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Zinc in PDB 8skp: X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid

Enzymatic activity of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid

All present enzymatic activity of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid:
3.5.2.6;

Protein crystallography data

The structure of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid, PDB code: 8skp was solved by J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.97 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.138, 59.185, 42.266, 90, 98.5, 90
R / Rfree (%) 20.2 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid (pdb code 8skp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid, PDB code: 8skp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8skp

Go back to Zinc Binding Sites List in 8skp
Zinc binding site 1 out of 2 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:12.0
occ:1.00
 O A:HOH436 1.9 15.4 1.0
ND1 A:HIS122 2.0 12.0 1.0
NE2 A:HIS189 2.0 13.7 1.0
NE2 A:HIS120 2.1 9.3 1.0
CD2 A:HIS189 3.0 11.3 1.0
CE1 A:HIS120 3.0 9.1 1.0
CE1 A:HIS122 3.0 12.5 1.0
CG A:HIS122 3.0 9.9 1.0
CE1 A:HIS189 3.1 14.4 1.0
CD2 A:HIS120 3.1 9.1 1.0
O A:HOH462 3.3 23.6 1.0
CB A:HIS122 3.4 8.9 1.0
ZN A:ZN302 3.5 15.5 1.0
O1 A:WAF303 3.6 19.0 1.0
SG A:CYS208 3.8 12.8 1.0
OD1 A:ASP124 4.0 12.5 1.0
CB A:CYS208 4.1 12.0 1.0
NE2 A:HIS122 4.1 12.1 1.0
ND1 A:HIS120 4.1 8.5 1.0
CD2 A:HIS122 4.1 10.4 1.0
ND1 A:HIS189 4.1 14.0 1.0
CG A:HIS189 4.1 14.0 1.0
CG A:HIS120 4.2 9.3 1.0
CG2 A:THR190 4.4 13.6 1.0
OD2 A:ASP124 4.5 11.3 1.0
CG A:ASP124 4.7 9.9 1.0
S A:WAF303 4.9 21.2 1.0
CA A:HIS122 4.9 8.0 1.0
N6 A:WAF303 4.9 21.5 1.0

Zinc binding site 2 out of 2 in 8skp

Go back to Zinc Binding Sites List in 8skp
Zinc binding site 2 out of 2 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia in Complex with 1-Hydroxypyridine-2(1H)-Thione-6-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:15.5
occ:1.00
 O A:HOH436 2.0 15.4 1.0
O1 A:WAF303 2.0 19.0 1.0
OD2 A:ASP124 2.1 11.3 1.0
NE2 A:HIS250 2.2 11.4 1.0
S A:WAF303 2.6 21.2 1.0
SG A:CYS208 2.7 12.8 1.0
N6 A:WAF303 2.7 21.5 1.0
C1 A:WAF303 3.0 22.8 1.0
CG A:ASP124 3.0 9.9 1.0
CE1 A:HIS250 3.1 12.1 1.0
CD2 A:HIS250 3.2 11.9 1.0
OD1 A:ASP124 3.3 12.5 1.0
ZN A:ZN301 3.5 12.0 1.0
CB A:CYS208 3.8 12.0 1.0
O A:HOH462 3.9 23.6 1.0
C5 A:WAF303 3.9 23.8 1.0
C2 A:WAF303 4.2 23.8 1.0
ND1 A:HIS250 4.3 12.0 1.0
CG A:HIS250 4.3 12.4 1.0
CB A:ASP124 4.3 9.2 1.0
NE2 A:HIS189 4.3 13.7 1.0
CE1 A:HIS189 4.5 14.4 1.0
C7 A:WAF303 4.5 22.4 1.0
CB A:SER249 4.8 11.0 1.0
O3 A:WAF303 4.8 23.9 1.0
NE2 A:HIS120 4.8 9.3 1.0
C4 A:WAF303 4.9 25.4 1.0

Reference:

J.B.Thoden, B.M.Benin, A.Priebe, W.S.Shin, R.Muthyala, Y.Y.Sham, H.M.Holden. Characterization of A Novel Inhibitor For the New Delhi Metallo-Beta-Lactamase-4: Implications For Drug Design and Combating Bacterial Drug Resistance. J.Biol.Chem. 05135 2023.
ISSN: ESSN 1083-351X
PubMed: 37549809
DOI: 10.1016/J.JBC.2023.105135
Page generated: Fri Aug 22 13:22:01 2025

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