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Nickel in PDB 1f5t: Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence

Protein crystallography data

The structure of Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence, PDB code: 1f5t was solved by S.Chen, A.White, J.Love, J.R.Murphy, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 3.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 116.178, 116.178, 142.919, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 27.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence (pdb code 1f5t). 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) Complexed with Nickel and Dtxr Consensus Binding Sequence, PDB code: 1f5t:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 1f5t

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Nickel binding site 1 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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 and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni251

b:49.4
occ:1.00
OE2 A:GLU1105 1.5 37.9 1.0
NE2 A:HIS1106 1.7 38.9 1.0
OD1 A:ASP1102 1.7 49.8 1.0
O A:ASP1102 1.8 41.2 1.0
O A:HOH201 1.9 49.4 1.0
SD A:MET1010 2.1 30.0 1.0
CD2 A:HIS1106 2.6 38.9 1.0
CD A:GLU1105 2.6 37.9 1.0
CE1 A:HIS1106 2.8 38.9 1.0
C A:ASP1102 2.9 41.2 1.0
CG A:ASP1102 3.0 49.8 1.0
CG A:GLU1105 3.2 37.9 1.0
CG A:MET1010 3.3 30.0 1.0
CA A:ASP1102 3.6 41.2 1.0
CE A:MET1010 3.6 30.0 1.0
OE1 A:GLU1105 3.7 37.9 1.0
CG A:HIS1106 3.8 38.9 1.0
CB A:ASP1102 3.8 49.8 1.0
ND1 A:HIS1106 3.8 38.9 1.0
OD2 A:ASP1102 3.9 49.8 1.0
O A:LEU1004 4.0 31.0 1.0
N A:ARG1103 4.0 36.7 1.0
CA A:ARG1103 4.4 36.7 1.0
NH1 A:ARG1013 4.5 42.9 1.0
CB A:GLU1105 4.7 37.9 1.0
CB A:MET1010 4.8 30.0 1.0
C A:LEU1004 4.9 31.0 1.0
N A:ASP1102 5.0 41.2 1.0

Nickel binding site 2 out of 8 in 1f5t

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Nickel binding site 2 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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 and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni252

b:49.4
occ:1.00
OE1 A:GLU1083 1.9 41.9 1.0
CE1 A:HIS1098 2.0 33.3 1.0
ND1 A:HIS1098 2.1 33.3 1.0
CD A:GLU1083 2.6 41.9 1.0
OE2 A:GLU1083 2.7 41.9 1.0
NE2 A:HIS1079 2.7 44.3 1.0
NE2 A:HIS1098 3.4 33.3 1.0
CD2 A:HIS1079 3.5 44.3 1.0
CG A:HIS1098 3.5 33.3 1.0
CE1 A:HIS1079 3.7 44.3 1.0
CD2 A:HIS1098 4.1 33.3 1.0
CG A:GLU1083 4.1 41.9 1.0
CB A:HIS1098 4.5 33.3 1.0
CG A:HIS1079 4.7 44.3 1.0
ND1 A:HIS1079 4.8 44.3 1.0

Nickel binding site 3 out of 8 in 1f5t

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Nickel binding site 3 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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) Complexed with Nickel and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni253

