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Zinc in PDB 2gfj: Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1)

Enzymatic activity of Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1)

All present enzymatic activity of Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1), PDB code: 2gfj was solved by L.Nauton, G.Garau, R.Kahn, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 1.80
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.880, 105.880, 197.860, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1) (pdb code 2gfj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1), PDB code: 2gfj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2gfj

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Zinc binding site 1 out of 4 in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1)


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 the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:17.0
occ:1.00
O21 A:VI1410 2.0 14.1 1.0
NE2 A:HIS196 2.1 16.0 1.0
ND1 A:HIS118 2.1 14.4 1.0
NE2 A:HIS116 2.1 10.8 1.0
O20 A:VI1410 2.7 14.0 1.0
C19 A:VI1410 2.7 16.5 1.0
CD2 A:HIS196 3.0 12.0 1.0
CD2 A:HIS116 3.0 8.6 1.0
CE1 A:HIS118 3.1 13.1 1.0
O A:HOH1470 3.1 16.6 1.0
CE1 A:HIS116 3.1 9.2 1.0
CG A:HIS118 3.1 14.6 1.0
CE1 A:HIS196 3.2 13.9 1.0
CB A:HIS118 3.5 13.7 1.0
ZN A:ZN402 3.6 16.7 1.0
OD1 A:ASP120 4.1 12.2 1.0
C3 A:VI1410 4.1 16.4 1.0
CG A:HIS116 4.1 11.8 1.0
ND1 A:HIS116 4.2 9.1 1.0
NE2 A:HIS118 4.2 14.0 1.0
CG A:HIS196 4.2 14.1 1.0
ND1 A:HIS196 4.2 14.2 1.0
CD2 A:HIS118 4.2 14.0 1.0
NE2 A:HIS121 4.3 11.5 1.0
O23 A:VI1410 4.3 19.5 1.0
CD2 A:HIS121 4.3 10.1 1.0
OD2 A:ASP120 4.7 14.4 1.0
C13 A:VI1410 4.8 17.1 1.0
CG A:ASP120 4.9 13.3 1.0
CA A:HIS118 5.0 14.3 1.0

Zinc binding site 2 out of 4 in 2gfj

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Zinc binding site 2 out of 4 in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1)


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 the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:16.7
occ:1.00
OD2 A:ASP120 2.0 14.4 1.0
O21 A:VI1410 2.1 14.1 1.0
NE2 A:HIS121 2.1 11.5 1.0
NE2 A:HIS263 2.1 13.1 1.0
O A:HOH1470 2.4 16.6 1.0
CG A:ASP120 2.9 13.3 1.0
CE1 A:HIS121 2.9 9.0 1.0
CE1 A:HIS263 3.0 13.6 1.0
C19 A:VI1410 3.1 16.5 1.0
OD1 A:ASP120 3.1 12.2 1.0
CD2 A:HIS263 3.1 15.8 1.0
CD2 A:HIS121 3.2 10.1 1.0
C3 A:VI1410 3.3 16.4 1.0
ZN A:ZN401 3.6 17.0 1.0
C4 A:VI1410 3.8 18.2 1.0
C2 A:VI1410 3.9 19.6 1.0
O23 A:VI1410 3.9 19.5 1.0
ND1 A:HIS121 4.1 11.6 1.0
NE2 A:HIS116 4.1 10.8 1.0
ND1 A:HIS263 4.1 12.5 1.0
CE1 A:HIS116 4.2 9.2 1.0
O20 A:VI1410 4.2 14.0 1.0
CG A:HIS121 4.2 10.7 1.0
CG A:HIS263 4.2 14.0 1.0
CB A:ASP120 4.3 14.2 1.0
C18 A:VI1410 4.3 19.3 1.0
C12 A:VI1410 4.4 19.8 1.0
C13 A:VI1410 4.5 17.1 1.0
N5 A:VI1410 4.5 19.6 1.0
N1 A:VI1410 4.5 18.9 1.0
OG A:SER221 4.6 13.1 1.0
NE2 A:HIS196 4.9 16.0 1.0

