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Nickel in PDB 1ddn: Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex

Protein crystallography data

The structure of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex, PDB code: 1ddn was solved by A.White, X.Ding, J.C.Vanderspek, J.R.Murphy, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 117.050, 117.050, 145.340, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 28

Nickel Binding Sites:

The binding sites of Nickel atom in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex (pdb code 1ddn). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex, PDB code: 1ddn:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 1ddn

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Nickel binding site 1 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


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)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni251

b:5.0
occ:1.00
 ND1 A:HIS98 2.1 64.6 1.0
OE2 A:GLU83 2.1 45.0 1.0
NE2 A:HIS79 2.1 20.2 1.0
CE1 A:HIS98 2.4 64.6 1.0
CD A:GLU83 2.5 45.0 1.0
OE1 A:GLU83 2.6 45.0 1.0
CE1 A:HIS79 3.0 20.2 1.0
CD2 A:HIS79 3.3 20.2 1.0
CG A:HIS98 3.4 64.6 1.0
NE2 A:HIS98 3.7 64.6 1.0
CG A:GLU83 3.8 45.0 1.0
ND1 A:HIS79 4.2 20.2 1.0
CD2 A:HIS98 4.2 64.6 1.0
CB A:HIS98 4.3 64.6 1.0
CG A:HIS79 4.3 20.2 1.0
CA A:HIS98 4.6 32.3 1.0

Nickel binding site 2 out of 8 in 1ddn

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Nickel binding site 2 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


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)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni252

b:5.0
occ:1.00
 O A:ASP102 1.9 29.8 1.0
OE2 A:GLU105 2.0 20.9 1.0
NE2 A:HIS106 2.0 20.2 1.0
OD1 A:ASP102 2.0 29.8 1.0
O A:HOH253 2.1 20.0 1.0
SD A:MET10 2.2 23.3 1.0
CD2 A:HIS106 3.0 20.2 1.0
CE1 A:HIS106 3.0 20.2 1.0
C A:ASP102 3.0 26.0 1.0
CD A:GLU105 3.1 20.9 1.0
CG A:ASP102 3.2 29.8 1.0
CG A:GLU105 3.5 20.9 1.0
CG A:MET10 3.6 23.3 1.0
CA A:ASP102 3.6 26.0 1.0
CE A:MET10 3.6 23.3 1.0
CB A:ASP102 4.0 29.8 1.0
ND1 A:HIS106 4.1 20.2 1.0
CG A:HIS106 4.2 20.2 1.0
OD2 A:ASP102 4.2 29.8 1.0
N A:ARG103 4.2 12.9 1.0
OE1 A:GLU105 4.2 20.9 1.0
O A:LEU4 4.2 8.8 1.0
CA A:ARG103 4.6 12.9 1.0
NH1 A:ARG13 4.7 18.5 1.0
CB A:MET10 4.9 23.3 1.0
N A:ASP102 5.0 26.0 1.0

Nickel binding site 3 out of 8 in 1ddn

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Nickel binding site 3 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni251

b:5.0
occ:1.00
 ND1 B:HIS98 2.1 65.5 1.0
OE2 B:GLU83 2.1 35.0 1.0
NE2 B:HIS79 2.2 23.2 1.0
OE1 B:GLU83 2.4 35.0 1.0
CE1 B:HIS98 2.5 65.5 1.0
CD B:GLU83 2.5 35.0 1.0
CE1 B:HIS79 3.1 23.2 1.0
CD2 B:HIS79 3.3 23.2 1.0
CG B:HIS98 3.4 65.5 1.0
NE2 B:HIS98 3.7 65.5 1.0
CG B:GLU83 3.9 35.0 1.0
CB B:HIS98 4.2 65.5 1.0
CD2 B:HIS98 4.2 65.5 1.0
ND1 B:HIS79 4.2 23.2 1.0
CG B:HIS79 4.4 23.2 1.0
CA B:HIS98 4.6 22.8 1.0

Nickel binding site 4 out of 8 in 1ddn

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Nickel binding site 4 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni252

b:5.0
occ:1.00
 O B:ASP102 2.0 44.1 1.0
O B:HOH253 2.0 20.0 1.0
NE2 B:HIS106 2.0 17.5 1.0
OE2 B:GLU105 2.0 32.3 1.0
OD1 B:ASP102 2.1 44.1 1.0
SD B:MET10 2.2 28.3 1.0
CD2 B:HIS106 3.0 17.5 1.0
CE1 B:HIS106 3.0 17.5 1.0
C B:ASP102 3.0 40.3 1.0
CD B:GLU105 3.1 32.3 1.0
CE B:MET10 3.2 28.3 1.0
CG B:ASP102 3.2 44.1 1.0
CG B:GLU105 3.5 32.3 1.0
CA B:ASP102 3.6 40.3 1.0
CG B:MET10 3.6 28.3 1.0
CB B:ASP102 4.0 44.1 1.0
ND1 B:HIS106 4.1 17.5 1.0
CG B:HIS106 4.1 17.5 1.0
N B:ARG103 4.2 17.4 1.0
OE1 B:GLU105 4.2 32.3 1.0
OD2 B:ASP102 4.2 44.1 1.0
O B:LEU4 4.4 5.0 1.0
CA B:ARG103 4.6 17.4 1.0
CB B:MET10 4.9 28.3 1.0
NH1 B:ARG13 4.9 19.4 1.0
N B:ASP102 5.0 40.3 1.0
O B:ALA101 5.0 30.7 1.0

