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Nickel in PDB 3od2: E. Coli Nikr Soaked with Excess Nickel Ions

Protein crystallography data

The structure of E. Coli Nikr Soaked with Excess Nickel Ions, PDB code: 3od2 was solved by C.M.Phillips, E.R.Schreiter, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.735, 50.735, 183.114, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 28.6

Nickel Binding Sites:

The binding sites of Nickel atom in the E. Coli Nikr Soaked with Excess Nickel Ions (pdb code 3od2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 11 binding sites of Nickel where determined in the E. Coli Nikr Soaked with Excess Nickel Ions, PDB code: 3od2:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11;

Nickel binding site 1 out of 11 in 3od2

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Nickel binding site 1 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni134

b:70.6
occ:1.00
NE2 A:HIS87 1.9 55.7 1.0
ND1 A:HIS89 2.1 68.1 1.0
SG A:CYS95 2.2 72.2 1.0
CE1 A:HIS87 2.8 53.5 1.0
CD2 A:HIS87 2.9 53.8 1.0
CE1 A:HIS89 3.0 60.6 1.0
CG A:HIS89 3.2 64.5 1.0
CB A:CYS95 3.4 67.3 1.0
CA A:HIS89 3.5 69.1 1.0
CB A:HIS89 3.6 65.7 1.0
CA A:CYS95 3.9 70.3 1.0
ND1 A:HIS87 4.0 55.5 1.0
N A:HIS89 4.0 67.4 1.0
CG A:HIS87 4.0 54.5 1.0
NE2 A:HIS89 4.1 63.1 1.0
CD2 A:HIS89 4.3 61.5 1.0
O A:VAL88 4.3 67.3 1.0
C A:VAL88 4.3 67.2 1.0
O A:ASP94 4.4 72.0 1.0
N A:CYS95 4.7 71.8 1.0
C A:ASP94 4.9 74.6 1.0
C A:HIS89 4.9 71.8 1.0
OH A:TYR60 5.0 71.8 1.0

Nickel binding site 2 out of 11 in 3od2

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Nickel binding site 2 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni135

b:0.7
occ:1.00
O B:HOH156 2.0 78.7 1.0
O A:MET1 2.2 71.4 1.0
O B:HOH145 2.2 0.1 1.0
O A:HOH149 2.3 91.1 1.0
O A:HOH150 2.7 54.9 1.0
CA A:MET1 2.7 72.0 1.0
C A:MET1 2.8 71.5 1.0
N A:MET1 2.8 63.6 1.0
N A:GLN2 4.1 71.3 1.0
CB A:MET1 4.2 73.3 1.0
OD1 B:ASP10 4.6 84.9 1.0
OD2 B:ASP10 4.7 86.4 1.0
CG A:MET1 4.9 79.7 1.0
CA A:GLN2 4.9 68.8 1.0

Nickel binding site 3 out of 11 in 3od2

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Nickel binding site 3 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni136

b:0.6
occ:1.00
O A:HOH148 2.2 35.3 1.0
NE2 B:HIS125 2.4 69.7 1.0
NE2 A:HIS125 2.4 62.0 1.0
O A:HOH147 2.5 65.4 1.0
CE1 A:HIS125 2.6 62.3 1.0
CD2 B:HIS125 2.9 64.8 1.0
CE1 B:HIS125 3.6 65.4 1.0
CD2 A:HIS125 3.7 64.2 1.0
ND1 A:HIS125 3.9 59.8 1.0
CG B:HIS125 4.2 64.2 1.0
ND1 B:HIS125 4.4 66.7 1.0
CG A:HIS125 4.5 62.9 1.0
O A:HOH159 4.5 51.2 1.0
O A:LEU126 4.5 56.3 1.0
OE1 A:GLN42 4.5 86.3 1.0
C60 B:3CM134 4.7 0.2 1.0
O4 B:3CM134 4.8 0.5 1.0
O60 B:3CM134 4.9 0.7 1.0
O A:HOH152 5.0 50.4 1.0

