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Platinum in PDB 2hr8: Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3

Enzymatic activity of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3

All present enzymatic activity of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3:
2.1.1.98;

Protein crystallography data

The structure of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3, PDB code: 2hr8 was solved by H.Yamamoto, M.Taketa, 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) 39.29 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.581, 104.581, 139.110, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.3

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 (pdb code 2hr8). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3, PDB code: 2hr8:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 2hr8

Go back to Platinum Binding Sites List in 2hr8
Platinum binding site 1 out of 5 in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt901

b:0.1
occ:0.79
SD A:MET1 2.0 0.9 1.0
N A:MET1 2.6 87.2 1.0
CB A:MET1 2.7 92.6 1.0
CG A:MET1 2.7 98.9 1.0
CA A:MET1 2.8 86.8 1.0
CE A:MET1 3.0 0.1 1.0
O A:GLU77 3.3 86.7 1.0
C A:GLU77 4.2 86.3 1.0
OD1 A:ASP79 4.3 78.4 1.0
C A:MET1 4.4 83.3 1.0
O A:ASN78 4.9 80.4 1.0
N A:ASN78 5.0 84.6 1.0
CA A:GLU77 5.0 87.4 1.0

Platinum binding site 2 out of 5 in 2hr8

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Platinum binding site 2 out of 5 in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt902

b:0.1
occ:0.36
SD A:MET174 2.2 93.3 1.0
CG A:MET174 3.1 85.8 1.0
CE A:MET174 3.8 86.6 1.0
CB A:MET174 4.1 80.9 1.0
CA A:MET174 4.2 77.2 1.0
O A:ARG173 4.8 80.0 1.0

Platinum binding site 3 out of 5 in 2hr8

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Platinum binding site 3 out of 5 in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt903

b:0.8
occ:0.47
SD A:MET220 2.5 71.6 1.0
CG A:MET220 3.7 67.8 1.0
O A:ASP200 3.9 67.0 1.0
CE A:MET220 3.9 70.1 1.0
OE2 A:GLU259 4.2 90.4 1.0
OD1 A:ASP200 4.4 75.8 1.0
CB A:ASP200 4.4 72.9 1.0
C A:ASP200 4.7 68.0 1.0
CG A:ASP200 4.8 75.6 1.0
CA A:ASP200 4.8 70.3 1.0
CB A:MET220 4.8 64.6 1.0

Platinum binding site 4 out of 5 in 2hr8

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Platinum binding site 4 out of 5 in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt904

b:0.1
occ:0.82
N B:MET1 2.0 83.3 1.0
SD B:MET1 2.0 95.3 1.0
CG B:MET1 2.7 88.7 1.0
CB B:MET1 2.7 86.0 1.0
CA B:MET1 2.8 82.7 1.0
OD1 B:ASP79 3.5 69.3 1.0
CE B:MET1 3.6 91.2 1.0
OD2 B:ASP79 3.7 71.1 1.0
CG B:ASP79 3.9 68.4 1.0
C B:MET1 4.2 80.0 1.0
N B:VAL2 4.4 76.3 1.0

Platinum binding site 5 out of 5 in 2hr8

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Platinum binding site 5 out of 5 in the Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt905

b:0.5
occ:0.43
SD B:MET174 2.1 0.8 1.0
CG B:MET174 2.8 99.4 1.0
CE B:MET174 3.8 0.4 1.0
OH B:TYR138 3.9 57.4 1.0
CB B:MET174 4.1 93.6 1.0
O B:TYR175 4.3 67.0 1.0
OE2 B:GLU180 4.5 63.8 1.0
OE1 B:GLU180 4.5 63.3 1.0
CZ B:TYR138 4.8 56.7 1.0
CD B:GLU180 4.9 62.3 1.0
CA B:MET174 5.0 88.6 1.0

Reference:

H.Yamamoto, M.Taketa, N.Kunishima. Crystal Structure of PH0725 From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Wed Dec 16 02:04:00 2020

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