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Zinc in PDB 5zr8: Crystal Structure of Ndm-1 Metallo-Beta-Lactamase

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase, PDB code: 5zr8 was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.56 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.080, 73.900, 77.750, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 16.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase (pdb code 5zr8). 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 Ndm-1 Metallo-Beta-Lactamase, PDB code: 5zr8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5zr8

Go back to Zinc Binding Sites List in 5zr8
Zinc binding site 1 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase


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 Ndm-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:10.0
occ:1.00
 ND1 A:HIS122 2.0 10.2 1.0
NE2 A:HIS189 2.0 9.1 1.0
NE2 A:HIS120 2.0 8.0 1.0
O A:HOH584 2.3 7.8 1.0
CE1 A:HIS120 3.0 8.9 1.0
CE1 A:HIS122 3.0 10.6 1.0
CG A:HIS122 3.0 9.1 1.0
CE1 A:HIS189 3.0 9.0 1.0
CD2 A:HIS189 3.0 8.7 1.0
CD2 A:HIS120 3.1 8.2 1.0
CB A:HIS122 3.4 6.9 1.0
ZN A:ZN302 3.7 11.3 1.0
OD1 A:ASP124 4.0 12.5 1.0
ND1 A:HIS120 4.1 8.2 1.0
NE2 A:HIS122 4.1 11.7 1.0
SG A:CYS208 4.1 9.3 1.0
CD2 A:HIS122 4.1 10.2 1.0
ND1 A:HIS189 4.1 8.5 1.0
CG A:HIS120 4.2 7.5 1.0
CG A:HIS189 4.2 9.6 1.0
CB A:CYS208 4.3 9.4 1.0
CG2 A:THR190 4.5 8.8 1.0
OD2 A:ASP124 4.7 12.0 1.0
CG A:ASP124 4.8 9.7 1.0
CA A:HIS122 4.8 6.7 1.0

Zinc binding site 2 out of 6 in 5zr8

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Zinc binding site 2 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase


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 Ndm-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.3
occ:1.00
 OD2 A:ASP124 1.9 12.0 1.0
NE2 A:HIS250 2.0 10.5 1.0
O A:HOH584 2.3 7.8 1.0
SG A:CYS208 2.3 9.3 1.0
CG A:ASP124 3.0 9.7 1.0
CE1 A:HIS250 3.0 10.2 1.0
CD2 A:HIS250 3.1 10.6 1.0
OD1 A:ASP124 3.3 12.5 1.0
CB A:CYS208 3.4 9.4 1.0
ZN A:ZN301 3.7 10.0 1.0
ND1 A:HIS250 4.1 10.6 1.0
CG A:HIS250 4.2 10.4 1.0
CB A:SER249 4.2 9.1 1.0
O A:HOH576 4.2 33.2 1.0
CB A:ASP124 4.3 7.7 1.0
CE1 A:HIS120 4.4 8.9 1.0
NE2 A:HIS189 4.5 9.1 1.0
NE2 A:HIS120 4.5 8.0 1.0
OG A:SER249 4.5 9.3 1.0
CA A:CYS208 4.6 8.0 1.0
CE1 A:HIS189 4.7 9.0 1.0
CE A:LYS125 4.9 8.7 1.0
CD A:LYS125 5.0 8.7 1.0

Zinc binding site 3 out of 6 in 5zr8

Go back to Zinc Binding Sites List in 5zr8
Zinc binding site 3 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase


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 Ndm-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:21.9
occ:1.00
 OD2 A:ASP223 2.0 16.9 1.0
OE2 A:GLU152 2.1 19.7 1.0
OE2 E:GLU227 2.1 35.1 1.0
OE1 E:GLU227 2.6 32.9 1.0
CD E:GLU227 2.6 29.1 1.0
OE1 A:GLU152 2.7 17.9 1.0
CD A:GLU152 2.7 16.2 1.0
CG A:ASP223 2.8 20.9 1.0
OD1 A:ASP223 2.9 21.2 1.0
O A:HOH514 3.9 18.2 1.0
NE2 E:HIS228 4.1 17.1 1.0
NE2 A:HIS122 4.1 11.7 1.0
CG E:GLU227 4.2 23.5 1.0
CB A:ASP223 4.2 15.6 1.0
CG A:GLU152 4.2 13.3 1.0
CE1 E:HIS228 4.3 16.1 1.0
O A:HOH411 4.3 35.3 1.0
O E:HOH523 4.6 29.2 1.0
CD2 A:HIS122 4.7 10.2 1.0
CB E:GLU227 4.9 17.9 1.0
O A:HOH456 4.9 20.4 1.0

