Atomistry » Nickel » PDB 1a5n-1fwb » 1ddn
Atomistry »
  Nickel »
    PDB 1a5n-1fwb »
      1ddn »

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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Go back to Nickel Binding Sites List in 1ddn
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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy