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Aluminium in PDB 6t66: Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4

Enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4

All present enzymatic activity of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66 was solved by P.Legrand, S.Quevillon-Cheruel, I.Li De La Sierra-Gallay, H.Walbott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.63 / 3.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.978, 123.292, 263.493, 90, 90, 90
R / Rfree (%) 25.5 / 27.6

Other elements in 6t66:

The structure of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 also contains other interesting chemical elements:

Fluorine (F) 24 atoms
Magnesium (Mg) 6 atoms

Aluminium Binding Sites:

The binding sites of Aluminium atom in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 (pdb code 6t66). This binding sites where shown within 5.0 Angstroms radius around Aluminium atom.
In total 6 binding sites of Aluminium where determined in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4, PDB code: 6t66:
Jump to Aluminium binding site number: 1; 2; 3; 4; 5; 6;

Aluminium binding site 1 out of 6 in 6t66

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Aluminium binding site 1 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 1 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Al503

b:175.6
occ:1.00
AL A:ALF503 0.0 175.6 1.0
F1 A:ALF503 1.8 175.6 1.0
F2 A:ALF503 1.8 175.2 1.0
F4 A:ALF503 1.8 176.0 1.0
F3 A:ALF503 1.8 175.5 1.0
O3B A:GDP501 2.0 151.9 1.0
OE1 A:GLU259 3.1 176.5 1.0
PB A:GDP501 3.2 152.1 1.0
O2B A:GDP501 3.5 151.4 1.0
MG A:MG502 3.8 63.7 1.0
NH1 B:ARG439 3.9 183.1 1.0
O3A A:GDP501 4.0 153.0 1.0
CD A:GLU259 4.0 184.8 1.0
OE2 A:GLU259 4.0 177.3 1.0
NZ A:LYS234 4.1 170.7 1.0
CE A:LYS234 4.3 164.3 1.0
O B:GLN407 4.3 149.3 1.0
NE B:ARG439 4.4 180.4 1.0
N A:SER231 4.4 144.5 1.0
O1B A:GDP501 4.4 152.4 1.0
CE1 A:TYR341 4.4 159.2 1.0
CZ B:ARG439 4.4 194.6 1.0
NZ B:LYS437 4.5 177.6 1.0
CA A:PRO230 4.6 145.4 1.0
CE B:LYS437 4.7 171.5 1.0
NE2 A:GLN381 4.7 185.1 1.0
CB A:PRO230 4.8 147.2 1.0
OH A:TYR341 4.9 166.0 1.0
CA B:GLN407 4.9 147.6 1.0
O B:GLU406 4.9 152.0 1.0

Aluminium binding site 2 out of 6 in 6t66

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Aluminium binding site 2 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 2 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Al503

b:160.6
occ:1.00
AL B:ALF503 0.0 160.6 1.0
F1 B:ALF503 1.8 160.2 1.0
F4 B:ALF503 1.8 161.0 1.0
F3 B:ALF503 1.8 160.5 1.0
F2 B:ALF503 1.8 160.8 1.0
O3B B:GDP501 2.0 146.2 1.0
OE1 B:GLU259 3.2 160.7 1.0
PB B:GDP501 3.2 146.1 1.0
O2B B:GDP501 3.5 145.8 1.0
MG B:MG502 3.9 52.1 1.0
NH1 C:ARG439 3.9 190.4 1.0
O3A B:GDP501 4.0 145.3 1.0
CD B:GLU259 4.0 171.8 1.0
OE2 B:GLU259 4.0 165.3 1.0
NZ B:LYS234 4.1 160.1 1.0
O C:GLN407 4.1 158.8 1.0
CE B:LYS234 4.3 151.9 1.0
N B:SER231 4.4 129.8 1.0
O1B B:GDP501 4.4 146.7 1.0
CE1 B:TYR341 4.4 144.8 1.0
CZ C:ARG439 4.5 202.7 1.0
NZ C:LYS437 4.6 196.7 1.0
NE C:ARG439 4.6 187.6 1.0
CA C:GLN407 4.6 156.9 1.0
CE C:LYS437 4.6 188.0 1.0
CA B:PRO230 4.7 130.6 1.0
O C:GLU406 4.7 161.3 1.0
NE2 B:GLN381 4.7 177.7 1.0
CB B:PRO230 4.8 132.3 1.0
C C:GLN407 4.8 159.3 1.0
OH B:TYR341 4.9 152.3 1.0

Aluminium binding site 3 out of 6 in 6t66

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Aluminium binding site 3 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 3 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Al503

b:161.9
occ:1.00
AL C:ALF503 0.0 161.9 1.0
F1 C:ALF503 1.8 161.8 1.0
F2 C:ALF503 1.8 161.8 1.0
F4 C:ALF503 1.8 161.8 1.0
F3 C:ALF503 1.8 162.0 1.0
O1B C:GDP501 2.0 142.9 1.0
OE1 C:GLU259 3.2 177.6 1.0
PB C:GDP501 3.2 142.3 1.0
O3B C:GDP501 3.5 142.2 1.0
NH1 D:ARG439 3.7 200.1 1.0
MG C:MG502 3.9 34.8 1.0
O3A C:GDP501 4.0 142.3 1.0
CD C:GLU259 4.0 186.5 1.0
OE2 C:GLU259 4.0 178.6 1.0
O D:GLN407 4.1 175.7 1.0
NZ C:LYS234 4.1 162.3 1.0
CE C:LYS234 4.3 155.6 1.0
CZ D:ARG439 4.4 212.2 1.0
N C:SER231 4.4 135.9 1.0
CE1 C:TYR341 4.4 156.3 1.0
O2B C:GDP501 4.4 142.2 1.0
NE D:ARG439 4.4 198.4 1.0
NZ D:LYS437 4.5 204.2 1.0
CA D:GLN407 4.6 173.3 1.0
CE D:LYS437 4.6 196.2 1.0
CA C:PRO230 4.7 137.3 1.0
O D:GLU406 4.7 176.9 1.0
NE2 C:GLN381 4.7 181.2 1.0
C D:GLN407 4.8 176.1 1.0
CB C:PRO230 4.8 139.2 1.0
OH C:TYR341 4.8 163.3 1.0

