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Nickel in PDB 2bj8: Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites

Protein crystallography data

The structure of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites, PDB code: 2bj8 was solved by T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.49 / 2.1
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 110.208, 110.208, 78.600, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 22.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites (pdb code 2bj8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites, PDB code: 2bj8:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 2bj8

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Nickel binding site 1 out of 6 in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1137

b:40.4
occ:1.00
ND1 A:HIS91 2.0 38.9 1.0
NE2 A:HIS89 2.1 41.2 1.0
SG A:CYS97 2.2 41.1 1.0
CE1 A:HIS91 2.9 32.2 1.0
CE1 A:HIS89 3.0 40.7 1.0
CG A:HIS91 3.1 40.4 1.0
CD2 A:HIS89 3.1 43.3 1.0
CB A:CYS97 3.3 38.6 1.0
CB A:HIS91 3.6 35.5 1.0
CA A:HIS91 3.6 38.3 1.0
NE2 A:HIS91 4.0 35.7 1.0
CA A:CYS97 4.1 43.2 1.0
ND1 A:HIS89 4.1 40.8 1.0
N A:HIS91 4.1 38.6 1.0
CD2 A:HIS91 4.2 35.7 1.0
CG A:HIS89 4.2 42.2 1.0
O A:VAL90 4.5 46.3 1.0
C A:VAL90 4.5 45.0 1.0
O A:ASN96 4.5 38.6 1.0
ND1 A:HIS64 4.7 53.7 1.0
N A:CYS97 4.8 41.6 1.0
C A:HIS91 4.9 42.7 1.0
C A:ASN96 4.9 45.6 1.0

Nickel binding site 2 out of 6 in 2bj8

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Nickel binding site 2 out of 6 in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1139

b:44.6
occ:1.00
ND1 B:HIS91 1.9 45.1 1.0
NE2 B:HIS89 2.0 44.8 1.0
SG B:CYS97 2.3 46.1 1.0
CE1 B:HIS91 2.7 35.4 1.0
CE1 B:HIS89 2.9 37.3 1.0
CG B:HIS91 3.1 43.2 1.0
CD2 B:HIS89 3.1 36.0 1.0
CB B:CYS97 3.2 44.5 1.0
CA B:HIS91 3.6 52.1 1.0
CB B:HIS91 3.6 45.8 1.0
CA B:CYS97 3.9 42.4 1.0
NE2 B:HIS91 3.9 40.9 1.0
ND1 B:HIS89 4.0 43.3 1.0
CD2 B:HIS91 4.1 38.3 1.0
N B:HIS91 4.1 44.0 1.0
CG B:HIS89 4.2 35.8 1.0
O B:VAL90 4.3 42.5 1.0
C B:VAL90 4.4 47.0 1.0
O B:ASN96 4.6 47.6 1.0
ND1 B:HIS64 4.7 53.8 1.0
N B:CYS97 4.7 43.2 1.0
C B:HIS91 4.9 48.6 1.0
C B:ASN96 5.0 46.8 1.0

Nickel binding site 3 out of 6 in 2bj8

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Nickel binding site 3 out of 6 in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1140

b:94.1
occ:1.00
NE2 B:HIS64 2.2 61.3 1.0
OD1 B:ASP65 2.3 69.0 1.0
OD2 B:ASP65 2.4 66.0 1.0
CG B:ASP65 2.7 68.0 1.0
CD2 B:HIS64 2.9 41.8 1.0
CE1 B:HIS64 3.3 55.8 1.0
CG B:HIS64 4.1 51.6 1.0
CB B:ASP65 4.2 57.9 1.0
O B:GLU94 4.3 57.2 1.0
ND1 B:HIS64 4.3 53.8 1.0
ND1 B:HIS95 4.8 76.0 1.0
CA B:ASP65 4.9 68.1 1.0
N B:ASP65 4.9 60.5 1.0

Nickel binding site 4 out of 6 in 2bj8

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Nickel binding site 4 out of 6 in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1141

b:79.8
occ:1.00
OD2 B:ASP75 2.3 58.0 1.0
CG B:ASP75 3.3 63.1 1.0
OD1 B:ASP75 4.0 65.9 1.0
CA B:ASP75 4.4 47.9 1.0
CB B:ASP75 4.4 52.5 1.0
O B:HOH2035 4.6 59.5 1.0
N B:ASP75 4.8 44.9 1.0

Nickel binding site 5 out of 6 in 2bj8

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Nickel binding site 5 out of 6 in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1142

b:86.7
occ:0.50
OD2 B:ASP36 2.7 55.8 1.0
OD1 B:ASP36 2.8 62.4 1.0
OE1 B:GLU32 2.9 91.6 1.0
CG B:ASP36 3.1 53.4 1.0
CG B:GLU32 3.2 74.5 1.0
CD B:GLU32 3.4 87.1 1.0
NH2 B:ARG39 4.0 68.5 1.0
O A:VAL123 4.0 43.7 1.0
O A:LEU120 4.1 44.8 1.0
O B:GLU32 4.2 42.0 1.0
CE2 B:TYR27 4.5 52.8 1.0
O B:HOH2019 4.5 77.9 1.0
CB B:GLU32 4.5 40.7 1.0
CB B:ASP36 4.6 38.0 1.0
CA A:LYS121 4.6 53.9 1.0
OE2 B:GLU32 4.6 93.1 1.0
C B:GLU32 4.7 38.1 1.0
O A:SER119 4.8 58.4 1.0
C A:LEU120 4.8 49.5 1.0
CD2 B:TYR27 4.9 50.8 1.0
N A:GLY122 4.9 42.3 1.0

Nickel binding site 6 out of 6 in 2bj8

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Nickel binding site 6 out of 6 in the Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Nikr in Closed Conformation and Nickel Bound to High and Low-Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1145

b:86.6
occ:0.30
OE1 B:GLU53 3.5 92.0 1.0
CD B:GLU53 4.3 86.3 1.0
O B:ASP82 4.6 52.4 1.0
O B:LYS104 4.7 48.8 1.0
CA B:GLY105 4.9 37.5 1.0
CG B:GLU53 5.0 74.1 1.0

Reference:

P.T.Chivers, T.H.Tahirov. Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications For the Regulation of Dna Recognition J.Mol.Biol. V. 348 597 2005.
ISSN: ISSN 0022-2836
PubMed: 15826657
DOI: 10.1016/J.JMB.2005.03.017
Page generated: Fri Sep 25 08:06:36 2020
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