Zinc in PDB 6ovz: Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label

The structure of Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label, PDB code: 6ovz was solved by A.F.Monzingo, W.Fast, P.W.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.56 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.023, 73.903, 145.584, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.1

The structure of Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label (pdb code 6ovz). 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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label, PDB code: 6ovz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label


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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.9 occ:1.00 NE2 A:HIS250 2.1 16.7 1.0 OD2 A:ASP124 2.2 18.1 1.0 O A:HOH1180 2.2 12.0 1.0 SG A:CYS208 2.3 13.9 1.0 O A:HOH1187 2.4 14.8 1.0 CE1 A:HIS250 3.0 15.7 1.0 CD2 A:HIS250 3.1 18.4 1.0 CG A:ASP124 3.2 15.2 1.0 CB A:CYS208 3.4 13.6 1.0 OD1 A:ASP124 3.5 14.2 1.0 ZN A:ZN1002 3.8 15.7 1.0 ND1 A:HIS250 4.1 15.3 1.0 CB A:SER249 4.1 15.0 1.0 CG A:HIS250 4.2 14.5 1.0 NE2 A:HIS189 4.3 15.2 1.0 CA A:CYS208 4.5 13.1 1.0 OG A:SER249 4.5 17.9 1.0 CB A:ASP124 4.6 12.4 1.0 CE1 A:HIS189 4.6 15.7 1.0 CE1 A:HIS120 4.8 16.3 1.0 CE A:LYS125 4.8 17.8 1.0 NE2 A:HIS120 4.8 14.2 1.0 O A:HOH1129 4.8 21.1 1.0 O A:HOH1192 4.9 26.4 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label


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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:15.7 occ:1.00 O A:HOH1187 1.9 14.8 1.0 NE2 A:HIS189 2.1 15.2 1.0 ND1 A:HIS122 2.1 15.3 1.0 NE2 A:HIS120 2.1 14.2 1.0 CD2 A:HIS189 2.9 9.4 1.0 CG A:HIS122 3.0 13.1 1.0 CE1 A:HIS120 3.1 16.3 1.0 CE1 A:HIS122 3.1 11.8 1.0 CD2 A:HIS120 3.1 9.1 1.0 CE1 A:HIS189 3.1 15.7 1.0 CB A:HIS122 3.3 11.7 1.0 O A:HOH1180 3.8 12.0 1.0 ZN A:ZN1001 3.8 16.9 1.0 SG A:CYS208 4.0 13.9 1.0 CG A:HIS189 4.1 13.4 1.0 CB A:CYS208 4.1 13.6 1.0 OD1 A:ASP124 4.2 14.2 1.0 ND1 A:HIS120 4.2 13.7 1.0 CD2 A:HIS122 4.2 13.9 1.0 ND1 A:HIS189 4.2 13.3 1.0 NE2 A:HIS122 4.2 13.8 1.0 ND2 A:ASN220 4.2 27.1 1.0 CG A:HIS120 4.2 11.0 1.0 CG2 A:THR190 4.4 11.9 1.0 CA A:HIS122 4.8 13.5 1.0 OD2 A:ASP124 4.9 18.1 1.0 CG A:ASP124 5.0 15.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label


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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:39.3 occ:1.00 OD2 A:ASP223 2.4 22.8 1.0 O A:HOH1198 2.4 18.6 1.0 OE1 A:GLU152 2.6 18.5 1.0 OE2 A:GLU152 2.7 21.9 1.0 O A:HOH1191 2.7 28.2 1.0 OD1 A:ASP223 3.0 22.2 1.0 CD A:GLU152 3.0 17.0 1.0 CG A:ASP223 3.1 17.7 1.0 NE2 A:HIS122 4.2 13.8 1.0 CG A:GLU152 4.5 11.9 1.0 CB A:ASP223 4.5 12.4 1.0 O A:HOH1146 4.6 19.7 1.0 O A:HOH1204 4.6 15.0 1.0 CD2 A:HIS122 4.8 13.9 1.0 O B:HOH1141 4.9 25.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label