Aluminium binding site 4 out of 6 in 6t66

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Aluminium binding site 4 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 4 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Al503

b:272.6
occ:1.00
AL D:ALF503 0.0 272.6 1.0
F4 D:ALF503 1.8 272.7 1.0
F3 D:ALF503 1.8 272.6 1.0
F1 D:ALF503 1.8 271.5 1.0
F2 D:ALF503 1.8 272.9 1.0
O1B D:GDP501 2.1 220.4 1.0
OE1 D:GLU259 3.2 199.3 1.0
PB D:GDP501 3.2 220.2 1.0
O3B D:GDP501 3.5 220.8 1.0
MG D:MG502 3.9 74.6 1.0
O3A D:GDP501 4.0 219.1 1.0
CD D:GLU259 4.0 206.1 1.0
OE2 D:GLU259 4.0 200.4 1.0
NZ D:LYS234 4.1 205.2 1.0
CE D:LYS234 4.3 197.6 1.0
N D:SER231 4.4 177.3 1.0
O2B D:GDP501 4.4 220.2 1.0
CE1 D:TYR341 4.4 166.8 1.0
CA D:PRO230 4.7 177.1 1.0
NE2 D:GLN381 4.7 207.1 1.0
CB D:PRO230 4.8 178.9 1.0
OH D:TYR341 4.9 174.4 1.0

Aluminium binding site 5 out of 6 in 6t66

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Aluminium binding site 5 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 5 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Al503

b:218.5
occ:1.00
AL E:ALF503 0.0 218.5 1.0
F3 E:ALF503 1.8 218.6 1.0
F1 E:ALF503 1.8 218.1 1.0
F4 E:ALF503 1.8 218.4 1.0
F2 E:ALF503 1.8 218.7 1.0
O3B E:GDP501 2.0 187.7 1.0
OE1 E:GLU259 3.2 229.7 1.0
PB E:GDP501 3.2 187.7 1.0
O2B E:GDP501 3.5 187.7 1.0
MG E:MG502 3.9 74.6 1.0
O3A E:GDP501 4.0 187.0 1.0
CD E:GLU259 4.0 235.3 1.0
NH1 F:ARG439 4.0 255.4 1.0
OE2 E:GLU259 4.0 232.1 1.0
NZ E:LYS234 4.1 239.7 1.0
O F:GLN407 4.3 227.2 1.0
CE E:LYS234 4.3 230.6 1.0
N E:SER231 4.4 200.0 1.0
O1B E:GDP501 4.4 187.9 1.0
CE1 E:TYR341 4.4 229.9 1.0
CZ F:ARG439 4.6 267.0 1.0
NE F:ARG439 4.6 252.1 1.0
CA E:PRO230 4.7 201.9 1.0
NE2 E:GLN381 4.7 259.0 1.0
CB E:PRO230 4.8 203.7 1.0
OH E:TYR341 4.9 236.2 1.0
NZ F:LYS437 4.9 264.0 1.0
CA F:GLN407 4.9 225.0 1.0

Aluminium binding site 6 out of 6 in 6t66

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Aluminium binding site 6 out of 6 in the Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4


Mono view


Stereo pair view

A full contact list of Aluminium with other atoms in the Al binding site number 6 of Crystal Structure of the Vibrio Cholerae Replicative Helicase (Dnab) with Gdp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Al503

b:287.8
occ:1.00
AL F:ALF503 0.0 287.8 1.0
F1 F:ALF503 1.8 287.7 1.0
F4 F:ALF503 1.8 288.0 1.0
F2 F:ALF503 1.8 287.2 1.0
F3 F:ALF503 1.8 287.9 1.0
O3B F:GDP501 2.0 216.0 1.0
OE1 F:GLU259 3.2 221.3 1.0
PB F:GDP501 3.2 215.3 1.0
O2B F:GDP501 3.5 215.6 1.0
MG F:MG502 3.9 92.1 1.0
O3A F:GDP501 4.0 214.3 1.0
CD F:GLU259 4.0 224.9 1.0
OE2 F:GLU259 4.0 219.5 1.0
NZ F:LYS234 4.1 233.4 1.0
CE F:LYS234 4.3 224.9 1.0
N F:SER231 4.4 199.5 1.0
O1B F:GDP501 4.4 215.1 1.0
CE1 F:TYR341 4.4 204.1 1.0
CA F:PRO230 4.7 200.3 1.0
NE2 F:GLN381 4.7 241.7 1.0
CB F:PRO230 4.8 202.2 1.0
OH F:TYR341 4.9 212.3 1.0

Reference:

S.Marsin, Y.Adam, C.Cargemel, J.Andreani, S.Baconnais, P.Legrand, I.Li De La Sierra-Gallay, A.Humbert, M.Aumont-Nicaise, C.Velours, F.Ochsenbein, D.Durand, E.Le Cam, H.Walbott, C.Possoz, S.Quevillon-Cheruel, J.-L.Ferat. Study of the Dnab:Dcia Interplay Reveals Insights Into the Primary Mode of Loading of the Bacterial Replicative Helicase To Be Published.
Page generated: Sat Jul 10 09:44:45 2021

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