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Aluminium in PDB 4esv: A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates

Enzymatic activity of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates

All present enzymatic activity of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates:
3.6.4.12;

Protein crystallography data

The structure of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates, PDB code: 4esv was solved by O.Itsathitphaisarn, R.A.Wing, W.K.Eliason, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 3.20
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 149.124, 180.321, 279.128, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.9

Other elements in 4esv:

The structure of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates also contains other interesting chemical elements:

Fluorine (F) 40 atoms
Calcium (Ca) 14 atoms

Aluminium Binding Sites:

The binding sites of Aluminium atom in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates (pdb code 4esv). This binding sites where shown within 5.0 Angstroms radius around Aluminium atom.
In total 10 binding sites of Aluminium where determined in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates, PDB code: 4esv:
Jump to Aluminium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Aluminium binding site 1 out of 10 in 4esv

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Aluminium binding site 1 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 1 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Al504

b:84.5
occ:1.00
AL A:ALF504 0.0 84.5 1.0
F2 A:ALF504 1.8 93.2 1.0
F3 A:ALF504 1.8 97.1 1.0
F4 A:ALF504 1.8 97.9 1.0
F1 A:ALF504 1.8 89.6 1.0
O3B A:GDP502 2.4 83.1 1.0
PB A:GDP502 3.3 81.8 1.0
O1B A:GDP502 3.3 70.6 1.0
NH2 F:ARG420 3.5 85.0 1.0
CA A:CA503 3.7 0.0 1.0
NZ A:LYS216 3.8 80.1 1.0
OE1 A:GLU241 3.8 0.1 1.0
O F:GLN388 4.0 81.1 1.0
O3A A:GDP502 4.0 85.9 1.0
OE1 A:GLN362 4.2 92.5 1.0
NZ F:LYS418 4.3 72.6 1.0
N A:SER213 4.3 84.7 1.0
CZ F:ARG420 4.5 83.0 1.0
OE2 A:GLU241 4.5 0.6 1.0
CD A:GLU241 4.5 0.9 1.0
NE F:ARG420 4.5 76.6 1.0
O2B A:GDP502 4.6 69.5 1.0
CA A:PRO212 4.6 75.7 1.0
CE F:LYS418 4.7 71.6 1.0
C F:GLN388 4.8 75.7 1.0
CA F:GLN388 4.8 72.6 1.0
CB A:PRO212 4.9 74.7 1.0
NE2 A:GLN362 4.9 77.9 1.0
CD A:GLN362 5.0 86.2 1.0

Aluminium binding site 2 out of 10 in 4esv

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Aluminium binding site 2 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 2 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Al503

b:70.4
occ:1.00
AL C:ALF503 0.0 70.4 1.0
F1 C:ALF503 1.8 80.6 1.0
F4 C:ALF503 1.8 66.7 1.0
F2 C:ALF503 1.8 88.6 1.0
F3 C:ALF503 1.8 86.8 1.0
O3B C:GDP501 2.3 67.3 1.0
O1B C:GDP501 3.2 66.6 1.0
PB C:GDP501 3.3 73.4 1.0
NH2 B:ARG420 3.4 65.9 1.0
NZ C:LYS216 3.7 74.3 1.0
CA C:CA502 3.8 0.2 1.0
OE1 C:GLU241 3.8 0.7 1.0
NZ B:LYS418 3.9 65.3 1.0
O3A C:GDP501 3.9 78.0 1.0
O B:GLN388 4.1 83.7 1.0
N C:SER213 4.3 79.7 1.0
OE1 C:GLN362 4.3 91.6 1.0
CE B:LYS418 4.4 70.3 1.0
CZ B:ARG420 4.4 64.0 1.0
OE2 C:GLU241 4.5 0.3 1.0
O2B C:GDP501 4.5 66.6 1.0
NE B:ARG420 4.5 64.1 1.0
CD C:GLU241 4.6 0.7 1.0
CA C:PRO212 4.6 72.8 1.0
CA B:GLN388 4.8 77.7 1.0
CB C:PRO212 4.9 73.2 1.0
C B:GLN388 4.9 79.6 1.0
C C:PRO212 5.0 74.8 1.0
CE C:LYS216 5.0 68.3 1.0