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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:19.3 occ:1.00 OD2 B:ASP124 2.1 15.6 1.0 NE2 B:HIS250 2.1 17.5 1.0 O B:HOH1130 2.2 12.4 1.0 SG B:CYS208 2.3 17.3 1.0 O B:HOH1139 2.6 16.2 1.0 CE1 B:HIS250 3.0 17.7 1.0 CG B:ASP124 3.1 18.0 1.0 CD2 B:HIS250 3.3 20.7 1.0 CB B:CYS208 3.4 16.1 1.0 OD1 B:ASP124 3.5 15.3 1.0 O2 B:FMT1005 3.8 26.2 1.0 ZN B:ZN1002 4.0 18.6 1.0 ND1 B:HIS250 4.2 18.3 1.0 CB B:SER249 4.3 11.8 1.0 CG B:HIS250 4.3 20.5 1.0 CAD B:N9J1006 4.4 25.8 1.0 CB B:ASP124 4.4 16.2 1.0 NE2 B:HIS189 4.5 13.9 1.0 CA B:CYS208 4.6 14.4 1.0 OG B:SER249 4.6 12.8 1.0 CE1 B:HIS189 4.7 16.5 1.0 CE1 B:HIS120 4.8 13.1 1.0 NE2 B:HIS120 4.9 16.4 1.0 CAG B:N9J1006 5.0 27.9 1.0 C B:FMT1005 5.0 26.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label


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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:18.6 occ:1.00 ND1 B:HIS122 2.0 18.1 1.0 O B:HOH1139 2.0 16.2 1.0 NE2 B:HIS189 2.1 13.9 1.0 NE2 B:HIS120 2.1 16.4 1.0 CG B:HIS122 2.9 19.4 1.0 CE1 B:HIS122 3.0 16.3 1.0 CD2 B:HIS189 3.0 12.9 1.0 CE1 B:HIS120 3.0 13.1 1.0 CD2 B:HIS120 3.1 12.8 1.0 CE1 B:HIS189 3.1 16.5 1.0 CB B:HIS122 3.2 11.8 1.0 O B:HOH1130 3.8 12.4 1.0 ZN B:ZN1001 4.0 19.3 1.0 NE2 B:HIS122 4.0 16.5 1.0 CD2 B:HIS122 4.0 17.8 1.0 SG B:CYS208 4.1 17.3 1.0 OD1 B:ASP124 4.1 15.3 1.0 ND1 B:HIS120 4.1 14.0 1.0 CG B:HIS189 4.2 12.8 1.0 CG B:HIS120 4.2 14.4 1.0 ND1 B:HIS189 4.2 15.9 1.0 CG2 B:THR190 4.3 12.9 1.0 CB B:CYS208 4.3 16.1 1.0 CA B:HIS122 4.7 12.8 1.0 OD2 B:ASP124 4.8 15.6 1.0 CG B:ASP124 4.9 18.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label


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 the New Delhi Metallo-Beta-Lactamase-1 Adduct with A Lysine-Targeted Affinity Label within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1003 b:60.8 occ:1.00 OE1 B:GLU152 2.7 23.4 1.0 OD2 B:ASP223 2.7 27.9 1.0 OE2 B:GLU152 3.0 30.6 1.0 OD1 B:ASP223 3.2 31.6 1.0 CD B:GLU152 3.2 24.5 1.0 CG B:ASP223 3.3 30.1 1.0 NE2 B:HIS122 4.2 16.5 1.0 O B:HOH1120 4.6 25.5 1.0 CG B:GLU152 4.7 19.9 1.0 CB B:ASP223 4.8 23.9 1.0 CD2 B:HIS122 4.8 17.8 1.0

P.W.Thomas, M.Cammarata, J.S.Brodbelt, A.F.Monzingo, R.F.Pratt, W.Fast. A Lysine-Targeted Affinity Label For Serine-Beta-Lactamase Also Covalently Modifies New Delhi Metallo-Beta-Lactamase-1 (Ndm-1). Biochemistry V. 58 2834 2019.
ISSN: ISSN 0006-2960
PubMed: 31145588
DOI: 10.1021/ACS.BIOCHEM.9B00393