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Cobalt in PDB 4rdy: Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl

Protein crystallography data

The structure of Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl, PDB code: 4rdy was solved by J.Hiblot, J.Bzdrenga, C.Champion, G.Gotthard, D.Gonzalez, E.Chabriere, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.75 / 2.00
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 174.740, 174.740, 61.550, 90.00, 90.00, 120.00
R / Rfree (%) 13.9 / 17.4

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl (pdb code 4rdy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl, PDB code: 4rdy:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 4rdy

Go back to Cobalt Binding Sites List in 4rdy
Cobalt binding site 1 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co401

b:17.3
occ:1.00
O A:HOH830 1.8 17.8 1.0
OD1 A:ASP257 2.1 14.2 1.0
OQ2 A:KCX138 2.1 15.8 1.0
NE2 A:HIS25 2.1 13.9 1.0
NE2 A:HIS23 2.2 14.7 1.0
OAC A:3M5403 2.4 44.3 0.8
CAB A:3M5403 2.8 40.5 0.8
CX A:KCX138 3.0 14.8 1.0
CG A:ASP257 3.0 15.3 1.0
CD2 A:HIS23 3.0 13.5 1.0
CE1 A:HIS25 3.1 13.2 1.0
CD2 A:HIS25 3.1 13.3 1.0
CE1 A:HIS23 3.2 14.0 1.0
OD2 A:ASP257 3.3 19.2 1.0
OQ1 A:KCX138 3.3 15.3 1.0
CO A:CO402 3.5 18.5 1.0
C A:3M5403 3.6 41.0 0.8
NZ A:KCX138 4.1 14.4 1.0
O A:3M5403 4.1 30.3 0.8
ND1 A:HIS25 4.2 14.3 1.0
CB A:3M5403 4.2 49.9 0.8
CG A:HIS23 4.2 13.2 1.0
CG A:HIS25 4.3 13.9 1.0
ND1 A:HIS23 4.3 14.0 1.0
CB A:LEU68 4.3 14.5 1.0
CB A:ASP257 4.4 14.4 1.0
CE1 A:HIS200 4.5 13.5 1.0
CA A:3M5403 4.6 48.5 0.8
NE2 A:HIS200 4.7 14.1 1.0
CA A:ASP257 4.8 14.7 1.0
OAL A:3M5403 5.0 46.5 0.8

Cobalt binding site 2 out of 4 in 4rdy

Go back to Cobalt Binding Sites List in 4rdy
Cobalt binding site 2 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co402

b:18.5
occ:1.00
OQ1 A:KCX138 1.9 15.3 1.0
O A:HOH830 2.1 17.8 1.0
ND1 A:HIS171 2.1 13.2 1.0
NE2 A:HIS200 2.2 14.1 1.0
O A:3M5403 2.4 30.3 0.8
CX A:KCX138 3.0 14.8 1.0
CE1 A:HIS171 3.0 14.9 1.0
C A:3M5403 3.0 41.0 0.8
CE1 A:HIS200 3.1 13.5 1.0
CG A:HIS171 3.1 14.1 1.0
OAC A:3M5403 3.2 44.3 0.8
CD2 A:HIS200 3.2 14.1 1.0
OQ2 A:KCX138 3.4 15.8 1.0
CB A:HIS171 3.4 13.5 1.0
CO A:CO401 3.5 17.3 1.0
NH1 A:ARG224 3.6 26.9 1.0
CE1 A:HIS23 4.0 14.0 1.0
NE2 A:HIS23 4.1 14.7 1.0
NZ A:KCX138 4.1 14.4 1.0
NE2 A:HIS171 4.1 15.9 1.0
OH A:TYR98 4.2 16.4 1.0
CD2 A:HIS171 4.2 15.0 1.0
ND1 A:HIS200 4.2 13.9 1.0
OD2 A:ASP257 4.2 19.2 1.0
CG A:HIS200 4.3 14.0 1.0
CA A:3M5403 4.3 48.5 0.8
CA A:HIS171 4.3 14.6 1.0
CE2 A:TYR98 4.3 14.2 1.0
CAB A:3M5403 4.4 40.5 0.8
CZ A:ARG224 4.5 19.5 1.0
CE A:KCX138 4.7 13.9 1.0
CZ A:TYR98 4.7 16.4 1.0
OD1 A:ASP257 4.8 14.2 1.0
NE A:ARG224 4.9 20.9 1.0
N A:3M5403 4.9 43.5 0.8
CG A:ASP257 4.9 15.3 1.0
CB A:3M5403 5.0 49.9 0.8

