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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: Mon Oct 28 18:36:33 2024

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