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Zinc in PDB 2gmn: Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum

Enzymatic activity of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum

All present enzymatic activity of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum, PDB code: 2gmn was solved by V.Calderone, M.Benvenuti, M.Stoczko, J.D.Docquier, G.M.Rossolini, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.501, 44.773, 76.966, 78.92, 89.51, 61.91
R / Rfree (%) 17.6 / 21.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum (pdb code 2gmn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum, PDB code: 2gmn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2gmn

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Zinc binding site 1 out of 6 in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:15.6
occ:1.00
 O A:HOH806 2.0 10.3 1.0
NE2 A:HIS177 2.0 9.5 1.0
NE2 A:HIS101 2.1 7.8 1.0
ND1 A:HIS103 2.1 8.7 1.0
CD2 A:HIS177 2.9 9.3 1.0
CE1 A:HIS103 3.0 9.2 1.0
CD2 A:HIS101 3.0 8.4 1.0
CE1 A:HIS101 3.0 9.3 1.0
CE1 A:HIS177 3.1 8.8 1.0
CG A:HIS103 3.1 8.6 1.0
O A:HOH879 3.2 20.9 1.0
O A:HOH807 3.3 8.4 1.0
ZN A:ZN802 3.4 12.8 1.0
CB A:HIS103 3.5 7.7 1.0
ND1 A:HIS101 4.1 9.7 1.0
CG A:HIS177 4.1 8.9 1.0
OD1 A:ASP105 4.1 9.2 1.0
CG A:HIS101 4.1 8.6 1.0
NE2 A:HIS103 4.1 10.3 1.0
ND1 A:HIS177 4.2 10.5 1.0
CD2 A:HIS106 4.2 8.2 1.0
NE2 A:HIS106 4.2 8.0 1.0
CD2 A:HIS103 4.2 9.1 1.0
O A:HOH848 4.6 15.6 1.0
OD2 A:ASP105 4.7 9.8 1.0
CG A:ASP105 4.8 8.6 1.0
O A:HOH1048 4.9 27.2 1.0
CA A:HIS103 4.9 7.6 1.0

Zinc binding site 2 out of 6 in 2gmn

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Zinc binding site 2 out of 6 in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:12.8
occ:1.00
 OD2 A:ASP105 2.1 9.8 1.0
NE2 A:HIS242 2.1 9.1 1.0
O A:HOH806 2.1 10.3 1.0
NE2 A:HIS106 2.1 8.0 1.0
O A:HOH807 2.5 8.4 1.0
CE1 A:HIS106 3.0 8.9 1.0
CG A:ASP105 3.0 8.6 1.0
CE1 A:HIS242 3.0 9.9 1.0
CD2 A:HIS242 3.0 9.2 1.0
CD2 A:HIS106 3.1 8.2 1.0
OD1 A:ASP105 3.3 9.2 1.0
ZN A:ZN801 3.4 15.6 1.0
NE2 A:HIS101 4.0 7.8 1.0
CE1 A:HIS101 4.0 9.3 1.0
ND1 A:HIS106 4.1 7.0 1.0
O A:HOH879 4.1 20.9 1.0
ND1 A:HIS242 4.1 8.5 1.0
CG A:HIS106 4.2 7.6 1.0
CG A:HIS242 4.2 9.5 1.0
O A:HOH1048 4.3 27.2 1.0
CB A:ASP105 4.3 7.9 1.0
CH2 A:TRP34 4.6 18.0 1.0
O A:HOH1144 4.7 37.9 1.0
CZ2 A:TRP34 4.8 18.0 1.0
NE2 A:HIS177 4.8 9.5 1.0

Zinc binding site 3 out of 6 in 2gmn

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Zinc binding site 3 out of 6 in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:22.1
occ:1.00
 NZ A:LYS229 2.0 18.6 1.0
O A:HOH858 2.0 18.2 1.0
ND1 A:HIS172 2.1 13.8 1.0
OE2 A:GLU158 2.1 16.3 1.0
CD A:GLU158 2.8 16.0 1.0
OE1 A:GLU158 2.9 16.6 1.0
CE1 A:HIS172 2.9 14.4 1.0
CE A:LYS229 3.1 18.8 1.0
CG A:HIS172 3.2 12.9 1.0
CB A:HIS172 3.6 12.3 1.0
CE A:MET233 4.0 21.2 1.0
NE2 A:HIS172 4.1 14.1 1.0
CA A:HIS172 4.1 11.8 1.0
CD2 A:HIS172 4.2 13.1 1.0
CG A:GLU158 4.2 15.5 1.0
O A:HOH1148 4.3 42.2 1.0
CD A:LYS229 4.4 17.2 1.0
O A:HOH1078 4.7 32.2 1.0
O A:ALA171 4.9 11.5 1.0
CG A:LYS229 4.9 15.9 1.0
N A:ALA173 4.9 12.3 1.0
C A:HIS172 5.0 11.9 1.0

