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Platinum in PDB 5v6i: Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative

Protein crystallography data

The structure of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative, PDB code: 5v6i was solved by K.Li, P.Zhang, Y.Gang, C.Xia, J.E.Polston, G.Li, S.Li, Z.Lin, L.-J.Yang, S.D.Bruner, Y.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.30 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.102, 55.237, 41.879, 90.00, 99.52, 90.00
R / Rfree (%) 16 / 19.4

Other elements in 5v6i:

The structure of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative (pdb code 5v6i). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative, PDB code: 5v6i:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 5v6i

Go back to Platinum Binding Sites List in 5v6i
Platinum binding site 1 out of 5 in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:20.4
occ:0.35
CL B:CL210 2.5 33.5 1.0
CL B:CL209 2.5 35.4 1.0
CL B:CL212 2.6 30.8 1.0
CL B:CL211 2.6 32.7 1.0
CD B:ARG100 3.6 17.2 1.0
NH2 B:ARG100 4.1 27.2 1.0
CG B:ARG100 4.3 18.8 1.0
NE B:ARG100 4.5 31.7 1.0
O B:HOH349 4.6 37.1 1.0
CZ B:ARG100 4.7 27.1 1.0

Platinum binding site 2 out of 5 in 5v6i

Go back to Platinum Binding Sites List in 5v6i
Platinum binding site 2 out of 5 in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:51.4
occ:0.25
PT B:PT202 0.0 51.4 0.2
PT B:PT202 1.6 43.8 0.2
SG B:CYS24 2.7 23.6 1.0
O B:HOH308 3.9 34.6 1.0
SG B:CYS101 3.9 18.4 1.0
CL B:CL213 4.0 53.8 1.0
NH1 B:ARG100 4.1 29.4 1.0
CB B:CYS24 4.1 20.5 1.0
NE B:ARG100 4.2 31.7 1.0
O B:ARG100 4.2 17.1 1.0
N B:CYS24 4.3 17.9 1.0
CB B:ARG100 4.4 16.9 1.0
CZ B:ARG100 4.6 27.1 1.0
O B:LEU22 4.6 26.5 1.0
CD1 B:LEU22 4.6 26.2 1.0
CA B:CYS24 4.8 16.4 1.0
C B:ARG100 4.8 16.8 1.0

Platinum binding site 3 out of 5 in 5v6i

Go back to Platinum Binding Sites List in 5v6i
Platinum binding site 3 out of 5 in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:43.8
occ:0.25
PT B:PT202 0.0 43.8 0.2
PT B:PT202 1.6 51.4 0.2
SG B:CYS24 2.5 23.6 1.0
CL B:CL213 2.6 53.8 1.0
CB B:CYS24 3.2 20.5 1.0
N B:CYS24 3.3 17.9 1.0
O B:HOH308 3.7 34.6 1.0
CA B:CYS24 3.8 16.4 1.0
C B:SER23 4.3 18.0 1.0
SG B:CYS101 4.3 18.4 1.0
CA B:SER23 4.4 17.3 1.0
O B:LEU22 4.5 26.5 1.0
C B:CYS24 5.0 22.9 1.0

Platinum binding site 4 out of 5 in 5v6i

Go back to Platinum Binding Sites List in 5v6i
Platinum binding site 4 out of 5 in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt203

b:31.9
occ:0.27
CL B:CL207 2.6 38.2 1.0
CL B:CL208 2.6 41.3 1.0
CL B:CL206 2.7 56.0 1.0
CL B:CL205 3.0 62.2 1.0
OG B:SER23 4.2 29.8 1.0
NE B:ARG106 4.5 39.8 1.0
CB B:SER23 4.6 23.9 1.0
NH2 B:ARG106 4.8 41.9 1.0
CZ B:ARG106 4.9 35.9 1.0
CG B:ARG106 5.0 18.3 1.0

Platinum binding site 5 out of 5 in 5v6i

Go back to Platinum Binding Sites List in 5v6i
Platinum binding site 5 out of 5 in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt204

b:37.5
occ:0.31
CL B:CL216 2.6 46.0 1.0
CL B:CL215 2.7 44.3 1.0
CL B:CL214 2.8 63.6 1.0
NH2 B:ARG55 3.5 22.7 1.0
NH1 B:ARG55 3.6 29.0 1.0
CZ B:ARG55 4.0 22.3 1.0
O B:HOH340 4.5 30.8 1.0
CE2 B:PHE74 4.6 19.2 1.0

Reference:

P.Zhang, K.Li, G.Yang, C.Xia, J.E.Polston, G.Li, S.Li, Z.Lin, L.J.Yang, S.D.Bruner, Y.Ding. Cytotoxic Protein From the Mushroom Coprinus Comatus Possesses A Unique Mode For Glycan Binding and Specificity. Proc. Natl. Acad. Sci. V. 114 8980 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28784797
DOI: 10.1073/PNAS.1706894114
Page generated: Wed Dec 16 02:05:32 2020

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