Aluminium binding site 3 out of 10 in 4esv

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Aluminium binding site 3 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 3 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Al504

b:77.9
occ:1.00
AL C:ALF504 0.0 77.9 1.0
F1 C:ALF504 1.7 67.4 1.0
F3 C:ALF504 1.8 74.6 1.0
F2 C:ALF504 1.8 92.7 1.0
F4 C:ALF504 1.8 94.9 1.0
O3B D:GDP501 2.2 65.8 1.0
CA D:CA502 3.2 90.6 1.0
PB D:GDP501 3.2 80.0 1.0
O1B D:GDP501 3.2 65.2 1.0
NH2 C:ARG420 3.4 83.4 1.0
OE1 D:GLU241 3.6 95.7 1.0
NZ D:LYS216 3.6 76.3 1.0
O3A D:GDP501 4.0 81.8 1.0
O D:HOH601 4.1 69.9 1.0
CZ C:ARG420 4.4 85.7 1.0
OE1 D:GLN362 4.4 91.4 1.0
CD D:GLU241 4.4 98.1 1.0
NE C:ARG420 4.5 81.1 1.0
O C:GLN388 4.5 78.2 1.0
N D:SER213 4.5 78.9 1.0
OE2 D:GLU241 4.5 0.9 1.0
O2B D:GDP501 4.5 65.6 1.0
NZ C:LYS418 4.6 70.9 1.0
CE D:LYS216 4.8 66.7 1.0
CA D:PRO212 4.9 73.9 1.0
CE C:LYS418 5.0 69.7 1.0
NE2 D:GLN362 5.0 74.2 1.0

Aluminium binding site 4 out of 10 in 4esv

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Aluminium binding site 4 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 4 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Al503

b:93.3
occ:1.00
AL D:ALF503 0.0 93.3 1.0
F1 D:ALF503 1.7 97.4 1.0
F4 D:ALF503 1.8 80.6 1.0
F3 D:ALF503 1.8 88.5 1.0
F2 D:ALF503 1.8 0.2 1.0
O3B E:GDP501 2.3 86.0 1.0
CA E:CA502 3.1 0.1 1.0
O1B E:GDP501 3.3 81.1 1.0
PB E:GDP501 3.3 92.0 1.0
NH2 D:ARG420 3.6 89.1 1.0
OE1 E:GLU241 3.6 0.2 1.0
NZ E:LYS216 3.6 80.6 1.0
O3A E:GDP501 4.1 88.0 1.0
O D:GLN388 4.3 89.2 1.0
CD E:GLU241 4.5 0.7 1.0
N E:SER213 4.5 80.0 1.0
OE1 E:GLN362 4.5 90.8 1.0
NE D:ARG420 4.5 87.2 1.0
CZ D:ARG420 4.5 88.8 1.0
O2B E:GDP501 4.6 72.4 1.0
OE2 E:GLU241 4.6 0.2 1.0
NZ D:LYS418 4.6 83.4 1.0
CE E:LYS216 4.8 72.8 1.0
CA E:PRO212 4.9 75.8 1.0

Aluminium binding site 5 out of 10 in 4esv

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Aluminium binding site 5 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 5 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Al503

b:88.3
occ:1.00
AL E:ALF503 0.0 88.3 1.0
F4 E:ALF503 1.8 0.6 1.0
F2 E:ALF503 1.8 88.4 1.0
F1 E:ALF503 1.8 92.3 1.0
F3 E:ALF503 1.8 0.8 1.0
O3B F:GDP501 2.4 81.7 1.0
NH2 E:ARG420 3.2 89.4 1.0
PB F:GDP501 3.4 90.1 1.0
CA F:CA502 3.5 92.1 1.0
O1B F:GDP501 3.5 93.2 1.0
OE1 F:GLU241 3.6 0.6 1.0
O3A F:GDP501 3.9 93.6 1.0
NZ F:LYS216 4.0 80.2 1.0
O E:GLN388 4.1 86.8 1.0
CZ E:ARG420 4.2 90.9 1.0
NZ E:LYS418 4.2 79.2 1.0
NE E:ARG420 4.2 89.2 1.0
CD F:GLU241 4.4 0.2 1.0
OE2 F:GLU241 4.4 0.7 1.0
N F:SER213 4.4 85.2 1.0
OE1 F:GLN362 4.7 95.9 1.0
CE E:LYS418 4.7 75.7 1.0
O2B F:GDP501 4.7 71.3 1.0
CA F:PRO212 4.8 75.5 1.0

Aluminium binding site 6 out of 10 in 4esv

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Aluminium binding site 6 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


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Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 6 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Al502

b:0.7
occ:1.00
AL G:ALF502 0.0 0.7 1.0
F4 G:ALF502 1.8 0.1 1.0
F3 G:ALF502 1.8 0.2 1.0
F2 G:ALF502 1.8 0.4 1.0
F1 G:ALF502 1.8 0.9 1.0
O3B G:GDP501 2.2 0.6 1.0
O1B G:GDP501 3.0 0.2 1.0
PB G:GDP501 3.2 0.7 1.0
OE1 G:GLU241 3.2 0.8 1.0
NZ G:LYS216 3.5 1.0 1.0
O3A G:GDP501 3.9 0.5 1.0
CD G:GLU241 4.3 0.0 1.0
OG1 G:THR217 4.3 0.0 1.0
O2B G:GDP501 4.4 0.9 1.0
NH2 L:ARG420 4.5 0.7 1.0
NE L:ARG420 4.5 0.3 1.0
O L:GLN388 4.5 0.3 1.0
OE1 G:GLN362 4.6 0.9 1.0
OE2 G:GLU241 4.7 0.7 1.0
CE G:LYS216 4.7 0.3 1.0
CZ L:ARG420 4.8 0.9 1.0
N G:SER213 4.9 0.5 1.0
NZ L:LYS418 4.9 0.8 1.0

Aluminium binding site 7 out of 10 in 4esv

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Aluminium binding site 7 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 7 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Al503

b:90.7
occ:1.00
AL I:ALF503 0.0 90.7 1.0
F3 I:ALF503 1.8 95.1 1.0
F1 I:ALF503 1.8 89.4 1.0
F2 I:ALF503 1.8 91.7 1.0
F4 I:ALF503 1.8 97.1 1.0
O3B I:GDP501 2.2 0.1 1.0
OE1 I:GLU241 3.1 0.6 1.0
CA I:CA502 3.3 0.6 1.0
PB I:GDP501 3.3 0.5 1.0
O1B I:GDP501 3.4 0.2 1.0
NZ I:LYS216 3.6 0.6 1.0
O3A I:GDP501 3.8 0.2 1.0
O H:GLN388 4.0 0.7 1.0
CD I:GLU241 4.1 0.6 1.0
NH2 H:ARG420 4.1 0.4 1.0
OE2 I:GLU241 4.3 0.3 1.0
NE H:ARG420 4.3 0.6 1.0
OE1 I:GLN362 4.4 0.5 1.0
NZ H:LYS418 4.4 0.5 1.0
O2B I:GDP501 4.6 74.4 1.0
CZ H:ARG420 4.6 0.1 1.0
N I:SER213 4.8 0.8 1.0
CE2 I:TYR321 4.9 0.6 1.0
CE I:LYS216 4.9 1.0 1.0
OG1 I:THR217 5.0 0.5 1.0
C H:GLN388 5.0 1.0 1.0

Aluminium binding site 8 out of 10 in 4esv

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Aluminium binding site 8 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 8 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Al502

b:0.4
occ:1.00
AL J:ALF502 0.0 0.4 1.0
F2 J:ALF502 1.8 0.8 1.0
F1 J:ALF502 1.8 0.0 1.0
F4 J:ALF502 1.8 0.2 1.0
F3 J:ALF502 1.8 0.7 1.0
O3B J:GDP501 2.3 1.0 1.0
O1B J:GDP501 3.2 0.8 1.0
OE1 J:GLU241 3.2 0.8 1.0
PB J:GDP501 3.3 0.0 1.0
NZ J:LYS216 3.4 0.4 1.0
O2B J:GDP501 4.0 0.7 1.0
OG1 J:THR217 4.2 0.1 1.0
O1A J:GDP501 4.3 0.8 1.0
CD J:GLU241 4.4 0.7 1.0
NE I:ARG420 4.4 0.7 1.0
NH2 I:ARG420 4.5 0.3 1.0
CE J:LYS216 4.5 0.4 1.0
OE1 J:GLN362 4.5 0.7 1.0
O3A J:GDP501 4.6 0.3 1.0
O I:GLN388 4.6 0.8 1.0
CZ I:ARG420 4.8 0.1 1.0
OE2 J:GLU241 4.8 0.3 1.0
N J:SER213 4.9 0.8 1.0
NZ I:LYS418 5.0 0.5 1.0

