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Cobalt in PDB 2vc7: Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities

Enzymatic activity of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities

All present enzymatic activity of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities:
3.1.8.1;

Protein crystallography data

The structure of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities, PDB code: 2vc7 was solved by M.Elias, J.Dupuy, L.Merone, L.Mandrich, S.Moniot, D.Rochu, C.Lecomte, M.Rossi, P.Masson, G.Manco, E.Chabriere, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.66 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.383, 104.124, 153.051, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.7

Other elements in 2vc7:

The structure of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities (pdb code 2vc7). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities, PDB code: 2vc7:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 2vc7

Go back to Cobalt Binding Sites List in 2vc7
Cobalt binding site 1 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1316

b:21.4
occ:1.00
 O A:HOH2200 2.1 15.8 1.0
OQ1 A:KCX137 2.2 17.4 1.0
NE2 A:HIS199 2.2 21.2 1.0
ND1 A:HIS170 2.3 20.9 1.0
CX A:KCX137 2.9 17.2 1.0
OQ2 A:KCX137 3.0 16.8 1.0
CE1 A:HIS199 3.1 21.2 1.0
O2 A:HT51335 3.1 49.0 0.7
SD A:HT51335 3.2 49.0 0.7
CG A:HIS170 3.2 20.9 1.0
CD2 A:HIS199 3.3 21.2 1.0
CE1 A:HIS170 3.3 21.1 1.0
FE A:FE1315 3.3 18.9 1.0
CB A:HIS170 3.4 20.8 1.0
C12 A:HT51335 3.5 49.0 0.7
CE2 A:TYR97 4.0 18.6 1.0
OH A:TYR97 4.0 18.9 1.0
NH1 A:ARG223 4.1 21.8 0.5
CE1 A:HIS22 4.1 19.5 1.0
NE2 A:HIS22 4.2 19.6 1.0
NZ A:KCX137 4.2 17.1 1.0
ND1 A:HIS199 4.2 20.9 1.0
OD1 A:ASP256 4.3 23.1 1.0
CA A:HIS170 4.3 20.9 1.0
CG A:HIS199 4.4 21.6 1.0
CD2 A:HIS170 4.4 20.9 1.0
NE2 A:HIS170 4.4 21.1 1.0
NH2 A:ARG223 4.4 20.1 0.5
CZ A:TYR97 4.5 18.8 1.0
CZ A:ARG223 4.6 21.7 0.5
C14 A:HT51335 4.7 49.0 0.7
OD2 A:ASP256 4.8 23.5 1.0
CG A:ASP256 4.8 23.2 1.0
C11 A:HT51335 4.9 49.0 0.7
CE A:KCX137 4.9 17.2 1.0
CZ A:ARG223 4.9 20.3 0.5
NH2 A:ARG223 5.0 21.5 0.5

Cobalt binding site 2 out of 4 in 2vc7

Go back to Cobalt Binding Sites List in 2vc7
Cobalt binding site 2 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1316

b:26.0
occ:1.00
 ND1 B:HIS170 2.0 21.9 1.0
NE2 B:HIS199 2.2 21.8 1.0
OQ1 B:KCX137 2.2 18.5 1.0
O B:HOH2161 2.3 25.6 1.0
CE1 B:HIS170 2.8 21.9 1.0
O2 B:HT51328 2.9 55.1 0.7
CE1 B:HIS199 3.0 22.1 1.0
CG B:HIS170 3.1 22.3 1.0
CX B:KCX137 3.2 19.6 1.0
CD2 B:HIS199 3.3 22.5 1.0
FE B:FE1315 3.5 19.8 1.0
OQ2 B:KCX137 3.5 19.0 1.0
NH2 B:ARG223 3.5 23.7 0.5
CB B:HIS170 3.6 22.6 1.0
C12 B:HT51328 3.8 55.2 0.7
NE2 B:HIS170 4.0 21.9 1.0
CD2 B:HIS170 4.1 22.1 1.0
ND1 B:HIS199 4.1 22.5 1.0
CE2 B:TYR97 4.2 23.9 1.0
OH B:TYR97 4.2 24.3 1.0
CZ B:ARG223 4.3 23.8 0.5
NZ B:KCX137 4.3 20.1 1.0
OD1 B:ASP256 4.3 26.7 1.0
NH1 B:ARG223 4.3 24.3 0.5
CA B:HIS170 4.3 22.6 1.0
CG B:HIS199 4.3 22.9 1.0
SD B:HT51328 4.4 55.2 0.7
CE1 B:HIS22 4.4 24.9 1.0
NE2 B:HIS22 4.4 24.9 1.0
NE B:ARG223 4.6 24.0 0.5
OD2 B:ASP256 4.7 26.9 1.0
CZ B:TYR97 4.7 23.9 1.0
CE B:KCX137 4.7 21.0 1.0
CG B:ASP256 4.8 27.0 1.0
CZ B:ARG223 4.9 24.3 0.5

Cobalt binding site 3 out of 4 in 2vc7

Go back to Cobalt Binding Sites List in 2vc7
Cobalt binding site 3 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1316

b:20.5
occ:1.00
 OQ1 C:KCX137 2.0 17.6 1.0
ND1 C:HIS170 2.1 19.0 1.0
NE2 C:HIS199 2.2 21.3 1.0
O C:HOH2189 2.4 24.9 1.0
CE1 C:HIS199 3.0 21.4 1.0
CE1 C:HIS170 3.0 18.6 1.0
CX C:KCX137 3.0 17.7 1.0
O2 C:HT51329 3.1 42.6 0.8
CG C:HIS170 3.1 18.9 1.0
OQ2 C:KCX137 3.2 17.7 1.0
CD2 C:HIS199 3.3 21.5 1.0
FE C:FE1315 3.4 18.2 1.0
CB C:HIS170 3.5 18.9 1.0
SD C:HT51329 3.6 42.6 0.8
C12 C:HT51329 3.6 42.5 0.8
NH1 C:ARG223 3.7 24.8 0.6
NE2 C:HIS170 4.1 18.6 1.0
ND1 C:HIS199 4.1 21.4 1.0
OH C:TYR97 4.2 20.4 1.0
CE2 C:TYR97 4.2 20.1 1.0
CE1 C:HIS22 4.2 19.8 1.0
CD2 C:HIS170 4.2 18.8 1.0
NZ C:KCX137 4.2 17.6 1.0
NH1 C:ARG223 4.2 22.5 0.4
NE2 C:HIS22 4.3 20.0 1.0
CA C:HIS170 4.3 19.0 1.0
CG C:HIS199 4.3 21.6 1.0
OD1 C:ASP256 4.4 22.8 1.0
CZ C:ARG223 4.4 24.7 0.6
CZ C:TYR97 4.7 20.1 1.0
CE C:KCX137 4.7 17.4 1.0
OD2 C:ASP256 4.8 22.7 1.0
NH2 C:ARG223 4.8 24.6 0.6
CZ C:ARG223 4.8 22.7 0.4
CG C:ASP256 4.9 23.0 1.0
NE C:ARG223 5.0 23.0 0.4
C11 C:HT51329 5.0 42.5 0.8

Cobalt binding site 4 out of 4 in 2vc7

Go back to Cobalt Binding Sites List in 2vc7
Cobalt binding site 4 out of 4 in the Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1316

b:27.2
occ:1.00
 O D:HOH2166 1.9 39.6 1.0
NE2 D:HIS199 2.1 30.0 1.0
OQ1 D:KCX137 2.1 22.1 1.0
ND1 D:HIS170 2.1 26.6 1.0
O2 D:HT51329 2.5 44.5 0.8
CE1 D:HIS170 3.0 26.5 1.0
CE1 D:HIS199 3.0 30.0 1.0
CD2 D:HIS199 3.0 30.0 1.0
CX D:KCX137 3.2 22.4 1.0
CG D:HIS170 3.2 27.0 1.0
OQ2 D:KCX137 3.4 22.2 1.0
FE D:FE1315 3.4 25.5 1.0
NH2 D:ARG223 3.5 29.4 0.5
C12 D:HT51329 3.5 44.5 0.8
CB D:HIS170 3.6 27.2 1.0
OD1 D:ASP256 4.1 28.8 1.0
ND1 D:HIS199 4.1 29.9 1.0
NE2 D:HIS170 4.1 26.6 1.0
NH1 D:ARG223 4.1 30.6 0.5
CG D:HIS199 4.1 30.1 1.0
NE2 D:HIS22 4.2 20.4 1.0
OH D:TYR97 4.2 24.1 1.0
CD2 D:HIS170 4.2 26.6 1.0
CE2 D:TYR97 4.3 24.1 1.0
CZ D:ARG223 4.3 29.6 0.5
NZ D:KCX137 4.3 22.5 1.0
CA D:HIS170 4.4 27.2 1.0
SD D:HT51329 4.4 44.6 0.8
CE1 D:HIS22 4.5 20.8 1.0
NE D:ARG223 4.6 29.8 0.5
C11 D:HT51329 4.6 44.5 0.8
CZ D:ARG223 4.6 30.7 0.5
CG D:ASP256 4.7 28.8 1.0
OD2 D:ASP256 4.7 28.7 1.0
CZ D:TYR97 4.7 24.2 1.0
CE D:KCX137 4.8 23.2 1.0

Reference:

M.Elias, J.Dupuy, L.Merone, L.Mandrich, E.Porzio, S.Moniot, D.Rochu, C.Lecomte, M.Rossi, P.Masson, G.Manco, E.Chabriere. Structural Basis For Natural Lactonase and Promiscuous Phosphotriesterase Activities. J.Mol.Biol. V. 379 1017 2008.
ISSN: ISSN 0022-2836
PubMed: 18486146
DOI: 10.1016/J.JMB.2008.04.022
Page generated: Tue Jul 30 15:31:07 2024

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