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Cadmium in PDB 3zr9: Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)

Enzymatic activity of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)

All present enzymatic activity of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1):
3.5.2.6;

Protein crystallography data

The structure of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1), PDB code: 3zr9 was solved by V.L.Green, A.Verma, R.J.Owens, S.E.V.Phillips, S.B.Carr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.56 / 1.91
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.300, 120.300, 88.100, 90.00, 90.00, 90.00
R / Rfree (%) 18.001 / 20.956

Other elements in 3zr9:

The structure of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1) also contains other interesting chemical elements:

Nickel (Ni) 4 atoms
Cobalt (Co) 1 atom
Zinc (Zn) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1) (pdb code 3zr9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total only one binding site of Cadmium was determined in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1), PDB code: 3zr9:

Cadmium binding site 1 out of 1 in 3zr9

Go back to Cadmium Binding Sites List in 3zr9
Cadmium binding site 1 out of 1 in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd276

b:29.6
occ:0.75
NE2 A:HIS250 2.3 36.7 1.0
O A:HOH2043 2.4 14.4 1.0
OD2 A:ASP124 2.4 31.8 1.0
O A:HOH2090 2.5 12.4 1.0
SG A:CYS208 2.6 36.5 1.0
O A:HOH2048 2.7 36.1 1.0
CE1 A:HIS250 3.3 32.4 1.0
CD2 A:HIS250 3.3 35.9 1.0
CG A:ASP124 3.4 33.8 1.0
CB A:CYS208 3.4 30.4 1.0
OD1 A:ASP124 3.6 28.4 1.0
ZN A:ZN273 3.6 28.4 1.0
ND1 A:HIS250 4.4 32.5 1.0
NE2 A:HIS189 4.4 26.6 1.0
CG A:HIS250 4.5 34.6 1.0
CB A:SER249 4.5 34.6 1.0
CE1 A:HIS189 4.6 22.7 1.0
CB A:ASP124 4.7 25.5 1.0
CA A:CYS208 4.8 29.3 1.0
CE1 A:HIS120 4.8 21.6 1.0
OG A:SER249 4.8 38.5 1.0
NE2 A:HIS120 4.8 23.8 1.0

Reference:

V.L.Green, A.Verma, R.J.Owens, S.E.Phillips, S.B.Carr. Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1). Acta Crystallogr.,Sect.F V. 67 1160 2011.
ISSN: ISSN 1744-3091
PubMed: 22102018
DOI: 10.1107/S1744309111029654
Page generated: Sat Dec 12 08:23:53 2020

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