Nickel binding site 5 out of 8 in 1ddn

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Nickel binding site 5 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni251

b:5.0
occ:1.00
 ND1 C:HIS98 2.1 65.2 1.0
OE2 C:GLU83 2.1 53.5 1.0
CE1 C:HIS98 2.1 65.2 1.0
NE2 C:HIS79 2.2 20.8 1.0
CD C:GLU83 2.8 53.5 1.0
OE1 C:GLU83 2.9 53.5 1.0
CE1 C:HIS79 3.1 20.8 1.0
CD2 C:HIS79 3.2 20.8 1.0
CG C:HIS98 3.5 65.2 1.0
NE2 C:HIS98 3.5 65.2 1.0
CG C:GLU83 4.1 53.5 1.0
CD2 C:HIS98 4.1 65.2 1.0
ND1 C:HIS79 4.3 20.8 1.0
CG C:HIS79 4.3 20.8 1.0
CB C:HIS98 4.4 65.2 1.0
CA C:HIS98 4.8 35.7 1.0

Nickel binding site 6 out of 8 in 1ddn

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Nickel binding site 6 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni252

b:5.0
occ:1.00
 O C:ASP102 2.0 27.4 1.0
OE2 C:GLU105 2.0 15.5 1.0
OD1 C:ASP102 2.0 27.4 1.0
NE2 C:HIS106 2.0 21.5 1.0
O C:HOH253 2.1 20.0 1.0
SD C:MET10 2.2 26.8 1.0
CD2 C:HIS106 2.8 21.5 1.0
C C:ASP102 3.0 48.7 1.0
CD C:GLU105 3.0 15.5 1.0
CE1 C:HIS106 3.1 21.5 1.0
CG C:ASP102 3.2 27.4 1.0
CG C:MET10 3.4 26.8 1.0
CG C:GLU105 3.5 15.5 1.0
CE C:MET10 3.5 26.8 1.0
CA C:ASP102 3.6 48.7 1.0
CB C:ASP102 3.9 27.4 1.0
CG C:HIS106 4.1 21.5 1.0
OE1 C:GLU105 4.1 15.5 1.0
ND1 C:HIS106 4.2 21.5 1.0
OD2 C:ASP102 4.2 27.4 1.0
N C:ARG103 4.2 18.2 1.0
O C:LEU4 4.3 14.1 1.0
NH1 C:ARG13 4.5 13.5 1.0
CA C:ARG103 4.6 18.2 1.0
CB C:MET10 4.8 26.8 1.0
N C:ASP102 5.0 48.7 1.0
CB C:GLU105 5.0 15.5 1.0
CZ C:ARG13 5.0 13.5 1.0

Nickel binding site 7 out of 8 in 1ddn

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Nickel binding site 7 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni251

b:5.0
occ:1.00
 ND1 D:HIS98 2.1 62.0 1.0
OE2 D:GLU83 2.1 54.7 1.0
NE2 D:HIS79 2.2 35.5 1.0
CE1 D:HIS98 2.3 62.0 1.0
CD D:GLU83 2.8 54.7 1.0
OE1 D:GLU83 3.0 54.7 1.0
CE1 D:HIS79 3.1 35.5 1.0
CD2 D:HIS79 3.2 35.5 1.0
CG D:HIS98 3.4 62.0 1.0
NE2 D:HIS98 3.6 62.0 1.0
CG D:GLU83 4.1 54.7 1.0
CD2 D:HIS98 4.1 62.0 1.0
ND1 D:HIS79 4.2 35.5 1.0
CG D:HIS79 4.3 35.5 1.0
CB D:HIS98 4.3 62.0 1.0
CA D:HIS98 4.7 30.0 1.0

Nickel binding site 8 out of 8 in 1ddn

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Nickel binding site 8 out of 8 in the Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Diphtheria Tox Repressor (C102D Mutant)/Tox Dna Operator Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni252

b:5.0
occ:1.00
 O D:ASP102 2.0 39.7 1.0
NE2 D:HIS106 2.0 17.2 1.0
OE2 D:GLU105 2.0 19.8 1.0
OD1 D:ASP102 2.0 39.7 1.0
O D:HOH253 2.1 80.0 1.0
SD D:MET10 2.1 24.0 1.0
CE1 D:HIS106 3.0 17.2 1.0
CD2 D:HIS106 3.0 17.2 1.0
C D:ASP102 3.1 25.3 1.0
CD D:GLU105 3.2 19.8 1.0
CG D:ASP102 3.2 39.7 1.0
CG D:MET10 3.5 24.0 1.0
CE D:MET10 3.5 24.0 1.0
CA D:ASP102 3.6 25.3 1.0
CG D:GLU105 3.7 19.8 1.0
CB D:ASP102 3.9 39.7 1.0
ND1 D:HIS106 4.1 17.2 1.0
CG D:HIS106 4.2 17.2 1.0
NH1 D:ARG13 4.2 10.7 1.0
OD2 D:ASP102 4.2 39.7 1.0
OE1 D:GLU105 4.2 19.8 1.0
N D:ARG103 4.2 8.9 1.0
CA D:ARG103 4.6 8.9 1.0
O D:LEU4 4.6 5.1 1.0
CB D:MET10 4.8 24.0 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: Wed Oct 9 14:46:57 2024

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