Zinc binding site 4 out of 6 in 5zr8

Go back to Zinc Binding Sites List in 5zr8
Zinc binding site 4 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase


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 Ndm-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:35.9
occ:1.00
 OD2 E:ASP223 2.0 19.9 1.0
OE2 A:GLU227 2.1 45.0 1.0
OE2 E:GLU152 2.1 26.3 1.0
O E:HOH548 2.3 35.9 1.0
OE1 E:GLU152 2.6 20.3 1.0
OE1 A:GLU227 2.7 54.4 1.0
CD A:GLU227 2.7 38.1 1.0
CD E:GLU152 2.8 21.3 1.0
CG E:ASP223 2.8 28.7 1.0
OD1 E:ASP223 2.9 30.9 1.0
O E:HOH543 4.0 18.3 1.0
NE2 E:HIS122 4.1 12.6 1.0
CE1 A:HIS228 4.2 18.3 1.0
NE2 A:HIS228 4.2 20.1 1.0
CG A:GLU227 4.2 25.1 1.0
CG E:GLU152 4.3 16.9 1.0
CB E:ASP223 4.3 20.4 1.0
CD2 E:HIS122 4.6 10.9 1.0
O E:HOH412 4.8 28.0 1.0

Zinc binding site 5 out of 6 in 5zr8

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Zinc binding site 5 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase


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 Ndm-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:11.1
occ:1.00
 NE2 E:HIS189 2.0 8.8 1.0
NE2 E:HIS120 2.0 8.6 1.0
ND1 E:HIS122 2.0 13.2 1.0
O E:HOH596 2.2 9.1 1.0
CE1 E:HIS120 3.0 8.9 1.0
CE1 E:HIS189 3.0 11.1 1.0
CE1 E:HIS122 3.0 12.2 1.0
CD2 E:HIS120 3.0 7.7 1.0
CD2 E:HIS189 3.1 9.9 1.0
CG E:HIS122 3.1 9.4 1.0
CB E:HIS122 3.4 8.2 1.0
ZN E:ZN302 3.7 12.4 1.0
OD1 E:ASP124 4.0 16.2 1.0
SG E:CYS208 4.1 10.1 1.0
ND1 E:HIS120 4.1 8.6 1.0
ND1 E:HIS189 4.1 11.1 1.0
NE2 E:HIS122 4.1 12.6 1.0
CG E:HIS120 4.2 7.5 1.0
CG E:HIS189 4.2 9.6 1.0
CD2 E:HIS122 4.2 10.9 1.0
CB E:CYS208 4.3 9.6 1.0
ND2 E:ASN220 4.5 53.3 1.0
CG2 E:THR190 4.5 10.3 1.0
OD2 E:ASP124 4.7 11.7 1.0
CG E:ASP124 4.8 13.1 1.0
CA E:HIS122 4.9 8.1 1.0
O E:HOH441 5.0 20.4 1.0

Zinc binding site 6 out of 6 in 5zr8

Go back to Zinc Binding Sites List in 5zr8
Zinc binding site 6 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase


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 Ndm-1 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn302

b:12.4
occ:1.00
 OD2 E:ASP124 2.0 11.7 1.0
NE2 E:HIS250 2.1 12.9 1.0
O E:HOH596 2.2 9.1 1.0
SG E:CYS208 2.3 10.1 1.0
CG E:ASP124 2.9 13.1 1.0
CE1 E:HIS250 3.0 13.1 1.0
CD2 E:HIS250 3.1 10.8 1.0
OD1 E:ASP124 3.3 16.2 1.0
CB E:CYS208 3.4 9.6 1.0
ZN E:ZN301 3.7 11.1 1.0
ND1 E:HIS250 4.2 12.8 1.0
CG E:HIS250 4.2 13.1 1.0
CB E:SER249 4.2 10.0 1.0
CB E:ASP124 4.3 10.0 1.0
O E:HOH514 4.3 40.2 1.0
NE2 E:HIS189 4.4 8.8 1.0
CE1 E:HIS120 4.4 8.9 1.0
NE2 E:HIS120 4.5 8.6 1.0
OG E:SER249 4.6 9.7 1.0
CE1 E:HIS189 4.6 11.1 1.0
CA E:CYS208 4.6 8.6 1.0
CE E:LYS125 4.8 9.4 1.0
CD E:LYS125 4.9 8.6 1.0

Reference:

J.Wachino, J.Wachino. N/A N/A.
Page generated: Mon Oct 28 17:06:58 2024

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