Zinc binding site 4 out of 6 in 2gmn

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Zinc binding site 4 out of 6 in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn803

b:13.0
occ:1.00
 O B:HOH882 2.0 10.3 1.0
NE2 B:HIS106 2.1 7.6 1.0
NE2 B:HIS242 2.1 9.4 1.0
OD2 B:ASP105 2.1 9.7 1.0
O B:HOH807 2.5 8.2 1.0
CE1 B:HIS106 2.9 7.8 1.0
CG B:ASP105 3.0 8.8 1.0
CE1 B:HIS242 3.1 9.7 1.0
CD2 B:HIS242 3.1 9.8 1.0
CD2 B:HIS106 3.1 7.2 1.0
OD1 B:ASP105 3.3 8.9 1.0
ZN B:ZN804 3.4 14.2 1.0
NE2 B:HIS101 4.0 9.7 1.0
CE1 B:HIS101 4.0 9.9 1.0
ND1 B:HIS106 4.1 6.9 1.0
O B:HOH855 4.1 20.5 1.0
ND1 B:HIS242 4.2 9.1 1.0
CG B:HIS106 4.2 7.3 1.0
CG B:HIS242 4.2 9.3 1.0
O B:HOH935 4.2 26.9 1.0
CH2 B:TRP34 4.4 24.0 1.0
CB B:ASP105 4.4 8.0 1.0
NE2 B:HIS177 4.7 8.4 1.0
CZ3 B:TRP34 4.7 24.5 1.0

Zinc binding site 5 out of 6 in 2gmn

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Zinc binding site 5 out of 6 in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn804

b:14.2
occ:1.00
 NE2 B:HIS177 2.0 8.4 1.0
O B:HOH882 2.0 10.3 1.0
NE2 B:HIS101 2.1 9.7 1.0
ND1 B:HIS103 2.1 8.7 1.0
CD2 B:HIS177 2.9 9.0 1.0
CD2 B:HIS101 3.0 9.2 1.0
CE1 B:HIS103 3.0 10.5 1.0
CE1 B:HIS101 3.0 9.9 1.0
CE1 B:HIS177 3.1 8.0 1.0
CG B:HIS103 3.2 9.5 1.0
O B:HOH855 3.2 20.5 1.0
O B:HOH807 3.3 8.2 1.0
ZN B:ZN803 3.4 13.0 1.0
CB B:HIS103 3.5 8.0 1.0
CG B:HIS177 4.1 9.3 1.0
ND1 B:HIS101 4.1 9.7 1.0
CG B:HIS101 4.1 8.8 1.0
ND1 B:HIS177 4.1 9.9 1.0
OD1 B:ASP105 4.2 8.9 1.0
NE2 B:HIS103 4.2 10.4 1.0
NE2 B:HIS106 4.2 7.6 1.0
CD2 B:HIS106 4.2 7.2 1.0
CD2 B:HIS103 4.3 9.6 1.0
O B:HOH849 4.6 17.2 1.0
OD2 B:ASP105 4.7 9.7 1.0
O B:HOH935 4.9 26.9 1.0
CG B:ASP105 4.9 8.8 1.0
CA B:HIS103 4.9 7.7 1.0
OG B:SER202 5.0 15.7 1.0

Zinc binding site 6 out of 6 in 2gmn

Go back to Zinc Binding Sites List in 2gmn
Zinc binding site 6 out of 6 in the Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Bjp-1, A Subclass B3 Metallo-Beta-Lactamase of Bradyrhizobium Japonicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn806

b:22.5
occ:1.00
 OE2 B:GLU158 2.0 17.8 1.0
NZ B:LYS229 2.0 19.7 1.0
O B:HOH864 2.1 18.7 1.0
ND1 B:HIS172 2.1 16.0 1.0
CD B:GLU158 2.8 17.7 1.0
OE1 B:GLU158 2.8 17.7 1.0
CE1 B:HIS172 2.9 16.9 1.0
CE B:LYS229 3.1 20.1 1.0
CG B:HIS172 3.2 14.4 1.0
CB B:HIS172 3.6 13.1 1.0
CE B:MET233 3.9 22.4 1.0
CA B:HIS172 4.1 13.0 1.0
NE2 B:HIS172 4.1 16.9 1.0
CG B:GLU158 4.2 16.4 1.0
CD2 B:HIS172 4.2 15.3 1.0
CD B:LYS229 4.5 18.8 1.0
CG B:LYS229 4.9 17.4 1.0
O B:ALA171 4.9 11.9 1.0
N B:ALA173 5.0 13.3 1.0
C B:HIS172 5.0 13.1 1.0

Reference:

M.Stoczko, J.M.Frere, G.M.Rossolini, J.D.Docquier. Postgenomic Scan of Metallo-Beta-Lactamase Homologues in Rhizobacteria: Identification and Characterization of Bjp-1, A Subclass B3 Ortholog From Bradyrhizobium Japonicum. Antimicrob.Agents Chemother. V. 50 1973 2006.
ISSN: ISSN 0066-4804
PubMed: 16723554
DOI: 10.1128/AAC.01551-05
Page generated: Thu Oct 17 00:20:06 2024

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