Nickel binding site 4 out of 11 in 3od2

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Nickel binding site 4 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni137

b:0.1
occ:1.00
NE2 A:HIS110 2.2 0.3 1.0
NE2 A:HIS78 2.2 97.3 1.0
OD2 A:ASP114 2.4 0.9 1.0
CE1 A:HIS78 2.8 97.2 1.0
O A:HOH144 2.9 86.1 1.0
CE1 A:HIS110 2.9 0.8 1.0
O A:HOH142 3.1 54.2 1.0
CD2 A:HIS110 3.3 0.4 1.0
CG A:ASP114 3.5 0.7 1.0
CD2 A:HIS78 3.5 95.5 1.0
O A:HOH143 3.9 52.7 1.0
ND1 A:HIS78 4.0 96.8 1.0
OD1 A:ASP114 4.0 0.8 1.0
ND1 A:HIS110 4.1 0.8 1.0
CG A:HIS110 4.3 0.7 1.0
CG A:HIS78 4.4 95.3 1.0
CB A:ASP114 4.6 0.9 1.0

Nickel binding site 5 out of 11 in 3od2

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Nickel binding site 5 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni138

b:0.7
occ:1.00
O A:HOH171 1.9 0.5 1.0
O A:HOH161 2.2 97.8 1.0
O A:HOH156 2.3 46.9 1.0
NE2 A:HIS79 2.5 0.7 1.0
O A:HOH162 2.9 0.6 1.0
O A:HOH163 3.2 45.8 1.0
CD2 A:HIS79 3.2 0.5 1.0
CE1 A:HIS79 3.6 0.6 1.0
CG A:HIS79 4.5 0.1 1.0
ND1 A:HIS79 4.6 0.6 1.0

Nickel binding site 6 out of 11 in 3od2

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Nickel binding site 6 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni139

b:0.6
occ:1.00
NE2 A:HIS123 2.1 83.2 1.0
O B:HOH165 2.3 97.9 1.0
O A:HOH153 2.5 81.2 1.0
O A:HOH164 2.7 79.8 1.0
CE1 A:HIS123 2.8 80.3 1.0
CD2 A:HIS123 3.2 80.5 1.0
O B:HOH163 3.5 66.4 1.0
O B:HOH141 3.7 65.7 1.0
O B:PRO130 3.7 78.5 1.0
C B:GLU132 4.0 91.9 1.0
ND1 A:HIS123 4.0 78.0 1.0
O B:GLU132 4.0 90.3 1.0
CG A:HIS123 4.2 77.3 1.0
O B:HOH157 4.3 73.2 1.0
N B:GLU132 4.6 92.2 1.0
CD A:ARG122 4.7 88.4 1.0
NH1 A:ARG122 4.8 96.8 1.0
C B:PRO130 4.9 83.6 1.0
CA B:GLU132 4.9 92.7 1.0

Nickel binding site 7 out of 11 in 3od2

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Nickel binding site 7 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni135

b:78.8
occ:1.00
ND1 B:HIS89 1.9 69.4 1.0
NE2 B:HIS87 2.1 63.9 1.0
SG B:CYS95 2.3 68.5 1.0
CE1 B:HIS89 2.5 65.6 1.0
CE1 B:HIS87 3.0 62.5 1.0
CG B:HIS89 3.1 68.2 1.0
CB B:CYS95 3.2 67.8 1.0
CD2 B:HIS87 3.2 59.3 1.0
NE2 B:HIS89 3.7 68.8 1.0
CB B:HIS89 3.8 66.3 1.0
CA B:HIS89 3.9 67.5 1.0
CA B:CYS95 4.0 66.6 1.0
CD2 B:HIS89 4.0 68.6 1.0
ND1 B:HIS87 4.1 60.2 1.0
CG B:HIS87 4.3 58.2 1.0
N B:HIS89 4.4 64.7 1.0
O B:ASP94 4.6 73.3 1.0
N B:CYS95 4.8 69.9 1.0
C B:VAL88 4.8 60.5 1.0
O B:VAL88 4.9 59.9 1.0

