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Nickel 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:

Cobalt (Co) 1 atom
Zinc (Zn) 1 atom
Cadmium (Cd) 1 atom

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1), PDB code: 3zr9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 3zr9

Go back to Nickel Binding Sites List in 3zr9
Nickel binding site 1 out of 4 in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni275

b:78.5
occ:1.00
O A:HOH2102 1.7 22.2 1.0
NE2 A:HIS228 2.4 53.3 1.0
CD2 A:HIS228 3.2 51.0 1.0
CE1 A:HIS228 3.4 56.8 1.0
CG A:HIS228 4.4 47.6 1.0
ND1 A:HIS228 4.4 54.0 1.0

Nickel binding site 2 out of 4 in 3zr9

Go back to Nickel Binding Sites List in 3zr9
Nickel binding site 2 out of 4 in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni277

b:23.2
occ:0.50
NE2 A:HIS159 2.2 22.6 1.0
CE1 A:HIS159 3.1 22.9 1.0
CD2 A:HIS159 3.3 26.0 1.0
O A:HOH2114 4.2 36.6 1.0
ND1 A:HIS159 4.2 22.9 1.0
O A:HOH2068 4.3 33.8 1.0
CG A:HIS159 4.3 21.6 1.0
O A:HOH2056 4.5 27.1 1.0

Nickel binding site 3 out of 4 in 3zr9

Go back to Nickel Binding Sites List in 3zr9
Nickel binding site 3 out of 4 in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni278

b:52.5
occ:1.00
O A:HOH2113 2.3 41.7 1.0
O A:HOH2115 2.5 23.6 1.0
ND1 A:HIS261 2.6 48.7 1.0
O A:HOH2116 2.6 30.4 1.0
O A:HOH2093 3.1 34.4 1.0
CG A:HIS261 3.5 41.8 1.0
CE1 A:HIS261 3.5 46.3 1.0
CB A:HIS261 3.7 40.0 1.0
O A:SER213 3.8 43.7 1.0
CA A:HIS261 4.3 39.3 1.0
NE2 A:HIS261 4.5 45.1 1.0
CD2 A:HIS261 4.6 41.3 1.0
C A:SER213 4.9 39.8 1.0

Nickel binding site 4 out of 4 in 3zr9

Go back to Nickel Binding Sites List in 3zr9
Nickel binding site 4 out of 4 in the Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of New Delhi Metallo-Beta-Lactamase 1 (Ndm-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni279

b:22.2
occ:1.00
OE1 A:GLU170 2.3 36.4 1.0
OE2 A:GLU170 2.3 38.2 1.0
CD A:GLU170 2.6 35.2 1.0
CG A:GLU170 4.2 29.1 1.0
CB A:ALA164 4.2 30.4 1.0
O A:HOH2071 4.5 19.0 1.0
CA A:ALA164 4.8 31.3 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: Wed Dec 16 01:28:45 2020

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