Cobalt in PDB 9b2p: Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group

Enzymatic activity of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group

All present enzymatic activity of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group:
3.1.1.81;

Protein crystallography data

The structure of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group, PDB code: 9b2p was solved by M.Corbella, J.A.Bravo, A.O.Demkiv, A.R.Calixto, K.Sompiyachoke, C.Bergonzi, S.C.L.Kamerlin, M.Elias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.93 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.77, 109.11, 97.17, 90, 116.42, 90
R / Rfree (%) 20.8 / 23.4

Other elements in 9b2p:

The structure of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group also contains other interesting chemical elements:

Iron (Fe) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group (pdb code 9b2p). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group, PDB code: 9b2p:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 9b2p

Go back to Cobalt Binding Sites List in 9b2p
Cobalt binding site 1 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co303

b:48.5
occ:1.00
 O A:HOH401 1.8 45.7 1.0
NE2 A:HIS198 2.0 47.4 1.0
OD2 A:ASP220 2.1 50.2 1.0
ND1 A:HIS120 2.1 43.4 1.0
NE2 A:HIS118 2.2 40.5 1.0
O A:HOH439 2.5 55.9 1.0
CE1 A:HIS198 2.9 50.5 1.0
CD2 A:HIS118 3.0 43.6 1.0
CD2 A:HIS198 3.0 43.7 1.0
CE1 A:HIS120 3.1 42.8 1.0
CG A:HIS120 3.2 43.5 1.0
CG A:ASP220 3.2 48.0 1.0
CE1 A:HIS118 3.3 50.4 1.0
FE A:FE304 3.5 41.4 1.0
CB A:HIS120 3.5 43.9 1.0
O A:HOH423 3.5 40.3 1.0
CB A:ASP220 3.7 46.9 1.0
ND1 A:HIS198 4.0 47.7 1.0
CG A:HIS198 4.1 44.1 1.0
NE2 A:HIS123 4.1 34.4 1.0
ND2 A:ASN122 4.2 70.7 1.0
NE2 A:HIS120 4.2 44.1 1.0
CD2 A:HIS123 4.2 41.1 1.0
CG A:HIS118 4.2 42.6 1.0
CD2 A:HIS120 4.3 50.5 1.0
OD1 A:ASP220 4.3 43.5 1.0
ND1 A:HIS118 4.3 45.6 1.0
OH A:TYR223 4.4 53.2 1.0
OD1 A:ASN122 4.5 68.7 1.0
CG A:ASN122 4.8 54.5 1.0
CE1 A:TYR223 4.9 52.4 1.0

Cobalt binding site 2 out of 3 in 9b2p

Go back to Cobalt Binding Sites List in 9b2p
Cobalt binding site 2 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Co305

b:46.9
occ:1.00
 NE2 P:HIS198 2.0 46.9 1.0
OD2 P:ASP220 2.0 47.2 1.0
O P:HOH402 2.1 55.5 1.0
NE2 P:HIS118 2.1 42.8 1.0
ND1 P:HIS120 2.2 42.7 1.0
O P:HOH422 2.7 51.6 1.0
CE1 P:HIS198 2.9 50.1 1.0
CD2 P:HIS198 3.1 41.4 1.0
CD2 P:HIS118 3.1 40.9 1.0
CE1 P:HIS118 3.1 45.8 1.0
CG P:ASP220 3.2 45.4 1.0
CE1 P:HIS120 3.2 49.3 1.0
CG P:HIS120 3.3 44.8 1.0
FE P:FE306 3.4 42.8 1.0
CB P:HIS120 3.6 43.9 1.0
O P:HOH441 3.6 41.3 1.0
CB P:ASP220 3.7 47.3 1.0
NE2 P:HIS123 4.0 39.1 1.0
ND1 P:HIS198 4.1 45.4 1.0
CD2 P:HIS123 4.1 48.0 1.0
CG P:HIS198 4.1 43.7 1.0
ND1 P:HIS118 4.2 43.6 1.0
CG P:HIS118 4.2 40.2 1.0
OD1 P:ASP220 4.2 44.6 1.0
NE2 P:HIS120 4.3 45.0 1.0
CD2 P:HIS120 4.4 49.1 1.0
ND2 P:ASN122 4.4 67.1 1.0
OH P:TYR223 4.5 46.9 1.0
OD1 P:ASN122 4.8 61.1 1.0
CE1 P:TYR223 4.9 51.4 1.0
CD1 P:ILE237 4.9 81.2 1.0
CE1 P:HIS123 5.0 46.2 1.0

Cobalt binding site 3 out of 3 in 9b2p

Go back to Cobalt Binding Sites List in 9b2p
Cobalt binding site 3 out of 3 in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Co303

b:48.4
occ:1.00
 O X:HOH403 2.1 54.2 1.0
OD2 X:ASP220 2.1 44.6 1.0
NE2 X:HIS198 2.1 47.4 1.0
NE2 X:HIS118 2.1 44.2 1.0
ND1 X:HIS120 2.1 42.9 1.0
O X:HOH412 2.7 49.4 1.0
CD2 X:HIS118 2.9 42.0 1.0
CE1 X:HIS120 3.0 48.1 1.0
CD2 X:HIS198 3.1 42.9 1.0
CE1 X:HIS198 3.1 49.9 1.0
CG X:ASP220 3.2 52.2 1.0
CG X:HIS120 3.2 44.8 1.0
CE1 X:HIS118 3.2 50.0 1.0
FE X:FE304 3.5 41.9 1.0
CB X:HIS120 3.6 46.4 1.0
CB X:ASP220 3.6 50.9 1.0
O X:HOH439 3.7 43.5 1.0
NE2 X:HIS123 4.0 41.1 1.0
CG X:HIS118 4.1 41.6 1.0
NE2 X:HIS120 4.2 45.0 1.0
CD2 X:HIS123 4.2 47.1 1.0
ND1 X:HIS198 4.2 45.8 1.0
CG X:HIS198 4.2 45.2 1.0
ND1 X:HIS118 4.2 45.9 1.0
OD1 X:ASP220 4.3 45.9 1.0
CD2 X:HIS120 4.3 47.7 1.0
OH X:TYR223 4.4 53.5 1.0
ND2 X:ASN122 4.6 60.7 1.0
CE1 X:TYR223 4.8 53.0 1.0
CD1 X:ILE237 4.9 90.6 1.0
CE1 X:HIS123 4.9 50.0 1.0

Reference:

M.Corbella, J.Bravo, A.O.Demkiv, A.R.Calixto, K.Sompiyachoke, C.Bergonzi, A.R.Brownless, M.H.Elias, S.C.L.Kamerlin. Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. Jacs Au V. 4 3519 2024.
ISSN: ESSN 2691-3704
PubMed: 39328773
DOI: 10.1021/JACSAU.4C00404
Page generated: Wed Nov 13 08:01:09 2024

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