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Aluminium in PDB 3sr0: Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site

Enzymatic activity of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site

All present enzymatic activity of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site, PDB code: 3sr0 was solved by Y.-J.Cho, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.79 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.950, 69.580, 85.670, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 18.9

Other elements in 3sr0:

The structure of Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 2 atoms

Aluminium Binding Sites:

The binding sites of Aluminium atom in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site (pdb code 3sr0). This binding sites where shown within 5.0 Angstroms radius around Aluminium atom.
In total 2 binding sites of Aluminium where determined in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site, PDB code: 3sr0:
Jump to Aluminium binding site number: 1; 2;

Aluminium binding site 1 out of 2 in 3sr0

Go back to Aluminium Binding Sites List in 3sr0
Aluminium binding site 1 out of 2 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site


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 Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Al210

b:19.5
occ:0.80
AL A:ALF210 0.0 19.5 0.8
F1 A:ALF210 1.8 20.0 0.8
F2 A:ALF210 1.8 19.0 0.8
F4 A:ALF210 1.8 20.7 0.8
F3 A:ALF210 1.8 20.9 0.8
O3P A:AMP208 2.0 17.7 1.0
O1B A:ADP207 2.2 9.9 1.0
HH12 A:ARG124 2.9 14.7 1.0
MG A:MG209 3.0 18.0 0.6
HH22 A:ARG85 3.3 16.5 0.6
P A:AMP208 3.3 14.3 1.0
O A:HOH712 3.4 16.0 0.9
PB A:ADP207 3.4 9.1 1.0
HH12 A:ARG161 3.4 26.9 1.0
HH22 A:ARG161 3.4 27.7 1.0
H A:GLY10 3.5 14.0 1.0
O3B A:ADP207 3.6 9.7 1.0
HH22 A:ARG124 3.6 14.2 1.0
HH12 A:ARG150 3.7 19.9 1.0
O1P A:AMP208 3.7 14.8 1.0
O A:HOH238 3.7 22.4 1.0
HH22 A:ARG150 3.8 19.3 1.0
HA A:PRO9 3.8 15.1 1.0
NH1 A:ARG124 3.8 12.3 1.0
HZ1 A:LYS13 3.8 16.0 1.0
O2P A:AMP208 3.9 15.4 1.0
O A:HOH232 3.9 15.5 0.7
O A:HOH332 4.0 23.8 1.0
NH2 A:ARG85 4.0 13.8 0.6
O2B A:ADP207 4.2 9.0 1.0
NH1 A:ARG161 4.2 22.4 1.0
HH21 A:ARG85 4.2 16.5 0.6
NH2 A:ARG161 4.2 23.1 1.0
HZ3 A:LYS13 4.3 16.0 1.0
NH2 A:ARG124 4.3 11.9 1.0
HH11 A:ARG124 4.3 14.7 1.0
N A:GLY10 4.4 11.7 1.0
NH1 A:ARG150 4.4 16.6 1.0
NZ A:LYS13 4.5 13.4 1.0
O5' A:AMP208 4.5 13.0 1.0
NH2 A:ARG150 4.5 16.1 1.0
O A:HOH314 4.5 16.9 1.0
CZ A:ARG124 4.5 10.9 1.0
HB3 A:PRO9 4.6 16.6 1.0
O3A A:ADP207 4.6 9.1 1.0
CA A:PRO9 4.6 12.6 1.0
CZ A:ARG161 4.7 23.0 1.0
HH22 A:ARG85 4.7 11.9 0.5
HH12 A:ARG85 4.8 16.7 0.6
HH11 A:ARG161 4.9 26.9 1.0
HH21 A:ARG161 4.9 27.7 1.0
O A:HOH232 4.9 8.3 0.3
HD21 A:LEU121 4.9 18.4 1.0
CZ A:ARG150 4.9 16.2 1.0
HE2 A:LYS13 5.0 16.7 1.0
H5'2 A:AMP208 5.0 13.4 1.0
HA2 A:GLY10 5.0 13.5 1.0