b:49.4
occ:1.00
OD1 B:ASP2102 1.7 52.6 1.0
OE2 B:GLU2105 1.7 44.3 1.0
NE2 B:HIS2106 1.7 35.6 1.0
O B:ASP2102 1.8 39.8 1.0
O B:HOH202 2.0 49.4 1.0
SD B:MET2010 2.0 32.3 1.0
CD2 B:HIS2106 2.6 35.6 1.0
CE1 B:HIS2106 2.8 35.6 1.0
CD B:GLU2105 2.9 44.3 1.0
C B:ASP2102 2.9 39.8 1.0
CG B:ASP2102 2.9 52.6 1.0
CG B:MET2010 3.3 32.3 1.0
CE B:MET2010 3.4 32.3 1.0
CA B:ASP2102 3.5 39.8 1.0
CG B:GLU2105 3.6 44.3 1.0
CB B:ASP2102 3.7 52.6 1.0
CG B:HIS2106 3.8 35.6 1.0
ND1 B:HIS2106 3.8 35.6 1.0
OD2 B:ASP2102 3.8 52.6 1.0
OE1 B:GLU2105 3.9 44.3 1.0
N B:ARG2103 4.1 47.6 1.0
NH1 B:ARG2013 4.1 36.3 1.0
O B:LEU2004 4.3 35.0 1.0
CA B:ARG2103 4.5 47.6 1.0
CB B:MET2010 4.7 32.3 1.0
N B:ASP2102 4.9 39.8 1.0
CB B:GLU2105 4.9 44.3 1.0

Nickel binding site 4 out of 8 in 1f5t

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Nickel binding site 4 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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) Complexed with Nickel and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni254

b:49.4
occ:1.00
OE1 B:GLU2083 2.0 42.1 1.0
CE1 B:HIS2098 2.0 29.7 1.0
ND1 B:HIS2098 2.0 29.7 1.0
NE2 B:HIS2079 2.4 45.9 1.0
OE2 B:GLU2083 2.6 42.1 1.0
CD B:GLU2083 2.6 42.1 1.0
CD2 B:HIS2079 3.1 45.9 1.0
NE2 B:HIS2098 3.3 29.7 1.0
CG B:HIS2098 3.4 29.7 1.0
CE1 B:HIS2079 3.6 45.9 1.0
CD2 B:HIS2098 4.0 29.7 1.0
CG B:GLU2083 4.2 42.1 1.0
CG B:HIS2079 4.3 45.9 1.0
CB B:HIS2098 4.4 29.7 1.0
ND1 B:HIS2079 4.5 45.9 1.0

Nickel binding site 5 out of 8 in 1f5t

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Nickel binding site 5 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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) Complexed with Nickel and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni255

b:49.4
occ:1.00
OE2 C:GLU3105 1.6 40.9 1.0
NE2 C:HIS3106 1.7 31.4 1.0
OD1 C:ASP3102 1.7 45.2 1.0
O C:ASP3102 1.8 35.3 1.0
O C:HOH203 1.9 49.4 1.0
SD C:MET3010 2.0 33.9 1.0
CD2 C:HIS3106 2.5 31.4 1.0
CD C:GLU3105 2.8 40.9 1.0
CE1 C:HIS3106 2.8 31.4 1.0
C C:ASP3102 2.9 35.3 1.0
CG C:ASP3102 3.0 45.2 1.0
CG C:MET3010 3.3 33.9 1.0
CG C:GLU3105 3.4 40.9 1.0
CE C:MET3010 3.5 33.9 1.0
CA C:ASP3102 3.6 35.3 1.0
CG C:HIS3106 3.7 31.4 1.0
ND1 C:HIS3106 3.8 31.4 1.0
OE1 C:GLU3105 3.8 40.9 1.0
CB C:ASP3102 3.8 45.2 1.0
OD2 C:ASP3102 3.9 45.2 1.0
N C:ARG3103 4.1 41.2 1.0
O C:LEU3004 4.1 34.7 1.0
CA C:ARG3103 4.5 41.2 1.0
NH1 C:ARG3013 4.6 47.8 1.0
CB C:MET3010 4.8 33.9 1.0
CB C:GLU3105 4.9 40.9 1.0
N C:ASP3102 5.0 35.3 1.0

