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Nickel in PDB 2cqz: Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3

Protein crystallography data

The structure of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3, PDB code: 2cqz was solved by N.K.Lokanath, Y.Terao, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.511, 101.166, 78.646, 90.00, 119.78, 90.00
R / Rfree (%) 19.5 / 22.5

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 (pdb code 2cqz). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3, PDB code: 2cqz:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 2cqz

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Nickel binding site 1 out of 6 in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:83.0
occ:1.00
OD1 A:ASP124 2.1 46.4 1.0
NE2 A:HIS33 2.3 30.5 1.0
OD2 A:ASP68 2.3 46.5 1.0
NE2 A:HIS67 2.4 38.1 1.0
CD2 A:HIS33 3.0 28.6 1.0
CG A:ASP124 3.1 36.9 1.0
CD2 A:HIS67 3.1 32.9 1.0
CG A:ASP68 3.3 40.4 1.0
CE1 A:HIS33 3.4 31.2 1.0
CE1 A:HIS67 3.5 35.7 1.0
OD1 A:ASP68 3.6 41.1 1.0
OD2 A:ASP124 3.6 41.4 1.0
NH1 A:ARG16 3.9 20.9 1.0
CG A:HIS33 4.2 32.5 1.0
CB A:ASP124 4.3 33.7 1.0
CG A:HIS67 4.4 36.1 1.0
ND1 A:HIS33 4.4 35.3 1.0
O A:HOH616 4.5 62.4 1.0
ND1 A:HIS67 4.5 39.4 1.0
CB A:ASP68 4.6 35.5 1.0
CG2 A:VAL37 4.6 24.1 1.0
CZ A:ARG16 4.7 27.4 1.0
NH2 A:ARG16 4.9 33.8 1.0
CA A:ASP124 5.0 33.3 1.0

Nickel binding site 2 out of 6 in 2cqz

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Nickel binding site 2 out of 6 in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni602

b:76.9
occ:1.00
OD2 B:ASP68 2.1 48.3 1.0
OD1 B:ASP124 2.3 39.1 1.0
NE2 B:HIS33 2.4 26.8 1.0
NE2 B:HIS67 2.4 42.4 1.0
CG B:ASP68 3.0 42.6 1.0
CD2 B:HIS33 3.1 28.1 1.0
CD2 B:HIS67 3.1 38.2 1.0
CG B:ASP124 3.3 35.3 1.0
OD1 B:ASP68 3.3 45.0 1.0
CE1 B:HIS67 3.5 46.5 1.0
CE1 B:HIS33 3.5 26.6 1.0
OD2 B:ASP124 3.8 38.7 1.0
O B:HOH614 3.9 64.2 1.0
NH1 B:ARG16 4.2 30.0 1.0
CG B:HIS67 4.3 39.6 1.0
CG B:HIS33 4.3 31.2 1.0
CB B:ASP68 4.4 39.4 1.0
CB B:ASP124 4.5 32.6 1.0
ND1 B:HIS67 4.5 43.6 1.0
ND1 B:HIS33 4.5 30.4 1.0
CG2 B:VAL37 4.7 32.7 1.0
CZ B:ARG16 4.9 30.9 1.0

Nickel binding site 3 out of 6 in 2cqz

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Nickel binding site 3 out of 6 in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni603

b:76.9
occ:1.00
OD2 C:ASP68 2.2 43.7 1.0
NE2 C:HIS67 2.3 31.3 1.0
OD1 C:ASP124 2.3 44.8 1.0
NE2 C:HIS33 2.5 34.8 1.0
CD2 C:HIS67 2.9 31.5 1.0
CG C:ASP68 3.0 39.4 1.0
CD2 C:HIS33 3.1 32.3 1.0
CG C:ASP124 3.3 40.6 1.0
OD1 C:ASP68 3.3 46.1 1.0
CE1 C:HIS67 3.4 35.4 1.0
CE1 C:HIS33 3.6 35.9 1.0
OD2 C:ASP124 3.8 46.0 1.0
O C:HOH628 4.0 51.2 1.0
CG C:HIS67 4.1 36.2 1.0
NH1 C:ARG16 4.3 30.4 1.0
CB C:ASP68 4.3 35.8 1.0
ND1 C:HIS67 4.3 36.2 1.0
CB C:ASP124 4.4 36.6 1.0
CG C:HIS33 4.4 29.4 1.0
ND1 C:HIS33 4.6 30.5 1.0
CG2 C:VAL37 4.7 26.0 1.0
OH C:TYR109 5.0 42.9 1.0

