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

Enzymatic activity of Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 2)

All present enzymatic activity of Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 2):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 2), PDB code: 2gfk 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) 19.51 / 1.90
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.350, 105.350, 197.080, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Zinc-Beta-Lactamase L1 From Stenotrophomonas Maltophilia (Inhibitor 2) (pdb code 2gfk). 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 2), PDB code: 2gfk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2gfk

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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 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.1
occ:1.00
O23 A:VII1410 2.1 11.5 1.0
NE2 A:HIS196 2.1 13.8 1.0
ND1 A:HIS118 2.1 14.2 1.0
NE2 A:HIS116 2.2 10.7 1.0
O22 A:VII1410 2.7 13.1 1.0
C18 A:VII1410 2.7 16.4 1.0
CD2 A:HIS196 3.0 11.7 1.0
CD2 A:HIS116 3.0 11.5 1.0
CE1 A:HIS118 3.0 12.6 1.0
CE1 A:HIS116 3.1 9.7 1.0
CE1 A:HIS196 3.1 10.8 1.0
O A:HOH1551 3.2 19.6 1.0
CG A:HIS118 3.2 13.4 1.0
CB A:HIS118 3.6 13.1 1.0
ZN A:ZN402 3.6 16.3 1.0
C9 A:VII1410 4.1 16.5 1.0
CG A:HIS196 4.1 12.3 1.0
CG A:HIS116 4.2 12.2 1.0
ND1 A:HIS116 4.2 11.7 1.0
OD1 A:ASP120 4.2 12.4 1.0
NE2 A:HIS118 4.2 11.4 1.0
ND1 A:HIS196 4.2 14.4 1.0
O21 A:VII1410 4.3 21.8 1.0
CD2 A:HIS118 4.3 10.7 1.0
CD2 A:HIS121 4.3 10.5 1.0
NE2 A:HIS121 4.4 15.0 1.0
C13 A:VII1410 4.8 16.4 1.0
OD2 A:ASP120 4.8 13.5 1.0
CE2 A:PHE156 4.9 26.9 1.0
CG A:ASP120 4.9 13.5 1.0
CA A:HIS118 5.0 13.1 1.0

Zinc binding site 2 out of 4 in 2gfk

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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 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:16.3
occ:1.00
OD2 A:ASP120 2.0 13.5 1.0
O23 A:VII1410 2.1 11.5 1.0
NE2 A:HIS263 2.1 11.6 1.0
NE2 A:HIS121 2.1 15.0 1.0
O A:HOH1551 2.5 19.6 1.0
CG A:ASP120 2.9 13.5 1.0
CE1 A:HIS121 3.0 13.1 1.0
CE1 A:HIS263 3.0 11.9 1.0
C18 A:VII1410 3.0 16.4 1.0
CD2 A:HIS121 3.1 10.5 1.0
OD1 A:ASP120 3.1 12.4 1.0
CD2 A:HIS263 3.1 13.1 1.0
C9 A:VII1410 3.2 16.5 1.0
ZN A:ZN401 3.6 16.1 1.0
C8 A:VII1410 3.8 19.7 1.0
O21 A:VII1410 3.8 21.8 1.0
C10 A:VII1410 3.8 18.5 1.0
ND1 A:HIS121 4.1 13.4 1.0
NE2 A:HIS116 4.1 10.7 1.0
ND1 A:HIS263 4.1 11.8 1.0
O22 A:VII1410 4.2 13.1 1.0
CG A:HIS121 4.2 14.2 1.0
CE1 A:HIS116 4.2 9.7 1.0
CG A:HIS263 4.2 12.9 1.0
CB A:ASP120 4.2 13.1 1.0
C19 A:VII1410 4.2 20.2 1.0
C12 A:VII1410 4.3 19.1 1.0
C13 A:VII1410 4.4 16.4 1.0
O11 A:VII1410 4.4 19.2 1.0
C7 A:VII1410 4.5 18.8 1.0
OG A:SER221 4.6 14.6 1.0
NE2 A:HIS196 4.9 13.8 1.0

