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Nickel in PDB 2bj7: Nikr in Closed Conformation and Nickel Bound to High- Affinity Sites

Protein crystallography data

The structure of Nikr in Closed Conformation and Nickel Bound to High- Affinity Sites, PDB code: 2bj7 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) 29.45 / 2.1
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.952, 109.952, 79.003, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 21.5

Other elements in 2bj7:

The structure of Nikr in Closed Conformation and Nickel Bound to High- Affinity Sites also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Nikr in Closed Conformation and Nickel Bound to High- Affinity Sites (pdb code 2bj7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Nikr in Closed Conformation and Nickel Bound to High- Affinity Sites, PDB code: 2bj7:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 2bj7

Go back to Nickel Binding Sites List in 2bj7
Nickel binding site 1 out of 4 in the Nikr in Closed Conformation and Nickel Bound to High- 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- Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1137

b:35.5
occ:1.00
NE2 A:HIS89 2.0 33.5 1.0
ND1 A:HIS91 2.1 29.6 1.0
SG A:CYS97 2.2 35.5 1.0
CE1 A:HIS91 2.9 30.2 1.0
CE1 A:HIS89 2.9 30.8 1.0
CD2 A:HIS89 3.1 32.6 1.0
CG A:HIS91 3.2 30.5 1.0
CB A:CYS97 3.3 37.1 1.0
CA A:HIS91 3.6 30.7 1.0
CB A:HIS91 3.7 31.6 1.0
CA A:CYS97 4.0 36.1 1.0
NE2 A:HIS91 4.1 31.4 1.0
ND1 A:HIS89 4.1 33.6 1.0
N A:HIS91 4.2 28.9 1.0
CG A:HIS89 4.2 32.5 1.0
CD2 A:HIS91 4.2 32.9 1.0
O A:VAL90 4.3 33.5 1.0
C A:VAL90 4.5 36.3 1.0
O A:ASN96 4.5 35.4 1.0
N A:CYS97 4.7 38.0 1.0
ND1 A:HIS64 4.8 48.8 1.0
C A:ASN96 4.9 38.0 1.0
C A:HIS91 4.9 36.4 1.0

Nickel binding site 2 out of 4 in 2bj7

Go back to Nickel Binding Sites List in 2bj7
Nickel binding site 2 out of 4 in the Nikr in Closed Conformation and Nickel Bound to High- 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- Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1140

b:38.5
occ:1.00
ND1 B:HIS91 1.9 39.8 1.0
NE2 B:HIS89 2.1 37.9 1.0
SG B:CYS97 2.3 40.3 1.0
CE1 B:HIS91 2.7 31.6 1.0
CE1 B:HIS89 2.9 37.4 1.0
CG B:HIS91 3.1 41.2 1.0
CD2 B:HIS89 3.2 34.4 1.0
CB B:CYS97 3.2 42.9 1.0
CA B:HIS91 3.6 44.6 1.0
CB B:HIS91 3.6 43.3 1.0
NE2 B:HIS91 3.9 37.4 1.0
CA B:CYS97 3.9 43.4 1.0
ND1 B:HIS89 4.1 38.7 1.0
CD2 B:HIS91 4.1 37.9 1.0
N B:HIS91 4.2 36.7 1.0
CG B:HIS89 4.2 36.1 1.0
O B:VAL90 4.3 38.3 1.0
C B:VAL90 4.5 42.0 1.0
ND1 B:HIS64 4.6 50.9 1.0
N B:CYS97 4.7 38.8 1.0
O B:ASN96 4.7 41.7 1.0
C B:HIS91 4.9 41.7 1.0
C B:ASN96 4.9 43.3 1.0

Nickel binding site 3 out of 4 in 2bj7

Go back to Nickel Binding Sites List in 2bj7
Nickel binding site 3 out of 4 in the Nikr in Closed Conformation and Nickel Bound to High- 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- Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1141

b:79.8
occ:1.00
NE2 B:HIS64 2.3 53.1 1.0
OD1 B:ASP65 2.3 59.3 1.0
OD2 B:ASP65 2.5 56.5 1.0
CG B:ASP65 2.7 61.8 1.0
CD2 B:HIS64 3.0 41.0 1.0
CE1 B:HIS64 3.4 51.0 1.0
CG B:HIS64 4.2 48.8 1.0
CB B:ASP65 4.2 57.5 1.0
ND1 B:HIS64 4.4 50.9 1.0
O B:GLU94 4.4 47.7 1.0
ND1 B:HIS95 4.7 64.7 1.0
CA B:ASP65 4.9 64.1 1.0
N B:ASP65 5.0 55.9 1.0

Nickel binding site 4 out of 4 in 2bj7

Go back to Nickel Binding Sites List in 2bj7
Nickel binding site 4 out of 4 in the Nikr in Closed Conformation and Nickel Bound to High- 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- Affinity Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1142

b:67.7
occ:1.00
OD2 B:ASP75 2.2 53.9 1.0
CG B:ASP75 3.3 58.6 1.0
OD1 B:ASP75 3.8 60.9 1.0
CB B:ASP75 4.5 48.8 1.0
CA B:ASP75 4.5 46.4 1.0
O B:HOH2039 4.8 48.8 1.0
N B:ASP75 4.9 43.9 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: Thu Oct 29 06:16:39 2020
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