Atomistry » Zinc » PDB 6c06-6cb1 » 6cac
Atomistry »
  Zinc »
    PDB 6c06-6cb1 »
      6cac »

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 6cac

Go back to Zinc Binding Sites List in 6cac
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:26.2
occ:1.00
 O A:HOH1191 2.0 23.6 1.0
ND1 A:HIS123 2.0 24.1 1.0
NE2 A:HIS121 2.0 23.3 1.0
NE2 A:HIS190 2.0 25.2 1.0
CD2 A:HIS190 2.9 25.1 1.0
CG A:HIS123 3.0 23.2 1.0
CE1 A:HIS121 3.0 23.3 1.0
CE1 A:HIS123 3.0 24.1 1.0
CD2 A:HIS121 3.0 23.9 1.0
CE1 A:HIS190 3.1 25.6 1.0
CB A:HIS123 3.3 21.0 1.0
CD A:CD1002 3.6 32.0 1.0
ND2 A:ASN221 3.7 23.7 1.0
OD1 A:ASP125 4.0 25.8 1.0
SG A:CYS209 4.1 28.4 1.0
O A:HOH1101 4.1 44.6 1.0
CG A:HIS190 4.1 24.4 1.0
CG A:HIS121 4.1 23.6 1.0
ND1 A:HIS121 4.1 24.6 1.0
CD2 A:HIS123 4.1 25.6 1.0
NE2 A:HIS123 4.1 25.4 1.0
ND1 A:HIS190 4.2 25.8 1.0
CB A:CYS209 4.3 25.2 1.0
CG2 A:THR191 4.5 25.6 1.0
OD2 A:ASP125 4.7 26.2 1.0
CG A:ASN221 4.7 42.6 1.0
CA A:HIS123 4.8 20.6 1.0
CG A:ASP125 4.8 25.1 1.0

Zinc binding site 2 out of 4 in 6cac

Go back to Zinc Binding Sites List in 6cac
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:30.5
occ:1.00
 ND1 B:HIS123 2.0 30.1 1.0
NE2 B:HIS121 2.0 26.0 1.0
O B:HOH1135 2.0 26.5 1.0
NE2 B:HIS190 2.1 26.9 1.0
CG B:HIS123 2.9 28.9 1.0
CD2 B:HIS190 2.9 27.7 1.0
CD2 B:HIS121 3.0 25.2 1.0
CE1 B:HIS121 3.0 25.8 1.0
CE1 B:HIS123 3.0 30.5 1.0
CE1 B:HIS190 3.2 27.2 1.0
CB B:HIS123 3.2 25.9 1.0
O B:HOH1180 3.4 39.2 1.0
CD B:CD1002 3.8 31.5 1.0
OD1 B:ASP125 4.0 31.6 1.0
SG B:CYS209 4.1 31.1 1.0
CG B:HIS121 4.1 24.9 1.0
CD2 B:HIS123 4.1 31.0 1.0
ND1 B:HIS121 4.1 26.2 1.0
CG B:HIS190 4.1 26.6 1.0
NE2 B:HIS123 4.1 31.1 1.0
ND1 B:HIS190 4.2 27.8 1.0
CB B:CYS209 4.3 26.8 1.0
CG2 B:THR191 4.4 27.1 1.0
O B:HOH1101 4.6 24.9 1.0
CA B:HIS123 4.7 25.4 1.0
OD2 B:ASP125 4.7 35.6 1.0
CG B:ASP125 4.8 34.4 1.0
ND2 B:ASN221 4.9 87.3 1.0

Zinc binding site 3 out of 4 in 6cac

Go back to Zinc Binding Sites List in 6cac
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:33.2
occ:1.00
 O C:HOH1140 1.9 33.1 1.0
ND1 C:HIS123 1.9 33.5 1.0
NE2 C:HIS121 2.0 31.0 1.0
NE2 C:HIS190 2.1 32.1 1.0
CG C:HIS123 2.9 32.3 1.0
CD2 C:HIS190 3.0 31.7 1.0
CE1 C:HIS123 3.0 33.8 1.0
CD2 C:HIS121 3.0 31.0 1.0
CE1 C:HIS121 3.0 30.3 1.0
CE1 C:HIS190 3.2 32.9 1.0
CB C:HIS123 3.2 29.5 1.0
O C:HOH1168 3.6 47.1 1.0
CD C:CD1002 3.8 34.9 1.0
OD1 C:ASP125 4.0 35.2 1.0
SG C:CYS209 4.0 34.0 1.0
CD2 C:HIS123 4.1 34.3 1.0
NE2 C:HIS123 4.1 34.5 1.0
CG C:HIS121 4.1 29.3 1.0
ND1 C:HIS121 4.1 31.0 1.0
CG C:HIS190 4.1 31.4 1.0
CB C:CYS209 4.2 30.3 1.0
ND1 C:HIS190 4.2 32.7 1.0
CG2 C:THR191 4.4 30.4 1.0
O C:HOH1251 4.6 31.8 1.0
OD2 C:ASP125 4.7 39.0 1.0
CA C:HIS123 4.7 28.8 1.0
CG C:ASP125 4.8 37.8 1.0

Zinc binding site 4 out of 4 in 6cac

Go back to Zinc Binding Sites List in 6cac
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:31.1
occ:1.00
 O D:HOH1106 1.9 27.4 1.0
ND1 D:HIS123 2.0 29.1 1.0
NE2 D:HIS121 2.0 29.8 1.0
NE2 D:HIS190 2.1 29.6 1.0
CD2 D:HIS190 3.0 28.9 1.0
CG D:HIS123 3.0 28.4 1.0
CE1 D:HIS121 3.0 29.5 1.0
CE1 D:HIS123 3.0 28.9 1.0
CD2 D:HIS121 3.0 29.6 1.0
CE1 D:HIS190 3.2 30.2 1.0
CB D:HIS123 3.3 26.2 1.0
CD D:CD1002 3.6 35.7 1.0
OD1 D:ASP125 4.0 32.2 1.0
SG D:CYS209 4.1 32.9 1.0
CG D:HIS121 4.1 28.0 1.0
ND1 D:HIS121 4.1 30.7 1.0
NE2 D:HIS123 4.1 29.3 1.0
CD2 D:HIS123 4.1 29.7 1.0
CG D:HIS190 4.1 29.2 1.0
ND1 D:HIS190 4.2 31.2 1.0
CB D:CYS209 4.3 29.5 1.0
O D:HOH1225 4.4 39.1 1.0
CG2 D:THR191 4.4 27.6 1.0
OD2 D:ASP125 4.7 32.8 1.0
CG D:ASP125 4.8 33.4 1.0
CA D:HIS123 4.8 25.5 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 Aug 21 13:01:00 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy