Zinc in PDB 8sko: X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound

All present enzymatic activity of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound:
3.5.2.6;

The structure of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound, PDB code: 8sko 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)	32.98 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.136, 59.265, 84.241, 90, 98.5, 90
R / Rfree (%)	19.9 / 22.3

The binding sites of Zinc atom in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound (pdb code 8sko). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound, PDB code: 8sko:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound


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 with L-Captopril Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.8 occ:1.00 ND1 A:HIS122 2.0 9.0 1.0 NE2 A:HIS120 2.1 7.5 1.0 NE2 A:HIS189 2.1 8.7 1.0 S A:X8Z303 2.3 15.2 0.8 CE1 A:HIS122 2.9 8.1 1.0 CE1 A:HIS120 3.0 7.4 1.0 CE1 A:HIS189 3.0 9.3 1.0 CG A:HIS122 3.0 7.1 1.0 CD2 A:HIS189 3.1 8.6 1.0 CD2 A:HIS120 3.1 7.4 1.0 C1 A:X8Z303 3.2 15.7 0.8 CB A:HIS122 3.4 6.9 1.0 ZN A:ZN302 3.6 13.7 1.0 SG A:CYS208 3.8 8.8 1.0 CB A:CYS208 4.0 8.1 1.0 OD1 A:ASP124 4.1 9.3 1.0 NE2 A:HIS122 4.1 7.6 1.0 ND1 A:HIS120 4.1 7.0 1.0 ND1 A:HIS189 4.2 8.7 1.0 CG A:HIS120 4.2 7.0 1.0 CD2 A:HIS122 4.2 7.5 1.0 CG A:HIS189 4.2 8.7 1.0 CG2 A:THR190 4.4 10.0 1.0 OD2 A:ASP124 4.7 8.6 1.0 C2 A:X8Z303 4.7 18.2 0.8 CG A:ASP124 4.8 7.6 1.0 CA A:HIS122 4.9 6.1 1.0 O A:HOH550 5.0 30.1 1.0

Zinc binding site 2 out of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound


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 with L-Captopril Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.7 occ:1.00 OD2 A:ASP124 2.0 8.6 1.0 S A:X8Z303 2.1 15.2 0.8 NE2 A:HIS250 2.1 6.4 1.0 SG A:CYS208 2.3 8.8 1.0 CG A:ASP124 2.9 7.6 1.0 CE1 A:HIS250 3.0 7.8 1.0 CD2 A:HIS250 3.1 7.2 1.0 C1 A:X8Z303 3.2 15.7 0.8 OD1 A:ASP124 3.3 9.3 1.0 CB A:CYS208 3.4 8.1 1.0 ZN A:ZN301 3.6 8.8 1.0 C2 A:X8Z303 3.8 18.2 0.8 ND1 A:HIS250 4.2 6.8 1.0 CG A:HIS250 4.2 7.8 1.0 CB A:ASP124 4.3 6.4 1.0 C4 A:X8Z303 4.3 20.8 0.8 CB A:SER249 4.4 6.8 1.0 NE2 A:HIS189 4.4 8.7 1.0 C5 A:X8Z303 4.4 23.3 0.8 N A:X8Z303 4.5 23.0 0.8 O A:HOH543 4.5 25.6 1.0 NE2 A:HIS120 4.6 7.5 1.0 OG A:SER249 4.6 6.7 1.0 CE1 A:HIS189 4.7 9.3 1.0 CA A:CYS208 4.7 9.0 1.0 CE1 A:HIS120 4.7 7.4 1.0

Zinc binding site 3 out of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:8.9 occ:1.00 ND1 B:HIS122 2.0 7.6 1.0 NE2 B:HIS189 2.1 9.6 1.0 NE2 B:HIS120 2.1 6.9 1.0 S B:X8Z303 2.3 14.3 0.8 CE1 B:HIS120 3.0 6.4 1.0 CE1 B:HIS122 3.0 7.5 1.0 CE1 B:HIS189 3.0 10.5 1.0 CG B:HIS122 3.0 7.4 1.0 CD2 B:HIS189 3.1 9.0 1.0 CD2 B:HIS120 3.1 6.7 1.0 C1 B:X8Z303 3.2 16.8 0.8 CB B:HIS122 3.4 6.7 1.0 ZN B:ZN302 3.6 12.8 1.0 SG B:CYS208 3.9 10.5 1.0 OD1 B:ASP124 4.0 8.1 1.0 CB B:CYS208 4.0 9.6 1.0 NE2 B:HIS122 4.1 8.0 1.0 ND1 B:HIS120 4.1 6.4 1.0 CD2 B:HIS122 4.1 7.8 1.0 ND1 B:HIS189 4.1 10.4 1.0 CG B:HIS120 4.2 6.8 1.0 CG B:HIS189 4.2 9.3 1.0 CG2 B:THR190 4.4 9.6 1.0 C2 B:X8Z303 4.6 18.7 0.8 OD2 B:ASP124 4.7 9.4 1.0 CG B:ASP124 4.8 7.8 1.0 CA B:HIS122 4.9 6.1 1.0 O1 B:X8Z303 5.0 18.9 0.8

Zinc binding site 4 out of 4 in the X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Structure of the Ndm-4 Beta-Lactamase From Klebsiella Pneumonia with L-Captopril Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.8 occ:1.00 OD2 B:ASP124 2.0 9.4 1.0 NE2 B:HIS250 2.1 8.3 1.0 S B:X8Z303 2.1 14.3 0.8 SG B:CYS208 2.4 10.5 1.0 CG B:ASP124 2.9 7.8 1.0 CE1 B:HIS250 3.0 9.8 1.0 CD2 B:HIS250 3.1 9.2 1.0 OD1 B:ASP124 3.2 8.1 1.0 C1 B:X8Z303 3.3 16.8 0.8 CB B:CYS208 3.4 9.6 1.0 ZN B:ZN301 3.6 8.9 1.0 C2 B:X8Z303 3.8 18.7 0.8 ND1 B:HIS250 4.2 9.8 1.0 C5 B:X8Z303 4.2 23.5 0.8 CG B:HIS250 4.2 10.2 1.0 CB B:ASP124 4.3 6.8 1.0 C4 B:X8Z303 4.3 21.1 0.8 CB B:SER249 4.3 7.0 1.0 N B:X8Z303 4.4 22.9 0.8 NE2 B:HIS189 4.4 9.6 1.0 O B:HOH548 4.6 28.1 1.0 OG B:SER249 4.6 7.6 1.0 NE2 B:HIS120 4.6 6.9 1.0 CE1 B:HIS189 4.6 10.5 1.0 CE1 B:HIS120 4.7 6.4 1.0 CA B:CYS208 4.7 9.3 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