Nickel binding site 6 out of 8 in 1f5t

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Nickel binding site 6 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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) Complexed with Nickel and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni256

b:49.4
occ:1.00
CE1 C:HIS3098 1.9 32.5 1.0
OE1 C:GLU3083 1.9 47.3 1.0
ND1 C:HIS3098 2.2 32.5 1.0
NE2 C:HIS3079 2.4 47.7 1.0
OE2 C:GLU3083 2.5 47.3 1.0
CD C:GLU3083 2.6 47.3 1.0
CD2 C:HIS3079 3.2 47.7 1.0
NE2 C:HIS3098 3.2 32.5 1.0
CG C:HIS3098 3.5 32.5 1.0
CE1 C:HIS3079 3.5 47.7 1.0
CD2 C:HIS3098 4.0 32.5 1.0
CG C:GLU3083 4.1 47.3 1.0
CG C:HIS3079 4.4 47.7 1.0
ND1 C:HIS3079 4.6 47.7 1.0
CB C:HIS3098 4.6 32.5 1.0

Nickel binding site 7 out of 8 in 1f5t

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Nickel binding site 7 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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) Complexed with Nickel and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni257

b:49.4
occ:1.00
OE2 D:GLU4105 1.6 45.9 1.0
NE2 D:HIS4106 1.7 37.0 1.0
OD1 D:ASP4102 1.8 52.2 1.0
O D:ASP4102 1.8 52.1 1.0
SD D:MET4010 2.0 31.0 1.0
O D:HOH204 2.1 49.4 1.0
CD2 D:HIS4106 2.6 37.0 1.0
CE1 D:HIS4106 2.7 37.0 1.0
CE D:MET4010 2.8 31.0 1.0
CD D:GLU4105 2.8 45.9 1.0
C D:ASP4102 3.0 52.1 1.0
CG D:ASP4102 3.0 52.2 1.0
CG D:GLU4105 3.6 45.9 1.0
CA D:ASP4102 3.6 52.1 1.0
CG D:MET4010 3.7 31.0 1.0
CG D:HIS4106 3.7 37.0 1.0
ND1 D:HIS4106 3.8 37.0 1.0
OE1 D:GLU4105 3.8 45.9 1.0
CB D:ASP4102 3.8 52.2 1.0
OD2 D:ASP4102 3.9 52.2 1.0
N D:ARG4103 4.1 46.7 1.0
O D:LEU4004 4.2 29.8 1.0
CA D:ARG4103 4.5 46.7 1.0
NH1 D:ARG4013 4.6 36.5 1.0
CB D:MET4010 4.6 31.0 1.0
CB D:GLU4105 5.0 45.9 1.0

Nickel binding site 8 out of 8 in 1f5t

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Nickel binding site 8 out of 8 in the Diphtheria Tox Repressor (C102D Mutant) Complexed with Nickel and Dtxr Consensus Binding Sequence


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) Complexed with Nickel and Dtxr Consensus Binding Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni258

b:49.4
occ:1.00
OE1 D:GLU4083 1.9 39.8 1.0
ND1 D:HIS4098 2.0 30.2 1.0
CE1 D:HIS4098 2.0 30.2 1.0
NE2 D:HIS4079 2.3 43.2 1.0
OE2 D:GLU4083 2.5 39.8 1.0
CD D:GLU4083 2.5 39.8 1.0
CD2 D:HIS4079 3.1 43.2 1.0
CE1 D:HIS4079 3.3 43.2 1.0
NE2 D:HIS4098 3.3 30.2 1.0
CG D:HIS4098 3.4 30.2 1.0
CD2 D:HIS4098 4.0 30.2 1.0
CG D:GLU4083 4.0 39.8 1.0
CG D:HIS4079 4.3 43.2 1.0
ND1 D:HIS4079 4.3 43.2 1.0
CB D:HIS4098 4.4 30.2 1.0

Reference:

C.S.Chen, A.White, J.Love, J.R.Murphy, D.Ringe. Methyl Groups of Thymine Bases Are Important For Nucleic Acid Recognition By Dtxr. Biochemistry V. 39 10397 2000.
ISSN: ISSN 0006-2960
PubMed: 10956029
DOI: 10.1021/BI0009284
Page generated: Wed Dec 16 01:11:48 2020

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