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Calcium in PDB 6cac: Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop

Enzymatic activity of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop

All present enzymatic activity of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop, PDB code: 6cac was solved by P.M.Alzari, E.Giannini, A.Palacios, M.Mojica, R.Bonomo, L.Llarrull, A.Vila, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.87 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.707, 91.737, 134.329, 90.00, 107.16, 90.00
R / Rfree (%) 16.3 / 18.1

Other elements in 6cac:

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop also contains other interesting chemical elements:

Nickel (Ni) 5 atoms
Cobalt (Co) 4 atoms
Zinc (Zn) 4 atoms
Cadmium (Cd) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop (pdb code 6cac). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop, PDB code: 6cac:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6cac

Go back to Calcium Binding Sites List in 6cac
Calcium binding site 1 out of 4 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop


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 Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1006

b:37.2
occ:1.00
 OD2 A:ASP96 2.3 38.5 1.0
O A:HOH1215 2.5 25.9 1.0
OD2 A:ASP131 2.5 48.8 1.0
O A:HOH1317 2.7 54.5 1.0
CG A:ASP96 3.1 35.4 1.0
CG A:ASP131 3.2 41.5 1.0
OD1 A:ASP96 3.3 35.7 1.0
CB A:ASP131 3.5 29.7 1.0
O A:HOH1103 4.2 46.4 1.0
OD1 A:ASP131 4.3 41.4 1.0
O A:GLY128 4.3 29.5 1.0
O A:HOH1134 4.3 53.5 1.0
O A:HOH1244 4.4 40.9 1.0
O A:HOH1190 4.5 34.1 1.0
CG2 A:VAL156 4.5 27.5 1.0
N A:ASP131 4.5 27.5 1.0
CB A:ASP96 4.6 30.1 1.0
O A:HOH1141 4.6 26.3 1.0
CA A:ASP131 4.6 26.9 1.0

Calcium binding site 2 out of 4 in 6cac

Go back to Calcium Binding Sites List in 6cac
Calcium binding site 2 out of 4 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop


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 Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1005

b:44.2
occ:1.00
 OD2 B:ASP96 2.4 43.8 1.0
O B:HOH1244 2.5 35.0 1.0
OD2 B:ASP131 2.5 53.7 1.0
O B:HOH1296 2.8 55.6 1.0
O B:HOH1131 3.0 58.9 1.0
CG B:ASP96 3.2 39.1 1.0
CG B:ASP131 3.4 44.1 1.0
OD1 B:ASP96 3.4 36.6 1.0
CB B:ASP131 3.7 34.2 1.0
O B:GLY128 4.2 33.2 1.0
OD1 B:ASP131 4.4 43.5 1.0
O B:HOH1197 4.4 39.9 1.0
O B:HOH1162 4.5 39.8 1.0
O B:HOH1129 4.5 27.9 1.0
CB B:ASP96 4.6 34.0 1.0
N B:ASP131 4.6 30.5 1.0
CG2 B:VAL156 4.7 33.0 1.0
CA B:ASP131 4.8 31.0 1.0

Calcium binding site 3 out of 4 in 6cac

Go back to Calcium Binding Sites List in 6cac
Calcium binding site 3 out of 4 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1005

b:36.5
occ:1.00
 O C:HOH1272 2.2 57.8 1.0
O C:HOH1246 2.2 54.1 1.0
OD2 C:ASP96 2.3 47.9 1.0
O C:HOH1209 2.5 32.4 1.0
OD2 C:ASP131 2.5 47.9 1.0
CG C:ASP96 3.2 45.4 1.0
CG C:ASP131 3.3 42.8 1.0
OD1 C:ASP96 3.4 47.5 1.0
CB C:ASP131 3.6 33.0 1.0
O C:GLY128 4.1 36.7 1.0
O C:HOH1183 4.3 37.1 1.0
OD1 C:ASP131 4.3 43.0 1.0
O C:HOH1133 4.5 30.2 1.0
O C:HOH1181 4.5 47.5 1.0
N C:ASP131 4.6 30.6 1.0
CB C:ASP96 4.6 34.8 1.0
CG2 C:VAL156 4.7 32.8 1.0
CA C:ASP131 4.7 31.0 1.0

Calcium binding site 4 out of 4 in 6cac

Go back to Calcium Binding Sites List in 6cac
Calcium binding site 4 out of 4 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase Harboring An Insertion of A Pro Residue in L3 Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1005

b:49.6
occ:1.00
 OD2 D:ASP96 2.3 49.3 1.0
OD2 D:ASP131 2.5 49.7 1.0
O D:HOH1215 2.6 30.9 1.0
CG D:ASP96 3.3 42.6 1.0
CG D:ASP131 3.3 44.5 1.0
OD1 D:ASP96 3.5 41.0 1.0
CB D:ASP131 3.7 33.3 1.0
O D:HOH1184 3.8 67.1 1.0
O D:HOH1101 3.9 41.4 1.0
O D:GLY128 4.3 31.7 1.0
OD1 D:ASP131 4.3 44.9 1.0
O D:HOH1194 4.4 39.4 1.0
O D:HOH1171 4.5 49.6 1.0
CG2 D:VAL156 4.6 30.4 1.0
CB D:ASP96 4.6 31.9 1.0
O D:HOH1156 4.6 30.5 1.0
N D:ASP131 4.7 29.1 1.0
CA D:ASP131 4.8 30.0 1.0

Reference:

A.R.Palacios, M.F.Mojica, E.Giannini, M.A.Taracila, C.R.Bethel, P.M.Alzari, L.H.Otero, S.Klinke, L.I.Llarrull, R.A.Bonomo, A.J.Vila. The Reaction Mechanism of Metallo-Beta-Lactamases Is Tuned By the Conformation of An Active-Site Mobile Loop. Antimicrob. Agents V. 63 2019CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 30348667
DOI: 10.1128/AAC.01754-18
Page generated: Wed Jul 9 13:02:13 2025

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