Cobalt binding site 3 out of 4 in 4rdy

Go back to Cobalt Binding Sites List in 4rdy
Cobalt binding site 3 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co401

b:16.3
occ:1.00
O B:HOH829 1.9 17.8 1.0
OD1 B:ASP257 2.0 14.0 1.0
OQ1 B:KCX138 2.1 18.8 1.0
NE2 B:HIS23 2.1 14.9 1.0
NE2 B:HIS25 2.1 15.1 1.0
OAC B:3M5403 2.6 46.4 0.8
CAB B:3M5403 2.9 42.5 0.8
CG B:ASP257 3.0 15.0 1.0
CD2 B:HIS23 3.0 13.8 1.0
CX B:KCX138 3.0 17.2 1.0
CE1 B:HIS25 3.1 14.0 1.0
CE1 B:HIS23 3.1 14.7 1.0
CD2 B:HIS25 3.1 13.7 1.0
OD2 B:ASP257 3.3 18.4 1.0
OQ2 B:KCX138 3.4 14.2 1.0
CO B:CO402 3.5 17.8 1.0
C B:3M5403 3.7 41.8 0.8
O B:3M5403 4.0 34.1 0.8
ND1 B:HIS23 4.2 15.2 1.0
NZ B:KCX138 4.2 14.6 1.0
CG B:HIS23 4.2 14.1 1.0
ND1 B:HIS25 4.2 13.1 1.0
CG B:HIS25 4.3 13.0 1.0
CB B:3M5403 4.3 55.6 0.8
CB B:ASP257 4.3 14.2 1.0
CB B:LEU68 4.4 15.2 1.0
CE1 B:HIS200 4.6 14.6 1.0
NE2 B:HIS200 4.7 14.5 1.0
CA B:3M5403 4.7 53.8 0.8
CA B:ASP257 4.8 16.3 1.0
OAL B:3M5403 4.9 44.1 0.8
O B:ASP257 5.0 15.8 1.0

Cobalt binding site 4 out of 4 in 4rdy

Go back to Cobalt Binding Sites List in 4rdy
Cobalt binding site 4 out of 4 in the Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Vmolac Bound to 3-Oxo-C10 Ahl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co402

b:17.8
occ:1.00
OQ2 B:KCX138 1.9 14.2 1.0
O B:HOH829 2.0 17.8 1.0
ND1 B:HIS171 2.1 13.7 1.0
NE2 B:HIS200 2.2 14.5 1.0
O B:3M5403 2.3 34.1 0.8
CX B:KCX138 3.0 17.2 1.0
CE1 B:HIS171 3.0 13.4 1.0
CE1 B:HIS200 3.1 14.6 1.0
C B:3M5403 3.1 41.8 0.8
CG B:HIS171 3.2 12.9 1.0
CD2 B:HIS200 3.2 13.8 1.0
OQ1 B:KCX138 3.3 18.8 1.0
OAC B:3M5403 3.4 46.4 0.8
CO B:CO401 3.5 16.3 1.0
CB B:HIS171 3.5 14.1 1.0
NH1 B:ARG224 3.7 28.4 1.0
CE1 B:HIS23 3.9 14.7 1.0
NE2 B:HIS23 4.1 14.9 1.0
OH B:TYR98 4.2 16.0 1.0
NE2 B:HIS171 4.2 14.1 1.0
NZ B:KCX138 4.2 14.6 1.0
OD2 B:ASP257 4.2 18.4 1.0
ND1 B:HIS200 4.2 13.3 1.0
CD2 B:HIS171 4.3 15.5 1.0
CE2 B:TYR98 4.3 14.9 1.0
CG B:HIS200 4.3 13.9 1.0
CA B:HIS171 4.3 14.8 1.0
CA B:3M5403 4.3 53.8 0.8
CZ B:ARG224 4.4 21.8 1.0
CAB B:3M5403 4.4 42.5 0.8
CE B:KCX138 4.6 13.3 1.0
CZ B:TYR98 4.7 15.3 1.0
OD1 B:ASP257 4.8 14.0 1.0
NE B:ARG224 4.8 21.5 1.0
N B:3M5403 4.9 51.6 0.8
CG B:ASP257 4.9 15.0 1.0

Reference:

J.Hiblot, J.Bzdrenga, C.Champion, E.Chabriere, M.Elias. Crystal Structure of Vmolac, A Tentative Quorum Quenching Lactonase From the Extremophilic Crenarchaeon Vulcanisaeta Moutnovskia. Sci Rep V. 5 8372 2015.
ISSN: ESSN 2045-2322
PubMed: 25670483
DOI: 10.1038/SREP08372
Page generated: Sun Dec 13 10:45:43 2020

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