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Platinum in PDB 3wu8: Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec

Enzymatic activity of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec

All present enzymatic activity of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec:
3.2.1.17;

Protein crystallography data

The structure of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec, PDB code: 3wu8 was solved by R.Mizutani, R.Saiga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.206, 79.206, 37.858, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.6

Platinum Binding Sites:

The binding sites of Platinum atom in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec (pdb code 3wu8). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec, PDB code: 3wu8:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 3wu8

Go back to Platinum Binding Sites List in 3wu8
Platinum binding site 1 out of 4 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt301

b:37.5
occ:0.15
O A:HOH463 2.7 18.8 1.0
O A:HOH445 4.2 43.1 1.0
NH1 A:ARG14 4.5 45.6 1.0
CD A:ARG14 4.8 33.9 1.0
CA A:ALA11 5.0 14.2 1.0

Platinum binding site 2 out of 4 in 3wu8

Go back to Platinum Binding Sites List in 3wu8
Platinum binding site 2 out of 4 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt302

b:34.3
occ:0.16
O A:HOH422 3.8 31.2 1.0
O A:HOH450 4.7 19.2 1.0
O A:HOH433 4.7 25.6 1.0

Platinum binding site 3 out of 4 in 3wu8

Go back to Platinum Binding Sites List in 3wu8
Platinum binding site 3 out of 4 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt303

b:34.2
occ:0.14
O A:HOH412 2.9 15.8 1.0
OD1 A:ASN65 3.3 24.5 1.0
O A:THR69 3.3 21.9 1.0
N A:THR69 3.4 17.0 1.0
O A:HOH440 3.7 26.9 1.0
C A:THR69 3.7 20.7 1.0
N A:GLY67 3.9 14.3 1.0
N A:ARG68 3.9 16.5 1.0
CB A:SER72 4.0 33.4 1.0
CA A:THR69 4.0 18.9 1.0
CA A:GLY67 4.0 15.4 1.0
C A:GLY67 4.0 17.1 1.0
CB A:THR69 4.3 16.6 1.0
C A:ARG68 4.4 17.5 1.0
CG A:ASN65 4.5 21.4 1.0
OD1 A:ASP66 4.5 12.3 1.0
OG A:SER72 4.5 36.4 1.0
N A:PRO70 4.6 24.3 1.0
CA A:ARG68 4.6 17.2 1.0
N A:ASP66 4.7 11.8 1.0
O A:GLY67 4.7 20.2 1.0
C A:ASP66 4.9 13.4 1.0
OG1 A:THR69 4.9 15.7 1.0
CA A:PRO70 5.0 25.8 1.0
N A:SER72 5.0 34.5 1.0

Platinum binding site 4 out of 4 in 3wu8

Go back to Platinum Binding Sites List in 3wu8
Platinum binding site 4 out of 4 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1080 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt304

b:39.4
occ:0.08
O A:HOH434 2.6 27.4 1.0
NH1 A:ARG14 2.6 45.6 1.0
CE1 A:HIS15 2.7 23.0 1.0
ND1 A:HIS15 3.6 23.4 1.0
NE2 A:HIS15 3.7 26.2 1.0
CZ A:ARG14 3.8 42.4 1.0
OD1 A:ASP87 4.2 25.9 1.0
NH2 A:ARG14 4.3 44.4 1.0
CB A:ALA11 4.6 15.9 1.0
NE A:ARG14 4.7 39.6 1.0
OG1 A:THR89 4.7 18.3 1.0
CG1 A:ILE88 4.8 16.9 1.0
CG A:HIS15 4.9 22.7 1.0
CD2 A:HIS15 4.9 23.7 1.0
CD A:ARG14 4.9 33.9 1.0
CG A:ASP87 4.9 26.0 1.0
N A:ILE88 5.0 17.0 1.0

Reference:

R.Mizutani, Y.Shimizu, R.Saiga, G.Ueno, Y.Nakamura, A.Takeuchi, K.Uesugi, Y.Suzuki. Spatiotemporal Development of Soaked Protein Crystal Sci Rep V. 4 5731 2014.
ISSN: ESSN 2045-2322
PubMed: 25043871
DOI: 10.1038/SREP05731
Page generated: Wed Dec 16 02:04:34 2020

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