Atomistry » Zinc » PDB 2gd8-2gze » 2gmn
Atomistry »
  Zinc »
    PDB 2gd8-2gze »
      2gmn »

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

Go back to Zinc Binding Sites List in 2gmn
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

Go back to Zinc Binding Sites List in 2gmn
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

Go back to Zinc Binding Sites List in 2gmn
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

Go back to Zinc Binding Sites List in 2gmn
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

Go back to Zinc Binding Sites List in 2gmn
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: Wed Dec 16 03:29:33 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy