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Platinum in PDB 3wu9: Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec

Enzymatic activity of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec

All present enzymatic activity of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec:
3.2.1.17;

Protein crystallography data

The structure of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec, PDB code: 3wu9 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 (°) 79.269, 79.269, 37.823, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.7

Platinum Binding Sites:

The binding sites of Platinum atom in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec (pdb code 3wu9). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec, PDB code: 3wu9:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 3wu9

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Platinum binding site 1 out of 5 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 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 1580 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt301

b:38.7
occ:0.08
 O A:HOH462 3.0 27.6 1.0
O A:HOH444 4.0 42.5 1.0
NH1 A:ARG14 4.6 48.9 1.0
CD A:ARG14 4.8 35.7 1.0

Platinum binding site 2 out of 5 in 3wu9

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Platinum binding site 2 out of 5 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 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 1580 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt302

b:34.6
occ:0.10
 O A:HOH422 3.6 32.0 1.0
O A:HOH449 4.7 20.3 1.0
O A:HOH432 4.7 30.3 1.0

Platinum binding site 3 out of 5 in 3wu9

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Platinum binding site 3 out of 5 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 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 1580 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt303

b:34.2
occ:0.06
 O A:ALA10 4.1 14.8 1.0
CB A:ALA10 4.4 16.5 1.0
CA A:ALA10 4.6 15.3 1.0
CD A:LYS13 4.7 31.1 1.0
OXT A:LEU129 4.7 67.2 1.0
C A:ALA10 4.7 14.9 1.0
CA A:LEU129 4.9 55.8 1.0

Platinum binding site 4 out of 5 in 3wu9

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Platinum binding site 4 out of 5 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 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 1580 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt304

b:34.8
occ:0.13
 OD1 A:ASN65 2.7 25.2 1.0
O A:HOH412 2.7 15.7 1.0
O A:HOH439 2.9 29.0 1.0
CB A:SER72 3.5 35.4 1.0
O A:THR69 3.5 21.9 1.0
CG A:ASN65 3.9 22.4 1.0
OG A:SER72 3.9 35.4 1.0
N A:GLY67 4.1 14.9 1.0
N A:THR69 4.2 16.8 1.0
C A:THR69 4.3 21.3 1.0
CA A:GLY67 4.4 16.6 1.0
N A:ASP66 4.5 12.3 1.0
CA A:SER72 4.6 36.0 1.0
N A:ARG68 4.6 17.1 1.0
CA A:THR69 4.6 18.9 1.0
CA A:ASN65 4.6 15.7 1.0
CB A:ASN65 4.6 17.9 1.0
N A:SER72 4.7 38.2 1.0
CB A:THR69 4.7 16.2 1.0
C A:GLY67 4.7 17.7 1.0
OD1 A:ASP66 4.8 12.9 1.0
ND2 A:ASN65 4.8 26.2 1.0
O A:SER72 5.0 29.4 1.0

Platinum binding site 5 out of 5 in 3wu9

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Platinum binding site 5 out of 5 in the Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Spatiotemporal Development of Soaked Protein Crystal; Derivative 1580 Sec within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt305

b:37.9
occ:0.13
 CE1 A:HIS15 2.5 25.6 1.0
O A:HOH433 2.6 27.4 1.0
NH1 A:ARG14 2.8 48.9 1.0
ND1 A:HIS15 3.4 26.7 1.0
NE2 A:HIS15 3.5 29.2 1.0
CZ A:ARG14 3.9 45.5 1.0
OD1 A:ASP87 4.3 27.7 1.0
NH2 A:ARG14 4.5 47.7 1.0
CG1 A:ILE88 4.5 16.8 1.0
OG1 A:THR89 4.6 19.6 1.0
CG A:HIS15 4.6 24.7 1.0
CB A:ALA11 4.6 15.8 1.0
CD2 A:HIS15 4.7 26.1 1.0
NE A:ARG14 4.8 42.2 1.0
N A:ILE88 4.9 17.4 1.0
CD A:ARG14 5.0 35.7 1.0
CG A:ASP87 5.0 27.6 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: Thu Oct 10 10:53:34 2024

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