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Cobalt 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
Zinc (Zn) 4 atoms
Cadmium (Cd) 4 atoms
Calcium (Ca) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 4 binding sites of Cobalt 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 Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in 6cac

Go back to Cobalt Binding Sites List in 6cac
Cobalt 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 Cobalt with other atoms in the Co 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:Co1005

b:20.0
occ:1.00
 OD2 A:ASP224 2.3 35.0 1.0
OE2 B:GLU228 2.3 43.0 1.0
OE1 A:GLU153 2.4 35.3 1.0
OE1 B:GLU228 2.5 55.7 1.0
OE2 A:GLU153 2.6 34.1 1.0
CD B:GLU228 2.7 48.5 1.0
CD A:GLU153 2.9 37.3 1.0
OD1 A:ASP224 2.9 36.1 1.0
CG A:ASP224 2.9 35.0 1.0
O B:HOH1254 3.7 72.8 1.0
NE2 A:HIS123 4.2 25.4 1.0
O A:HOH1231 4.2 28.2 1.0
CG B:GLU228 4.3 34.2 1.0
O B:HOH1263 4.3 74.2 1.0
CG A:GLU153 4.4 29.9 1.0
CB A:ASP224 4.4 25.9 1.0
O A:HOH1205 4.4 53.1 1.0
NE2 B:HIS229 4.4 32.7 1.0
CE1 B:HIS229 4.7 32.5 1.0
CD2 A:HIS123 4.7 25.6 1.0
O B:HOH1191 4.8 38.6 1.0

Cobalt binding site 2 out of 4 in 6cac

Go back to Cobalt Binding Sites List in 6cac
Cobalt 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 Cobalt with other atoms in the Co 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:Co1004

b:24.3
occ:1.00
 O B:HOH1275 2.2 46.0 1.0
OD2 B:ASP224 2.2 36.3 1.0
OE2 A:GLU228 2.4 47.4 1.0
OE1 A:GLU228 2.4 40.4 1.0
OE1 B:GLU153 2.4 35.9 1.0
OE2 B:GLU153 2.6 37.9 1.0
CD A:GLU228 2.8 46.8 1.0
OD1 B:ASP224 2.8 39.2 1.0
CG B:ASP224 2.8 37.5 1.0
CD B:GLU153 2.9 40.5 1.0
O B:HOH1211 4.1 31.9 1.0
NE2 B:HIS123 4.2 31.1 1.0
CG A:GLU228 4.3 37.4 1.0
CB B:ASP224 4.3 33.3 1.0
NE2 A:HIS229 4.3 31.4 1.0
O B:HOH1290 4.3 59.8 1.0
O B:HOH1136 4.4 57.4 1.0
CG B:GLU153 4.4 28.4 1.0
O A:HOH1157 4.5 63.8 1.0
CE1 A:HIS229 4.5 30.2 1.0
O B:HOH1115 4.8 35.4 1.0
CD2 B:HIS123 4.8 31.0 1.0
O A:HOH1227 4.8 36.1 1.0

Cobalt binding site 3 out of 4 in 6cac

Go back to Cobalt Binding Sites List in 6cac
Cobalt 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 Cobalt with other atoms in the Co 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:Co1004

b:30.8
occ:1.00
 OE2 D:GLU228 2.2 49.0 1.0
O C:HOH1270 2.2 50.7 1.0
OD2 C:ASP224 2.2 51.1 1.0
OE1 C:GLU153 2.4 48.8 1.0
OE2 C:GLU153 2.5 41.8 1.0
OE1 D:GLU228 2.5 51.8 1.0
CD D:GLU228 2.7 58.0 1.0
CD C:GLU153 2.8 44.0 1.0
CG C:ASP224 2.9 47.1 1.0
OD1 C:ASP224 2.9 48.0 1.0
NE2 C:HIS123 4.1 34.5 1.0
O C:HOH1166 4.1 38.5 1.0
CG D:GLU228 4.2 45.8 1.0
NE2 D:HIS229 4.3 37.3 1.0
CG C:GLU153 4.3 36.8 1.0
CB C:ASP224 4.4 36.1 1.0
CE1 D:HIS229 4.6 36.0 1.0
CD2 C:HIS123 4.6 34.3 1.0
O C:HOH1182 4.7 42.3 1.0
O D:HOH1111 4.7 46.6 1.0

Cobalt binding site 4 out of 4 in 6cac

Go back to Cobalt Binding Sites List in 6cac
Cobalt 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 Cobalt with other atoms in the Co 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:Co1004

b:26.6
occ:1.00
 OE2 C:GLU228 2.3 50.3 1.0
OD2 D:ASP224 2.3 40.3 1.0
OE1 D:GLU153 2.5 41.0 1.0
OE2 D:GLU153 2.5 42.6 1.0
OE1 C:GLU228 2.5 52.7 1.0
O D:HOH1258 2.6 32.2 1.0
CD C:GLU228 2.7 62.4 1.0
CD D:GLU153 2.9 47.1 1.0
OD1 D:ASP224 2.9 40.2 1.0
CG D:ASP224 2.9 41.2 1.0
NE2 D:HIS123 4.2 29.3 1.0
CG C:GLU228 4.2 46.9 1.0
O D:HOH1191 4.3 32.8 1.0
NE2 C:HIS229 4.3 37.1 1.0
CG D:GLU153 4.4 36.4 1.0
CB D:ASP224 4.4 37.1 1.0
CE1 C:HIS229 4.6 36.5 1.0
CD2 D:HIS123 4.7 29.7 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: Tue Jul 30 18:29:17 2024

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