Zinc binding site 3 out of 4 in 2gfj

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Zinc binding site 3 out of 4 in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1)


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 the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:19.0
occ:1.00
O21 B:VI2410 1.9 14.3 1.0
NE2 B:HIS116 2.1 12.9 1.0
NE2 B:HIS196 2.1 16.5 1.0
ND1 B:HIS118 2.2 18.8 1.0
C19 B:VI2410 2.6 20.3 1.0
O20 B:VI2410 2.7 18.6 1.0
CD2 B:HIS116 3.0 12.6 1.0
CD2 B:HIS196 3.0 16.1 1.0
CE1 B:HIS118 3.1 17.0 1.0
CE1 B:HIS116 3.1 12.4 1.0
CE1 B:HIS196 3.2 13.6 1.0
CG B:HIS118 3.2 14.9 1.0
CB B:HIS118 3.5 14.3 1.0
ZN B:ZN402 3.6 18.0 1.0
C3 B:VI2410 4.1 20.9 1.0
CG B:HIS116 4.1 13.5 1.0
ND1 B:HIS116 4.1 12.1 1.0
OD1 B:ASP120 4.1 15.6 1.0
CG B:HIS196 4.2 15.9 1.0
NE2 B:HIS118 4.2 15.5 1.0
ND1 B:HIS196 4.2 13.7 1.0
CD2 B:HIS118 4.3 17.0 1.0
CD2 B:HIS121 4.3 13.7 1.0
NE2 B:HIS121 4.3 14.7 1.0
O23 B:VI2410 4.4 23.1 1.0
C17 B:VI2410 4.7 23.5 1.0
OD2 B:ASP120 4.9 16.9 1.0
CG2 B:THR197 4.9 14.5 1.0
CA B:HIS118 5.0 14.6 1.0
CG B:ASP120 5.0 15.2 1.0

Zinc binding site 4 out of 4 in 2gfj

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Zinc binding site 4 out of 4 in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1)


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 the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:18.0
occ:1.00
NE2 B:HIS263 2.1 13.6 1.0
NE2 B:HIS121 2.1 14.7 1.0
OD2 B:ASP120 2.2 16.9 1.0
O21 B:VI2410 2.2 14.3 1.0
CE1 B:HIS121 2.9 16.4 1.0
CG B:ASP120 2.9 15.2 1.0
CE1 B:HIS263 3.0 16.9 1.0
C19 B:VI2410 3.1 20.3 1.0
OD1 B:ASP120 3.1 15.6 1.0
CD2 B:HIS121 3.1 13.7 1.0
CD2 B:HIS263 3.1 15.0 1.0
C3 B:VI2410 3.2 20.9 1.0
ZN B:ZN401 3.6 19.0 1.0
C4 B:VI2410 3.7 23.3 1.0
O23 B:VI2410 3.8 23.1 1.0
C2 B:VI2410 3.8 24.5 1.0
ND1 B:HIS121 4.0 11.5 1.0
NE2 B:HIS116 4.1 12.9 1.0
ND1 B:HIS263 4.1 14.8 1.0
CE1 B:HIS116 4.2 12.4 1.0
CG B:HIS121 4.2 15.2 1.0
C18 B:VI2410 4.2 24.3 1.0
CG B:HIS263 4.2 17.5 1.0
O20 B:VI2410 4.2 18.6 1.0
CB B:ASP120 4.3 14.8 1.0
C12 B:VI2410 4.4 23.9 1.0
N5 B:VI2410 4.4 24.9 1.0
N1 B:VI2410 4.5 25.4 1.0
C17 B:VI2410 4.6 23.5 1.0
OG B:SER221 4.6 16.5 1.0
NE2 B:HIS196 4.8 16.5 1.0

Reference:

L.Nauton, R.Kahn, G.Garau, J.F.Hernandez, O.Dideberg. Structural Insights Into the Design of Inhibitors For the L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia. J.Mol.Biol. V. 375 257 2008.
ISSN: ISSN 0022-2836
PubMed: 17999929
DOI: 10.1016/J.JMB.2007.10.036
Page generated: Wed Dec 16 03:29:25 2020

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