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Nickel in PDB 2tdx: Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel

Protein crystallography data

The structure of Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel, PDB code: 2tdx was solved by A.White, X.Ding, H.Zheng, N.Schiering, D.Ringe, J.R.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 64.500, 64.500, 105.700, 90.00, 90.00, 120.00
R / Rfree (%) 24.6 / 32.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel (pdb code 2tdx). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel, PDB code: 2tdx:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2tdx

Go back to Nickel Binding Sites List in 2tdx
Nickel binding site 1 out of 2 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni551

b:2.0
occ:1.00
NE2 A:HIS79 2.1 14.8 1.0
ND1 A:HIS98 2.1 16.3 1.0
OE2 A:GLU83 2.1 18.8 1.0
CE1 A:HIS98 2.3 18.3 1.0
CD2 A:HIS79 3.0 15.7 1.0
CE1 A:HIS79 3.2 20.2 1.0
CD A:GLU83 3.3 18.9 1.0
CG A:HIS98 3.5 19.7 1.0
NE2 A:HIS98 3.6 17.7 1.0
OE1 A:GLU83 3.9 23.8 1.0
CG A:HIS79 4.2 16.9 1.0
CD2 A:HIS98 4.2 18.6 1.0
ND1 A:HIS79 4.2 19.8 1.0
CB A:HIS98 4.3 21.6 1.0
CG A:GLU83 4.5 16.7 1.0
CA A:HIS98 4.7 20.7 1.0

Nickel binding site 2 out of 2 in 2tdx

Go back to Nickel Binding Sites List in 2tdx
Nickel binding site 2 out of 2 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni552

b:2.0
occ:1.00
OD1 A:ASP102 2.0 16.1 1.0
O A:HOH251 2.1 20.7 1.0
O A:ASP102 2.1 15.5 1.0
NE2 A:HIS106 2.1 17.7 1.0
OE2 A:GLU105 2.2 17.9 1.0
SD A:MET10 2.5 21.6 1.0
CD2 A:HIS106 3.0 15.0 1.0
C A:ASP102 3.1 15.4 1.0
CE1 A:HIS106 3.2 18.2 1.0
CG A:ASP102 3.2 16.0 1.0
CD A:GLU105 3.2 19.4 1.0
CE A:MET10 3.4 21.9 1.0
CA A:ASP102 3.5 14.6 1.0
CG A:MET10 3.6 22.5 1.0
CG A:GLU105 3.7 17.0 1.0
CB A:ASP102 3.9 14.4 1.0
NH2 A:ARG13 4.2 15.7 1.0
O A:LEU4 4.2 27.1 1.0
OD2 A:ASP102 4.2 21.7 1.0
CG A:HIS106 4.2 13.7 1.0
ND1 A:HIS106 4.3 15.2 1.0
OE1 A:GLU105 4.3 20.5 1.0
N A:ARG103 4.3 14.0 1.0
CA A:ARG103 4.8 12.9 1.0
N A:ASP102 4.9 12.1 1.0
CB A:MET10 4.9 17.8 1.0
O A:ALA101 5.0 11.1 1.0

Reference:

A.White, X.Ding, J.C.Vanderspek, J.R.Murphy, D.Ringe. Structure of the Metal-Ion-Activated Diphtheria Toxin Repressor/Tox Operator Complex. Nature V. 394 502 1998.
ISSN: ISSN 0028-0836
PubMed: 9697776
DOI: 10.1038/28893
Page generated: Fri Sep 25 08:14:18 2020
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