Zinc binding site 3 out of 4 in 2gfk

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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 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:18.3
occ:1.00
O23 B:VII2410 1.9 19.4 1.0
NE2 B:HIS116 2.0 12.6 1.0
NE2 B:HIS196 2.1 15.1 1.0
ND1 B:HIS118 2.1 13.4 1.0
C18 B:VII2410 2.6 20.0 1.0
O22 B:VII2410 2.7 19.6 1.0
CD2 B:HIS196 2.9 12.5 1.0
CD2 B:HIS116 2.9 11.0 1.0
CE1 B:HIS116 3.0 11.0 1.0
CE1 B:HIS118 3.1 14.8 1.0
O B:HOH2540 3.2 18.4 1.0
CG B:HIS118 3.2 13.3 1.0
CE1 B:HIS196 3.2 8.4 1.0
CB B:HIS118 3.5 12.8 1.0
ZN B:ZN402 3.6 18.9 1.0
ND1 B:HIS116 4.0 11.0 1.0
CG B:HIS116 4.0 12.0 1.0
C9 B:VII2410 4.1 22.3 1.0
CG B:HIS196 4.1 12.0 1.0
OD1 B:ASP120 4.1 14.7 1.0
NE2 B:HIS118 4.2 15.4 1.0
ND1 B:HIS196 4.2 12.0 1.0
O21 B:VII2410 4.2 21.1 1.0
CD2 B:HIS118 4.3 12.2 1.0
NE2 B:HIS121 4.3 13.0 1.0
CD2 B:HIS121 4.3 13.9 1.0
C13 B:VII2410 4.8 22.6 1.0
OD2 B:ASP120 4.9 15.9 1.0
CA B:HIS118 5.0 13.6 1.0
CG B:ASP120 5.0 13.9 1.0
CG2 B:THR197 5.0 12.8 1.0
C8 B:VII2410 5.0 23.4 1.0

Zinc binding site 4 out of 4 in 2gfk

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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 2)


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 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:18.9
occ:1.00
NE2 B:HIS121 2.0 13.0 1.0
OD2 B:ASP120 2.1 15.9 1.0
NE2 B:HIS263 2.1 11.3 1.0
O23 B:VII2410 2.2 19.4 1.0
O B:HOH2540 2.4 18.4 1.0
CG B:ASP120 2.8 13.9 1.0
CE1 B:HIS121 2.9 14.5 1.0
OD1 B:ASP120 3.0 14.7 1.0
CE1 B:HIS263 3.0 15.0 1.0
C18 B:VII2410 3.0 20.0 1.0
CD2 B:HIS121 3.1 13.9 1.0
CD2 B:HIS263 3.2 15.0 1.0
C9 B:VII2410 3.2 22.3 1.0
ZN B:ZN401 3.6 18.3 1.0
C8 B:VII2410 3.7 23.4 1.0
O21 B:VII2410 3.8 21.1 1.0
C10 B:VII2410 3.8 24.0 1.0
ND1 B:HIS121 4.0 13.9 1.0
NE2 B:HIS116 4.0 12.6 1.0
CE1 B:HIS116 4.1 11.0 1.0
ND1 B:HIS263 4.1 13.2 1.0
CG B:HIS121 4.2 14.2 1.0
C19 B:VII2410 4.2 25.2 1.0
O22 B:VII2410 4.2 19.6 1.0
CG B:HIS263 4.2 14.9 1.0
CB B:ASP120 4.2 13.8 1.0
C12 B:VII2410 4.3 24.6 1.0
C13 B:VII2410 4.4 22.6 1.0
O11 B:VII2410 4.5 25.6 1.0
C7 B:VII2410 4.5 24.4 1.0
OG B:SER221 4.7 13.4 1.0
NE2 B:HIS196 4.9 15.1 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: Sat Sep 26 02:08:01 2020
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