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Nickel 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:

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

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 5 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in 6cac

Go back to Nickel Binding Sites List in 6cac
Nickel binding site 1 out of 5 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 Nickel with other atoms in the Ni 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:Ni1003

b:22.1
occ:1.00
 O A:HOH1207 1.9 38.1 1.0
O A:HOH1203 2.0 28.2 1.0
O A:HOH1223 2.0 27.5 1.0
NE2 A:HIS160 2.1 22.8 1.0
NE2 D:HIS160 2.1 24.6 1.0
O D:HOH1220 2.2 30.9 1.0
CE1 A:HIS160 3.1 22.4 1.0
CE1 D:HIS160 3.1 24.8 1.0
CD2 A:HIS160 3.1 23.1 1.0
CD2 D:HIS160 3.2 24.9 1.0
ND1 A:HIS160 4.2 22.5 1.0
CG A:HIS160 4.2 22.3 1.0
ND1 D:HIS160 4.3 26.0 1.0
CG D:HIS160 4.3 24.4 1.0
O A:HOH1123 4.3 27.9 1.0
O D:HOH1155 4.3 27.5 1.0
O D:HOH1276 4.3 53.7 1.0
O A:HOH1193 4.3 35.6 1.0
O D:HOH1278 4.3 58.0 1.0
O D:HOH1133 4.4 37.9 1.0
O D:HOH1212 4.4 50.2 1.0
O A:HOH1121 4.5 33.0 1.0

Nickel binding site 2 out of 5 in 6cac

Go back to Nickel Binding Sites List in 6cac
Nickel binding site 2 out of 5 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 Nickel with other atoms in the Ni 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
A:Ni1004

b:38.1
occ:0.50
 NE2 A:HIS262 2.2 37.2 1.0
CD2 A:HIS262 3.1 37.9 1.0
CE1 A:HIS262 3.2 36.0 1.0
O A:SER214 4.1 39.4 1.0
CG A:HIS262 4.2 34.6 1.0
ND1 A:HIS262 4.3 35.4 1.0
O A:ALA216 4.4 38.6 1.0

Nickel binding site 3 out of 5 in 6cac

Go back to Nickel Binding Sites List in 6cac
Nickel binding site 3 out of 5 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 Nickel with other atoms in the Ni 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
B:Ni1003

b:28.5
occ:1.00
 NE2 B:HIS160 2.0 25.7 1.0
O B:HOH1226 2.1 32.3 1.0
CE1 B:HIS160 3.0 25.4 1.0
CD2 B:HIS160 3.1 26.2 1.0
ND1 B:HIS160 4.1 25.7 1.0
O B:HOH1205 4.2 36.0 1.0
CG B:HIS160 4.2 24.2 1.0
O B:HOH1117 4.6 28.7 1.0

Nickel binding site 4 out of 5 in 6cac

Go back to Nickel Binding Sites List in 6cac
Nickel binding site 4 out of 5 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 Nickel with other atoms in the Ni 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
C:Ni1003

b:26.9
occ:1.00
 NE2 C:HIS160 2.1 25.2 1.0
CE1 C:HIS160 2.9 25.3 1.0
CD2 C:HIS160 3.2 24.6 1.0
ND1 C:HIS160 4.1 25.6 1.0
O C:HOH1129 4.2 32.1 1.0
CG C:HIS160 4.2 23.0 1.0
O C:HOH1127 4.5 25.3 1.0
O B:HOH1196 4.8 46.1 1.0

Nickel binding site 5 out of 5 in 6cac

Go back to Nickel Binding Sites List in 6cac
Nickel binding site 5 out of 5 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 Nickel with other atoms in the Ni binding site number 5 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:Ni1003

b:44.5
occ:1.00
 ND1 D:HIS262 2.1 44.7 1.0
CG D:HIS262 3.1 41.5 1.0
CE1 D:HIS262 3.1 43.9 1.0
CA D:HIS262 3.3 36.9 1.0
CB D:HIS262 3.4 37.6 1.0
O D:HIS262 3.9 41.9 1.0
C D:HIS262 4.1 41.5 1.0
CD2 D:HIS262 4.2 42.5 1.0
NE2 D:HIS262 4.2 43.2 1.0
N D:HIS262 4.3 37.1 1.0
O D:HOH1221 4.5 57.3 1.0
CB D:ARG265 4.6 40.6 1.0
O D:THR261 4.9 39.9 1.0
C D:THR261 5.0 40.7 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: Thu Oct 10 08:21:13 2024

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