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Nickel in PDB 4tzb: Structure of Ndm-Metallo-Beta-Lactamase

Protein crystallography data

The structure of Structure of Ndm-Metallo-Beta-Lactamase, PDB code: 4tzb was solved by J.A.Ferguson, A.Makena, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.05 / 2.03
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.244, 120.244, 89.192, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.6

Other elements in 4tzb:

The structure of Structure of Ndm-Metallo-Beta-Lactamase 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 Ndm-Metallo-Beta-Lactamase (pdb code 4tzb). 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 Ndm-Metallo-Beta-Lactamase, PDB code: 4tzb:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4tzb

Go back to Nickel Binding Sites List in 4tzb
Nickel binding site 1 out of 4 in the Structure of Ndm-Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Ndm-Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:62.5
occ:1.00
NE2 A:HIS228 2.0 55.7 1.0
CE1 A:HIS228 2.9 53.1 1.0
CD2 A:HIS228 3.0 52.4 1.0
ND1 A:HIS228 4.1 52.2 1.0
CG A:HIS228 4.1 50.2 1.0
O A:HOH458 4.1 52.2 1.0

Nickel binding site 2 out of 4 in 4tzb

Go back to Nickel Binding Sites List in 4tzb
Nickel binding site 2 out of 4 in the Structure of Ndm-Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Ndm-Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni305

b:32.7
occ:1.00
NE2 A:HIS159 2.0 25.6 1.0
CE1 A:HIS159 2.9 26.4 1.0
CD2 A:HIS159 3.0 26.1 1.0
ND1 A:HIS159 4.1 25.9 1.0
O A:HOH401 4.1 46.6 1.0
CG A:HIS159 4.1 26.0 1.0
O A:HOH552 4.2 50.3 1.0
O A:HOH431 4.4 45.8 1.0
O A:HOH436 4.5 40.1 1.0

Nickel binding site 3 out of 4 in 4tzb

Go back to Nickel Binding Sites List in 4tzb
Nickel binding site 3 out of 4 in the Structure of Ndm-Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Ndm-Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni306

b:59.6
occ:1.00
ND1 A:HIS261 1.9 54.3 1.0
O A:HOH523 2.0 59.2 1.0
O A:HOH451 2.0 59.7 1.0
CE1 A:HIS261 2.8 54.7 1.0
O A:HOH536 3.0 50.9 1.0
CG A:HIS261 3.1 52.0 1.0
O A:HOH561 3.1 56.3 1.0
CB A:HIS261 3.6 47.0 1.0
O A:SER213 3.7 43.4 1.0
NE2 A:HIS261 3.9 53.6 1.0
CD2 A:HIS261 4.1 52.7 1.0
CA A:HIS261 4.2 42.4 1.0
C A:SER213 4.8 43.3 1.0

Nickel binding site 4 out of 4 in 4tzb

Go back to Nickel Binding Sites List in 4tzb
Nickel binding site 4 out of 4 in the Structure of Ndm-Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Ndm-Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni307

b:22.0
occ:1.00
OE2 A:GLU170 2.0 28.9 1.0
OE1 A:GLU170 2.0 27.3 1.0
CD A:GLU170 2.3 27.9 1.0
CG A:GLU170 3.8 28.9 1.0
CB A:ALA164 4.2 33.9 1.0
O A:HOH505 4.6 40.9 1.0
CB A:GLU170 4.7 30.2 1.0
O A:HOH464 4.7 30.2 1.0
CA A:ALA164 4.9 33.8 1.0

Reference:

J.A.Ferguson, A.Makena, J.Brem, M.A.Mcdonough, C.J.Schofield. Structure of Metallo-Beta-Lactamase To Be Published.
Page generated: Wed Dec 16 01:35:16 2020

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