Aluminium binding site 2 out of 2 in 3sr0

Go back to Aluminium Binding Sites List in 3sr0
Aluminium binding site 2 out of 2 in the Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site


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 Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: Adp/ALF4/Amp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Al210

b:19.5
occ:0.77
AL B:ALF210 0.0 19.5 0.8
F4 B:ALF210 1.8 19.0 0.8
F3 B:ALF210 1.8 19.8 0.8
F1 B:ALF210 1.8 22.0 0.8
F2 B:ALF210 1.8 17.6 0.8
O2B B:ADP207 2.3 9.2 1.0
O2P B:AMP208 2.4 17.3 1.0
HH12 B:ARG124 2.9 13.7 1.0
MG B:MG209 3.1 29.6 0.9
HH12 B:ARG150 3.3 14.4 1.0
P B:AMP208 3.4 12.1 1.0
HH22 B:ARG161 3.4 14.1 0.5
PB B:ADP207 3.4 9.2 1.0
HH22 B:ARG150 3.4 13.1 1.0
O B:HOH389 3.4 17.6 0.8
HH12 B:ARG161 3.5 14.5 0.5
HH22 B:ARG124 3.5 11.5 1.0
O3B B:ADP207 3.5 9.3 1.0
O B:HOH635 3.6 14.2 0.8
O B:HOH310 3.6 17.5 1.0
NH1 B:ARG124 3.7 11.5 1.0
H B:GLY10 3.7 11.4 1.0
O3P B:AMP208 3.8 13.1 1.0
O1P B:AMP208 3.8 11.4 1.0
HA B:PRO9 3.8 12.0 1.0
HH11 B:ARG161 3.8 17.8 0.5
HZ1 B:LYS13 4.0 15.9 1.0
O B:HOH348 4.0 22.1 1.0
NH1 B:ARG150 4.1 12.1 1.0
NH2 B:ARG150 4.2 10.9 1.0
NH2 B:ARG161 4.2 11.8 0.5
HH11 B:ARG124 4.2 13.7 1.0
NH2 B:ARG124 4.2 9.6 1.0
NH1 B:ARG161 4.3 12.1 0.5
O1B B:ADP207 4.3 8.8 1.0
HH12 B:ARG161 4.4 17.8 0.5
CZ B:ARG124 4.4 10.7 1.0
NH1 B:ARG161 4.4 14.9 0.5
HZ3 B:LYS13 4.4 15.9 1.0
HB3 B:PRO9 4.5 14.5 1.0
N B:GLY10 4.5 9.6 1.0
O3A B:ADP207 4.6 8.4 1.0
CZ B:ARG150 4.6 11.3 1.0
NZ B:LYS13 4.6 13.2 1.0
O B:HOH216 4.6 21.6 1.0
HH12 B:ARG85 4.7 22.5 1.0
CA B:PRO9 4.7 10.1 1.0
HH11 B:ARG150 4.7 14.4 1.0
O5' B:AMP208 4.7 12.5 1.0
CZ B:ARG161 4.7 12.5 0.5
HH21 B:ARG150 4.8 13.1 1.0
HH21 B:ARG161 4.8 14.1 0.5
O B:HOH369 4.8 16.1 0.3
HE2 B:LYS13 4.9 14.0 1.0
CB B:PRO9 4.9 12.1 1.0
HH21 B:ARG124 5.0 11.5 1.0
HH11 B:ARG161 5.0 14.5 0.5
HB2 B:PRO9 5.0 14.5 1.0
HD21 B:LEU121 5.0 13.4 1.0

Reference:

S.J.Kerns, R.V.Agafonov, Y.J.Cho, F.Pontiggia, R.Otten, D.V.Pachov, S.Kutter, L.A.Phung, P.N.Murphy, V.Thai, T.Alber, M.F.Hagan, D.Kern. The Energy Landscape of Adenylate Kinase During Catalysis. Nat.Struct.Mol.Biol. V. 22 124 2015.
ISSN: ISSN 1545-9993
PubMed: 25580578
DOI: 10.1038/NSMB.2941
Page generated: Sun Jul 6 21:49:25 2025

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