Calcium 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:

Zinc

(Zn)

6 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca1004 b:23.1 occ:1.00 OD2 A:ASP130 2.3 24.5 1.0 OD2 A:ASP95 2.3 19.1 1.0 O A:HOH1200 2.4 25.8 1.0 O A:HOH1210 2.4 20.7 1.0 O A:HOH1154 2.4 23.6 1.0 O A:HOH1158 2.5 26.7 1.0 O A:HOH1142 2.6 17.4 1.0 CG A:ASP130 3.3 23.0 1.0 CG A:ASP95 3.3 18.7 1.0 OD1 A:ASP95 3.7 13.9 1.0 CB A:ASP130 3.7 15.6 1.0 O A:HOH1223 4.1 23.9 1.0 O A:HOH1176 4.3 16.8 1.0 O A:HOH1203 4.3 13.9 1.0 O A:GLY127 4.4 15.2 1.0 OD1 A:ASP130 4.4 23.9 1.0 CB A:ASP95 4.7 14.0 1.0 O A:HOH1115 4.8 14.4 1.0 N A:ASP130 4.8 18.3 1.0 CA A:ASP130 4.9 17.1 1.0 CG2 A:VAL155 5.0 15.8 1.0

Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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 B:Ca1004 b:25.8 occ:1.00 OD2 B:ASP95 2.4 24.1 1.0 OD2 B:ASP130 2.5 20.4 1.0 O B:HOH1112 2.6 19.4 1.0 O B:HOH1157 2.7 15.4 1.0 CG B:ASP95 3.5 20.4 1.0 CG B:ASP130 3.5 21.6 1.0 OD1 B:ASP95 3.8 17.1 1.0 O B:HOH1118 3.9 26.1 1.0 CB B:ASP130 3.9 20.1 1.0 O B:HOH1163 4.3 13.5 1.0 O B:GLY127 4.4 15.9 1.0 OD1 B:ASP130 4.6 23.7 1.0 O B:HOH1184 4.6 15.9 1.0 O B:HOH1147 4.7 15.0 1.0 CB B:ASP95 4.8 14.7 1.0 CG2 B:VAL155 4.8 18.2 1.0 N B:ASP130 4.9 15.4 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