Nickel binding site 4 out of 6 in 2cqz

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Nickel binding site 4 out of 6 in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni604

b:76.1
occ:1.00
OD2 D:ASP68 1.9 49.0 1.0
NE2 D:HIS67 2.4 33.4 1.0
OD1 D:ASP124 2.6 44.4 1.0
NE2 D:HIS33 2.7 34.7 1.0
CG D:ASP68 2.9 40.7 1.0
CD2 D:HIS67 3.1 30.4 1.0
CD2 D:HIS33 3.1 33.0 1.0
OD1 D:ASP68 3.2 46.6 1.0
CE1 D:HIS67 3.5 35.5 1.0
CG D:ASP124 3.7 40.9 1.0
CE1 D:HIS33 3.9 34.3 1.0
NH1 D:ARG16 4.1 25.6 1.0
CB D:ASP68 4.2 37.0 1.0
OD2 D:ASP124 4.2 49.3 1.0
CG D:HIS67 4.2 34.0 1.0
O D:HOH633 4.3 59.9 1.0
ND1 D:HIS67 4.4 37.2 1.0
CG D:HIS33 4.4 33.0 1.0
CB D:ASP124 4.8 35.5 1.0
ND1 D:HIS33 4.8 33.1 1.0
CZ D:ARG16 4.9 28.7 1.0
CG2 D:VAL37 4.9 30.4 1.0

Nickel binding site 5 out of 6 in 2cqz

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Nickel binding site 5 out of 6 in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni605

b:85.2
occ:1.00
NE2 E:HIS33 2.1 32.4 1.0
OD2 E:ASP68 2.1 39.5 1.0
OD1 E:ASP124 2.3 46.1 1.0
NE2 E:HIS67 2.5 39.1 1.0
CD2 E:HIS33 2.7 27.3 1.0
CG E:ASP68 3.2 37.6 1.0
CE1 E:HIS33 3.3 29.8 1.0
CD2 E:HIS67 3.3 38.0 1.0
CG E:ASP124 3.4 37.9 1.0
CE1 E:HIS67 3.5 38.4 1.0
OD1 E:ASP68 3.6 41.4 1.0
NH1 E:ARG16 3.9 24.1 1.0
O E:HOH614 4.0 43.9 1.0
CG E:HIS33 4.0 30.4 1.0
OD2 E:ASP124 4.0 41.9 1.0
ND1 E:HIS33 4.2 31.1 1.0
CB E:ASP124 4.5 32.8 1.0
CB E:ASP68 4.5 35.8 1.0
CG E:HIS67 4.5 36.0 1.0
ND1 E:HIS67 4.6 39.9 1.0
CZ E:ARG16 4.6 28.6 1.0
CG2 E:VAL37 4.6 26.1 1.0
NH2 E:ARG16 4.8 29.6 1.0

Nickel binding site 6 out of 6 in 2cqz

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Nickel binding site 6 out of 6 in the Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni606

b:77.6
occ:1.00
OD1 F:ASP124 2.1 42.3 1.0
OD2 F:ASP68 2.2 42.0 1.0
NE2 F:HIS33 2.2 27.2 1.0
NE2 F:HIS67 2.3 33.7 1.0
CD2 F:HIS33 2.9 26.1 1.0
CG F:ASP68 3.1 34.7 1.0
CD2 F:HIS67 3.1 27.3 1.0
CG F:ASP124 3.2 35.1 1.0
CE1 F:HIS33 3.3 24.5 1.0
CE1 F:HIS67 3.4 35.4 1.0
OD1 F:ASP68 3.5 36.7 1.0
OD2 F:ASP124 3.8 39.4 1.0
NH1 F:ARG16 4.1 32.8 1.0
CG F:HIS33 4.2 26.5 1.0
CG F:HIS67 4.3 30.8 1.0
CB F:ASP124 4.3 33.4 1.0
ND1 F:HIS33 4.3 31.7 1.0
ND1 F:HIS67 4.4 37.7 1.0
CB F:ASP68 4.4 32.0 1.0
CG2 F:VAL37 4.5 31.0 1.0
CZ F:ARG16 4.9 35.7 1.0
CA F:ASP124 4.9 32.8 1.0

Reference:

N.K.Lokanath, Y.Terao, N.Kunishima. Crystal Structure of PH0347 Protein From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Wed Dec 16 01:17:39 2020

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