Nickel binding site 8 out of 11 in 3od2

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Nickel binding site 8 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni136

b:74.0
occ:1.00
O B:HOH146 1.8 62.3 1.0
O B:HOH158 2.1 80.8 1.0
O B:HOH148 2.3 80.5 1.0
OD2 B:ASP114 2.4 61.6 1.0
NE2 B:HIS78 2.4 65.8 1.0
NE2 B:HIS110 2.5 47.9 1.0
CG B:ASP114 3.1 59.1 1.0
CE1 B:HIS110 3.1 49.5 1.0
CE1 B:HIS78 3.2 61.5 1.0
OD1 B:ASP114 3.4 61.0 1.0
O B:HOH167 3.6 49.1 1.0
CD2 B:HIS78 3.6 66.4 1.0
CD2 B:HIS110 3.6 46.1 1.0
O B:HOH159 4.2 48.5 1.0
ND1 B:HIS110 4.3 48.4 1.0
CB B:ASP114 4.4 58.1 1.0
ND1 B:HIS78 4.4 63.9 1.0
CG B:HIS110 4.6 48.8 1.0
CG B:HIS78 4.6 65.8 1.0

Nickel binding site 9 out of 11 in 3od2

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Nickel binding site 9 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni137

b:0.1
occ:1.00
O A:HOH160 2.1 0.3 1.0
O A:HOH165 2.2 81.5 1.0
O B:HOH149 2.2 85.7 1.0
NE2 B:HIS123 2.5 68.8 1.0
O B:HOH169 2.5 96.8 1.0
O B:HOH168 3.1 73.4 1.0
CE1 B:HIS123 3.1 69.2 1.0
CD2 B:HIS123 3.7 69.8 1.0
OE1 A:GLU132 4.1 0.6 1.0
NH2 B:ARG122 4.2 77.9 1.0
ND1 B:HIS123 4.3 68.5 1.0
O A:PRO130 4.3 75.7 1.0
CG B:HIS123 4.6 68.3 1.0
NE B:ARG122 4.8 79.2 1.0

Nickel binding site 10 out of 11 in 3od2

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Nickel binding site 10 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni138

b:0.5
occ:1.00
O B:HOH164 2.2 0.8 1.0
O B:HOH161 2.3 88.0 1.0
O B:HOH160 2.3 89.8 1.0
O B:HOH162 2.4 57.2 1.0
NE2 B:HIS79 2.5 69.6 1.0
CD2 B:HIS79 3.4 68.0 1.0
CE1 B:HIS79 3.4 66.6 1.0
OD2 B:ASP80 3.7 86.5 1.0
OD1 B:ASP80 4.1 80.0 1.0
CG B:ASP80 4.3 81.3 1.0
O B:HOH144 4.4 46.5 1.0
ND1 B:HIS79 4.5 66.0 1.0
CG B:HIS79 4.5 67.5 1.0

Nickel binding site 11 out of 11 in 3od2

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Nickel binding site 11 out of 11 in the E. Coli Nikr Soaked with Excess Nickel Ions


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 11 of E. Coli Nikr Soaked with Excess Nickel Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni139

b:1.0
occ:1.00
O A:HOH157 2.0 97.5 1.0
O A:HOH158 2.0 96.4 1.0
O B:HOH142 2.2 93.6 1.0
O B:HOH170 2.3 78.0 1.0
O B:MET1 2.7 97.6 1.0
N B:MET1 2.7 97.2 1.0
C B:MET1 3.0 97.1 1.0
CA B:MET1 3.4 98.0 1.0
N B:GLN2 3.8 95.6 1.0
CA B:GLN2 4.3 91.7 1.0
OD2 A:ASP10 4.4 98.5 1.0
CB B:MET1 4.5 0.9 1.0
OD1 A:ASP10 4.8 96.7 1.0
CG A:ASP10 4.9 98.1 1.0

Reference:

C.M.Phillips, E.R.Schreiter, C.M.Stultz, C.L.Drennan. Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor Nikr From Escherichia Coli. Biochemistry V. 49 7830 2010.
ISSN: ISSN 0006-2960
PubMed: 20704276
DOI: 10.1021/BI100923J
Page generated: Fri Sep 25 08:31:13 2020
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