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Nickel in PDB 4tz9: Structure of Metallo-Beta-Lactamase

Protein crystallography data

The structure of Structure of Metallo-Beta-Lactamase, PDB code: 4tz9 was solved by J.A.Ferguson, J.Brem, A.Makena, A.M.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 2.19 / 2.13
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.908, 120.908, 90.190, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 24.9

Other elements in 4tz9:

The structure of Structure of 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 Metallo-Beta-Lactamase (pdb code 4tz9). 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 Metallo-Beta-Lactamase, PDB code: 4tz9:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 4tz9

Go back to Nickel Binding Sites List in 4tz9
Nickel binding site 1 out of 4 in the Structure of 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 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni303

b:76.9
occ:1.00
NE2 A:HIS228 2.0 52.5 1.0
O A:HOH474 2.0 49.4 1.0
CD2 A:HIS228 2.9 48.0 1.0
CE1 A:HIS228 3.0 53.5 1.0
CG A:HIS228 4.1 47.1 1.0
ND1 A:HIS228 4.1 50.3 1.0
O A:HOH514 4.9 39.5 1.0

Nickel binding site 2 out of 4 in 4tz9

Go back to Nickel Binding Sites List in 4tz9
Nickel binding site 2 out of 4 in the Structure of 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 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni305

b:27.1
occ:1.00
NE2 A:HIS159 2.0 26.9 1.0
CE1 A:HIS159 2.9 25.8 1.0
CD2 A:HIS159 3.1 26.5 1.0
ND1 A:HIS159 4.0 25.2 1.0
CG A:HIS159 4.2 25.4 1.0
O A:HOH429 4.4 40.3 1.0

Nickel binding site 3 out of 4 in 4tz9

Go back to Nickel Binding Sites List in 4tz9
Nickel binding site 3 out of 4 in the Structure of 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 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni306

b:55.4
occ:1.00
O A:HOH488 2.0 39.8 1.0
ND1 A:HIS261 2.0 47.5 1.0
O A:HOH496 2.3 52.3 1.0
O A:HOH494 2.4 50.3 1.0
O A:HOH455 2.7 41.0 1.0
CE1 A:HIS261 2.8 48.5 1.0
CG A:HIS261 3.1 44.1 1.0
CB A:HIS261 3.6 42.9 1.0
NE2 A:HIS261 4.0 45.5 1.0
CA A:HIS261 4.1 42.5 1.0
O A:SER213 4.1 44.6 1.0
CD2 A:HIS261 4.1 42.5 1.0
CD A:ARG264 4.8 50.3 1.0

Nickel binding site 4 out of 4 in 4tz9

Go back to Nickel Binding Sites List in 4tz9
Nickel binding site 4 out of 4 in the Structure of 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 Metallo-Beta-Lactamase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni307

b:21.3
occ:1.00
OE2 A:GLU170 2.0 46.9 1.0
OE1 A:GLU170 2.0 43.1 1.0
CD A:GLU170 2.3 41.6 1.0
CG A:GLU170 3.8 35.1 1.0
CB A:ALA164 4.2 31.7 1.0
CB A:GLU170 4.7 33.1 1.0
CA A:ALA164 4.9 31.0 1.0
O A:HOH476 4.9 39.0 1.0

Reference:

J.A.Ferguson, A.Makena, J.Brem, A.M.Mcdonough, C.J.Schofield. Structure of Metallo-Beta-Lactamase To Be Published.
Page generated: Wed Dec 16 01:35:17 2020

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