Aluminium binding site 9 out of 10 in 4esv

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Aluminium binding site 9 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 9 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Al502

b:0.0
occ:1.00
AL K:ALF502 0.0 0.0 1.0
F1 K:ALF502 1.8 0.9 1.0
F4 K:ALF502 1.8 0.4 1.0
F3 K:ALF502 1.8 0.9 1.0
F2 K:ALF502 1.8 0.8 1.0
O3B K:GDP501 2.3 0.2 1.0
PB K:GDP501 3.0 0.5 1.0
O2B K:GDP501 3.0 0.0 1.0
OE1 K:GLU241 3.2 0.6 1.0
O1B K:GDP501 3.3 0.0 1.0
NZ K:LYS216 3.5 0.5 1.0
O J:GLN388 4.3 0.1 1.0
CD K:GLU241 4.3 0.2 1.0
NH2 J:ARG420 4.4 0.6 1.0
NZ J:LYS418 4.4 0.8 1.0
OG1 K:THR217 4.5 0.6 1.0
O3A K:GDP501 4.5 1.0 1.0
OE1 K:GLN362 4.6 0.6 1.0
NE J:ARG420 4.6 0.3 1.0
CE K:LYS216 4.7 0.6 1.0
OE2 K:GLU241 4.7 0.9 1.0
N K:SER213 4.8 0.0 1.0
O1A K:GDP501 4.8 0.4 1.0
CZ J:ARG420 4.9 0.4 1.0

Aluminium binding site 10 out of 10 in 4esv

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Aluminium binding site 10 out of 10 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 10 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Al502

b:0.5
occ:1.00
AL L:ALF502 0.0 0.5 1.0
F3 L:ALF502 1.8 0.9 1.0
F4 L:ALF502 1.8 0.3 1.0
F1 L:ALF502 1.8 0.6 1.0
F2 L:ALF502 1.8 0.8 1.0
O3B L:GDP501 2.4 1.0 1.0
O1B L:GDP501 3.5 0.0 1.0
OE1 L:GLU241 3.5 0.1 1.0
PB L:GDP501 3.5 0.1 1.0
NZ L:LYS216 3.7 0.7 1.0
CA L:CA503 3.9 0.7 1.0
O K:GLN388 4.0 0.5 1.0
NZ K:LYS418 4.0 0.6 1.0
NH2 K:ARG420 4.4 0.1 1.0
CD L:GLU241 4.4 0.8 1.0
N L:SER213 4.4 0.8 1.0
O3A L:GDP501 4.4 0.8 1.0
OE1 L:GLN362 4.4 0.9 1.0
O2B L:GDP501 4.6 0.6 1.0
NE K:ARG420 4.6 0.1 1.0
OE2 L:GLU241 4.6 0.3 1.0
CE K:LYS418 4.7 0.6 1.0
CA L:PRO212 4.7 0.7 1.0
CE2 L:TYR321 4.8 0.8 1.0
CB L:PRO212 4.8 0.1 1.0
C K:GLN388 4.9 0.4 1.0
CA K:GLN388 4.9 0.6 1.0
CZ K:ARG420 4.9 0.6 1.0
NE2 L:GLN362 4.9 0.5 1.0

Reference:

O.Itsathitphaisarn, R.A.Wing, W.K.Eliason, J.Wang, T.A.Steitz. The Hexameric Helicase Dnab Adopts A Nonplanar Conformation During Translocation. Cell(Cambridge,Mass.) V. 151 267 2012.
ISSN: ISSN 0092-8674
PubMed: 23022319
DOI: 10.1016/J.CELL.2012.09.014
Page generated: Sun Jul 6 21:52:06 2025

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