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Zinc in PDB 3s0z: Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1)

Protein crystallography data

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1), PDB code: 3s0z was solved by Y.Guo, J.Wang, G.J.Niu, W.Q.Shui, Y.N.Sun, Z.Y.Lou, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 40.696, 40.696, 215.292, 90.00, 90.00, 120.00
R / Rfree (%) 23.4 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1) (pdb code 3s0z). 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 New Delhi Metallo-Beta-Lactamase (Ndm-1), PDB code: 3s0z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3s0z

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Zinc binding site 1 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:11.8
occ:1.00
O A:HOH368 2.0 27.3 1.0
SG A:CYS208 2.0 16.8 1.0
OD2 A:ASP124 2.8 18.1 1.0
ZN A:ZN1002 3.1 38.5 1.0
NE2 A:HIS250 3.2 15.7 1.0
CB A:CYS208 3.7 14.6 1.0
NE2 A:HIS189 3.7 10.3 1.0
CD2 A:HIS250 3.8 16.9 1.0
CG A:ASP124 3.9 16.9 1.0
CE1 A:HIS189 4.1 12.8 1.0
CE1 A:HIS250 4.3 14.9 1.0
CA A:CYS208 4.6 14.5 1.0
NZ A:LYS211 4.6 6.1 1.0
OD1 A:ASP124 4.6 16.3 1.0
CD2 A:HIS189 4.7 11.0 1.0
CB A:ASP124 4.8 15.6 1.0
OG A:SER249 4.9 20.7 1.0
CE A:LYS125 4.9 12.7 1.0
CE A:LYS211 4.9 6.2 1.0
CB A:ASN220 5.0 20.2 1.0

Zinc binding site 2 out of 4 in 3s0z

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Zinc binding site 2 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:38.5
occ:1.00
NE2 A:HIS189 2.2 10.3 1.0
CD2 A:HIS189 2.9 11.0 1.0
NE2 A:HIS120 3.0 16.4 1.0
CD2 A:HIS122 3.0 12.8 1.0
SG A:CYS208 3.1 16.8 1.0
ZN A:ZN1001 3.1 11.8 1.0
CG A:HIS122 3.1 13.5 1.0
OD2 A:ASP124 3.2 18.1 1.0
CE1 A:HIS189 3.4 12.8 1.0
OD1 A:ASP124 3.4 16.3 1.0
CB A:HIS122 3.6 14.4 1.0
NE2 A:HIS122 3.6 11.2 1.0
CG A:ASP124 3.7 16.9 1.0
ND1 A:HIS122 3.7 13.0 1.0
CB A:CYS208 3.8 14.6 1.0
CE1 A:HIS120 3.8 17.2 1.0
CE1 A:HIS122 3.9 12.9 1.0
CD2 A:HIS120 4.1 16.5 1.0
O A:HOH368 4.1 27.3 1.0
CG A:HIS189 4.2 12.4 1.0
ND1 A:HIS189 4.4 13.3 1.0
CG A:LYS125 4.8 16.2 1.0

Zinc binding site 3 out of 4 in 3s0z

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Zinc binding site 3 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:20.2
occ:1.00
SG B:CYS208 1.9 24.4 1.0
OD2 B:ASP124 2.7 21.1 1.0
O B:HOH341 2.8 30.5 1.0
NE2 B:HIS250 3.1 21.0 1.0
CE1 B:HIS250 3.2 19.1 1.0
CB B:CYS208 3.3 19.7 1.0
CG B:ASP124 3.6 20.1 1.0
ZN B:ZN1002 3.8 25.9 1.0
O B:HOH44 3.8 19.3 1.0
CA B:CYS208 4.1 19.5 1.0
CD2 B:HIS250 4.2 20.2 1.0
NE2 B:HIS189 4.3 12.4 1.0
OD1 B:ASP124 4.3 21.3 1.0
CE1 B:HIS189 4.3 12.4 1.0
ND1 B:HIS250 4.4 19.1 1.0
CB B:ASP124 4.5 18.4 1.0
CG B:HIS250 4.9 19.9 1.0
O B:CYS208 4.9 19.2 1.0

Zinc binding site 4 out of 4 in 3s0z

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Zinc binding site 4 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:25.9
occ:1.00
NE2 B:HIS120 2.1 10.9 1.0
ND1 B:HIS122 2.5 17.8 1.0
CB B:HIS122 2.9 17.2 1.0
CE1 B:HIS120 2.9 8.7 1.0
NE2 B:HIS189 2.9 12.4 1.0
CG B:HIS122 3.1 17.4 1.0
CD2 B:HIS189 3.1 12.6 1.0
CD2 B:HIS120 3.2 11.7 1.0
SG B:CYS208 3.2 24.4 1.0
CB B:CYS208 3.4 19.7 1.0
OD1 B:ASP124 3.5 21.3 1.0
OD2 B:ASP124 3.6 21.1 1.0
CE1 B:HIS122 3.7 16.4 1.0
ZN B:ZN1001 3.8 20.2 1.0
CG B:ASP124 4.0 20.1 1.0
CE1 B:HIS189 4.1 12.4 1.0
ND1 B:HIS120 4.1 11.4 1.0
CG B:HIS120 4.3 12.9 1.0
CG B:HIS189 4.3 12.6 1.0
CD2 B:HIS122 4.3 16.7 1.0
CA B:HIS122 4.4 16.9 1.0
CG B:LYS125 4.5 15.2 1.0
NE2 B:HIS122 4.6 15.8 1.0
ND1 B:HIS189 4.8 10.8 1.0
O B:HOH341 4.8 30.5 1.0
CG2 B:THR190 4.9 9.8 1.0
CA B:CYS208 4.9 19.5 1.0
C B:HIS122 5.0 17.0 1.0
N B:HIS122 5.0 16.2 1.0

Reference:

Y.Guo, J.Wang, G.Niu, W.Shui, Y.Sun, H.Zhou, Y.Zhang, C.Yang, Z.Lou, Z.Rao. A Structural View of the Antibiotic Degradation Enzyme Ndm-1 From A Superbug. Protein Cell 2011.
ISSN: ESSN 1674-8018
PubMed: 21637961
DOI: 10.1007/S13238-011-1055-9
Page generated: Wed Dec 16 04:48:28 2020

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