Zinc in PDB 8sk2: X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia, Apo Form

All present enzymatic activity of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia, Apo Form:
3.5.2.6;

The structure of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia, Apo Form, PDB code: 8sk2 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)	33.91 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.927, 59.312, 41.815, 90, 98.65, 90
R / Rfree (%)	17.8 / 19.9

The binding sites of Zinc atom in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia, Apo Form (pdb code 8sk2). 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, Apo Form, PDB code: 8sk2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.8 occ:1.00 O A:HOH455 1.8 11.9 1.0 NE2 A:HIS189 2.0 9.5 1.0 NE2 A:HIS120 2.0 6.7 1.0 ND1 A:HIS122 2.1 9.0 1.0 CE1 A:HIS120 3.0 6.9 1.0 CD2 A:HIS189 3.0 9.6 1.0 CE1 A:HIS122 3.0 10.0 1.0 CE1 A:HIS189 3.0 10.1 1.0 CD2 A:HIS120 3.1 6.5 1.0 CG A:HIS122 3.1 8.0 1.0 O A:HOH440 3.4 25.6 1.0 CB A:HIS122 3.4 7.3 1.0 ZN A:ZN302 3.5 16.0 1.0 SG A:CYS208 3.8 11.8 1.0 O A:HOH537 3.9 15.3 1.0 OD1 A:ASP124 4.0 10.4 1.0 CB A:CYS208 4.1 9.9 1.0 ND1 A:HIS120 4.1 7.0 1.0 CG A:HIS189 4.1 9.8 1.0 NE2 A:HIS122 4.1 9.5 1.0 CG A:HIS120 4.2 6.8 1.0 ND1 A:HIS189 4.2 9.9 1.0 CD2 A:HIS122 4.2 9.0 1.0 O A:HOH475 4.4 22.8 1.0 CG2 A:THR190 4.5 10.7 1.0 OD2 A:ASP124 4.5 9.7 1.0 CG A:ASP124 4.7 8.5 1.0 CA A:HIS122 4.9 6.8 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia, Apo Form


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, Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.0 occ:1.00 O A:HOH475 2.0 22.8 1.0 O A:HOH455 2.0 11.9 1.0 O A:HOH537 2.1 15.3 1.0 NE2 A:HIS250 2.1 8.8 1.0 OD2 A:ASP124 2.1 9.7 1.0 SG A:CYS208 2.5 11.8 1.0 CE1 A:HIS250 3.1 11.4 1.0 CG A:ASP124 3.2 8.5 1.0 CD2 A:HIS250 3.2 9.6 1.0 OD1 A:ASP124 3.5 10.4 1.0 ZN A:ZN301 3.5 9.8 1.0 CB A:CYS208 3.5 9.9 1.0 O A:HOH559 3.9 21.4 1.0 O A:HOH440 3.9 25.6 1.0 NE2 A:HIS189 4.2 9.5 1.0 ND1 A:HIS250 4.2 9.4 1.0 CG A:HIS250 4.3 10.0 1.0 CE1 A:HIS189 4.3 10.1 1.0 CB A:ASP124 4.5 7.5 1.0 CB A:SER249 4.6 7.9 1.0 NE2 A:HIS120 4.7 6.7 1.0 CA A:CYS208 4.8 9.9 1.0 CE1 A:HIS120 4.9 6.9 1.0 OG A:SER249 4.9 8.4 1.0

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