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Cadmium 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
Calcium (Ca) 4 atoms

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 4 in 6cac

Go back to Cadmium Binding Sites List in 6cac
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1002

b:32.0
occ:1.00
 O A:HOH1191 2.1 23.6 1.0
NE2 A:HIS251 2.2 27.8 1.0
OD2 A:ASP125 2.2 26.2 1.0
SG A:CYS209 2.3 28.4 1.0
O A:HOH1101 2.4 44.6 1.0
CE1 A:HIS251 3.1 28.7 1.0
CG A:ASP125 3.2 25.1 1.0
CD2 A:HIS251 3.2 28.9 1.0
CB A:CYS209 3.4 25.2 1.0
OD1 A:ASP125 3.4 25.8 1.0
ZN A:ZN1001 3.6 26.2 1.0
OD1 A:ASN221 4.1 31.3 1.0
NE2 A:HIS190 4.1 25.2 1.0
ND2 A:ASN221 4.3 23.7 1.0
ND1 A:HIS251 4.3 29.7 1.0
CG A:HIS251 4.3 28.4 1.0
CB A:SER250 4.4 25.3 1.0
CE1 A:HIS190 4.4 25.6 1.0
CE1 A:HIS121 4.5 23.3 1.0
NE2 A:HIS121 4.5 23.3 1.0
CB A:ASP125 4.5 23.5 1.0
CA A:CYS209 4.6 25.3 1.0
CG A:ASN221 4.7 42.6 1.0
OG A:SER250 4.8 28.4 1.0
CE A:LYS126 4.9 30.4 1.0
O A:HOH1136 4.9 30.8 1.0
CD A:LYS126 5.0 26.1 1.0

Cadmium binding site 2 out of 4 in 6cac

Go back to Cadmium Binding Sites List in 6cac
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1002

b:31.5
occ:1.00
 NE2 B:HIS251 2.3 32.5 1.0
OD2 B:ASP125 2.3 35.6 1.0
O B:HOH1135 2.3 26.5 1.0
SG B:CYS209 2.5 31.1 1.0
O B:HOH1101 2.5 24.9 1.0
CE1 B:HIS251 3.2 32.4 1.0
CG B:ASP125 3.3 34.4 1.0
CD2 B:HIS251 3.3 32.9 1.0
CB B:CYS209 3.5 26.8 1.0
OD1 B:ASP125 3.6 31.6 1.0
ZN B:ZN1001 3.8 30.5 1.0
ND2 B:ASN221 4.1 87.3 1.0
NE2 B:HIS190 4.3 26.9 1.0
O B:HOH1180 4.4 39.2 1.0
ND1 B:HIS251 4.4 32.4 1.0
CG B:HIS251 4.4 31.2 1.0
CE1 B:HIS190 4.5 27.2 1.0
CB B:SER250 4.5 27.4 1.0
CB B:ASP125 4.6 27.4 1.0
CA B:CYS209 4.6 26.4 1.0
OG B:SER250 4.8 31.2 1.0
NE2 B:HIS121 4.8 26.0 1.0
CE1 B:HIS121 4.8 25.8 1.0
OD1 B:ASN221 4.9 95.2 1.0
CG B:ASN221 5.0 96.2 1.0

Cadmium binding site 3 out of 4 in 6cac

Go back to Cadmium Binding Sites List in 6cac
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1002

b:34.9
occ:1.00
 NE2 C:HIS251 2.2 33.2 1.0
OD2 C:ASP125 2.3 39.0 1.0
O C:HOH1140 2.4 33.1 1.0
O C:HOH1251 2.4 31.8 1.0
SG C:CYS209 2.5 34.0 1.0
CE1 C:HIS251 3.2 33.1 1.0
CD2 C:HIS251 3.3 33.9 1.0
CG C:ASP125 3.3 37.8 1.0
CB C:CYS209 3.4 30.3 1.0
OD1 C:ASP125 3.6 35.2 1.0
ZN C:ZN1001 3.8 33.2 1.0
NE2 C:HIS190 4.3 32.1 1.0
ND1 C:HIS251 4.4 35.3 1.0
CG C:HIS251 4.4 34.3 1.0
CE1 C:HIS190 4.4 32.9 1.0
CB C:SER250 4.4 30.5 1.0
O C:HOH1168 4.4 47.1 1.0
CA C:CYS209 4.6 29.7 1.0
CB C:ASP125 4.6 32.9 1.0
OG C:SER250 4.7 31.8 1.0
NE2 C:HIS121 4.8 31.0 1.0
CE1 C:HIS121 4.9 30.3 1.0

Cadmium binding site 4 out of 4 in 6cac

Go back to Cadmium Binding Sites List in 6cac
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1002

b:35.7
occ:1.00
 NE2 D:HIS251 2.2 32.5 1.0
OD2 D:ASP125 2.3 32.8 1.0
O D:HOH1106 2.3 27.4 1.0
SG D:CYS209 2.4 32.9 1.0
O D:HOH1225 2.5 39.1 1.0
CE1 D:HIS251 3.2 32.9 1.0
CD2 D:HIS251 3.3 33.5 1.0
CG D:ASP125 3.3 33.4 1.0
CB D:CYS209 3.4 29.5 1.0
OD1 D:ASP125 3.6 32.2 1.0
ZN D:ZN1001 3.6 31.1 1.0
NE2 D:HIS190 4.1 29.6 1.0
ND1 D:HIS251 4.4 34.5 1.0
CE1 D:HIS190 4.4 30.2 1.0
CG D:HIS251 4.4 33.4 1.0
CB D:SER250 4.5 31.3 1.0
CB D:ASP125 4.6 27.7 1.0
NE2 D:HIS121 4.6 29.8 1.0
CE1 D:HIS121 4.6 29.5 1.0
CA D:CYS209 4.7 29.9 1.0
O D:HOH1181 4.7 52.7 1.0
OG D:SER250 4.8 30.2 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: Fri Jul 19 19:04:55 2024

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