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Iron 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:

Cobalt (Co) 3 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 3 binding sites of Iron where determined in the Structure of the Quorum Quenching Lactonase Gcl D122N Mutant - Bimetallic Metal Center - C2 Space Group, PDB code: 9b2p:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 9b2p

Go back to Iron Binding Sites List in 9b2p
Iron 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 Iron with other atoms in the Fe 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:Fe304

b:41.4
occ:1.00
 OD1 A:ASN122 1.8 68.7 1.0
NE2 A:HIS123 2.0 34.4 1.0
O A:HOH423 2.1 40.3 1.0
O A:HOH401 2.1 45.7 1.0
NE2 A:HIS266 2.1 40.7 1.0
OD2 A:ASP220 2.2 50.2 1.0
OD1 A:ASP220 2.8 43.5 1.0
CG A:ASP220 2.8 48.0 1.0
CG A:ASN122 2.8 54.5 1.0
CD2 A:HIS123 3.0 41.1 1.0
CE1 A:HIS266 3.0 48.8 1.0
CE1 A:HIS123 3.1 51.1 1.0
CD2 A:HIS266 3.1 51.6 1.0
ND2 A:ASN122 3.3 70.7 1.0
O A:HOH439 3.3 55.9 1.0
CO A:CO303 3.5 48.5 1.0
ND1 A:HIS266 4.1 46.6 1.0
CG A:HIS123 4.1 40.4 1.0
CB A:ASN122 4.2 57.5 1.0
ND1 A:HIS123 4.2 35.5 1.0
CG A:HIS266 4.2 47.3 1.0
NE2 A:HIS118 4.2 40.5 1.0
CE1 A:HIS118 4.3 50.4 1.0
CB A:ASP220 4.3 46.9 1.0
CE1 A:TYR223 4.5 52.4 1.0
NE2 A:HIS198 4.9 47.4 1.0

Iron binding site 2 out of 3 in 9b2p

Go back to Iron Binding Sites List in 9b2p
Iron 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 Iron with other atoms in the Fe 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:Fe306

b:42.8
occ:1.00
 NE2 P:HIS123 2.0 39.1 1.0
OD1 P:ASN122 2.1 61.1 1.0
NE2 P:HIS266 2.1 37.5 1.0
O P:HOH441 2.1 41.3 1.0
OD2 P:ASP220 2.2 47.2 1.0
O P:HOH402 2.6 55.5 1.0
OD1 P:ASP220 2.8 44.6 1.0
CG P:ASP220 2.8 45.4 1.0
CD2 P:HIS123 2.9 48.0 1.0
CE1 P:HIS123 3.0 46.2 1.0
CE1 P:HIS266 3.0 48.4 1.0
CG P:ASN122 3.1 52.4 1.0
CD2 P:HIS266 3.2 52.3 1.0
ND2 P:ASN122 3.4 67.1 1.0
CO P:CO305 3.4 46.9 1.0
O P:HOH422 3.5 51.6 1.0
ND1 P:HIS123 4.1 36.7 1.0
CG P:HIS123 4.1 40.5 1.0
ND1 P:HIS266 4.1 42.9 1.0
CG P:HIS266 4.3 45.2 1.0
CE1 P:HIS118 4.3 45.8 1.0
CB P:ASP220 4.3 47.3 1.0
NE2 P:HIS118 4.3 42.8 1.0
CB P:ASN122 4.4 56.0 1.0
CE1 P:TYR223 4.4 51.4 1.0
NE2 P:HIS198 5.0 46.9 1.0

Iron binding site 3 out of 3 in 9b2p

Go back to Iron Binding Sites List in 9b2p
Iron 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 Iron with other atoms in the Fe 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:Fe304

b:41.9
occ:1.00
 NE2 X:HIS123 1.9 41.1 1.0
O X:HOH403 2.1 54.2 1.0
NE2 X:HIS266 2.1 42.1 1.0
O X:HOH439 2.2 43.5 1.0
OD2 X:ASP220 2.2 44.6 1.0
OD1 X:ASN122 2.3 57.5 1.0
OD1 X:ASP220 2.8 45.9 1.0
CG X:ASP220 2.8 52.2 1.0
CE1 X:HIS123 2.8 50.0 1.0
CD2 X:HIS123 2.9 47.1 1.0
CD2 X:HIS266 3.1 56.7 1.0
CE1 X:HIS266 3.1 50.4 1.0
CG X:ASN122 3.3 54.5 1.0
CO X:CO303 3.5 48.4 1.0
ND2 X:ASN122 3.5 60.7 1.0
O X:HOH412 3.5 49.4 1.0
ND1 X:HIS123 4.0 35.0 1.0
CG X:HIS123 4.0 41.2 1.0
NE2 X:HIS118 4.2 44.2 1.0
ND1 X:HIS266 4.2 41.8 1.0
CG X:HIS266 4.3 50.0 1.0
CE1 X:HIS118 4.3 50.0 1.0
CB X:ASP220 4.3 50.9 1.0
CE1 X:TYR223 4.4 53.0 1.0
CB X:ASN122 4.6 50.9 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 10:37:40 2024

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