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Chlorine 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:

Platinum (Pt) 5 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Glycan Binding Protein Y3 From Mushroom Coprinus Comatus Possesses Anti-Leukemic Activity - Pt Derivative, PDB code: 5v6i:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5v6i

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Chlorine binding site 1 out of 12 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 Chlorine with other atoms in the Cl 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:Cl205

b:62.2
occ:1.00
PT B:PT203 3.0 31.9 0.3
CD1 B:LEU116 3.6 23.9 1.0
NE B:ARG106 3.7 39.8 1.0
CG B:ARG106 3.8 18.3 1.0
CL B:CL208 3.8 41.3 1.0
CL B:CL214 3.9 63.6 1.0
CL B:CL207 4.1 38.2 1.0
CD B:ARG106 4.4 27.3 1.0
NH2 B:ARG106 4.6 41.9 1.0
CZ B:ARG106 4.6 35.9 1.0
CD2 B:LEU116 4.8 15.4 1.0
CG B:LEU116 4.8 18.6 1.0
O A:PHE130 5.0 32.1 1.0

Chlorine binding site 2 out of 12 in 5v6i

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Chlorine binding site 2 out of 12 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 Chlorine with other atoms in the Cl 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:Cl206

b:56.0
occ:1.00
PT B:PT203 2.7 31.9 0.3
OG B:SER23 2.9 29.8 1.0
CL B:CL207 3.7 38.2 1.0
CB B:SER23 3.9 23.9 1.0
CL B:CL208 3.9 41.3 1.0
CB B:PRO21 4.8 16.1 1.0

Chlorine binding site 3 out of 12 in 5v6i

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Chlorine binding site 3 out of 12 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 Chlorine with other atoms in the Cl 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:Cl207

b:38.2
occ:1.00
PT B:PT203 2.6 31.9 0.3
O B:ARG106 3.4 12.0 1.0
OG B:SER23 3.5 29.8 1.0
CL B:CL206 3.7 56.0 1.0
CB B:SER23 3.8 23.9 1.0
N B:SER23 4.0 16.4 1.0
CB B:PRO21 4.0 16.1 1.0
CA B:GLY107 4.0 11.5 1.0
CG B:PRO21 4.1 17.6 1.0
C B:ARG106 4.1 11.3 1.0
CG B:ARG106 4.1 18.3 1.0
CL B:CL205 4.1 62.2 1.0
O B:PRO21 4.2 13.3 1.0
C B:PRO21 4.3 17.8 1.0
N B:GLY107 4.4 9.6 1.0
N B:LEU22 4.5 14.0 1.0
CD1 B:LEU116 4.5 23.9 1.0
CA B:SER23 4.5 17.3 1.0
CD B:ARG106 4.5 27.3 1.0
C B:LEU22 4.5 25.8 1.0
CA B:LEU22 4.7 19.0 1.0
NE B:ARG106 4.7 39.8 1.0
CA B:PRO21 4.8 17.7 1.0

Chlorine binding site 4 out of 12 in 5v6i

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Chlorine binding site 4 out of 12 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 Chlorine with other atoms in the Cl 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:Cl208

b:41.3
occ:1.00
PT B:PT203 2.6 31.9 0.3
CL B:CL205 3.8 62.2 1.0
CL B:CL206 3.9 56.0 1.0

Chlorine binding site 5 out of 12 in 5v6i

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Chlorine binding site 5 out of 12 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 Chlorine with other atoms in the Cl 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:Cl209

b:35.4
occ:1.00
O B:HOH349 2.5 37.1 1.0
PT B:PT201 2.5 20.4 0.3
NH2 B:ARG100 2.9 27.2 1.0
CL B:CL212 3.5 30.8 1.0
CG B:PCA19 3.6 23.6 1.0
CD B:ARG100 3.8 17.2 1.0
CL B:CL211 3.8 32.7 1.0
CB B:PCA19 4.0 18.0 1.0
CZ B:ARG100 4.0 27.1 1.0
CB B:ALA96 4.3 11.8 1.0
NE B:ARG100 4.3 31.7 1.0
O B:PCA19 4.5 20.7 1.0
CD B:PCA19 4.7 21.3 1.0
O B:HOH312 4.8 34.6 1.0
O B:HOH336 4.9 25.4 1.0
CL B:CL210 5.0 33.5 1.0

Chlorine binding site 6 out of 12 in 5v6i

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Chlorine binding site 6 out of 12 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl210

b:33.5
occ:1.00
PT B:PT201 2.5 20.4 0.3
O B:HOH301 3.3 39.3 1.0
CL B:CL211 3.4 32.7 1.0
CL B:CL212 3.6 30.8 1.0
OD1 B:ASN99 4.0 46.3 1.0
CG B:ARG100 4.7 18.8 1.0
CD B:ARG100 4.8 17.2 1.0
CL B:CL209 5.0 35.4 1.0

Chlorine binding site 7 out of 12 in 5v6i

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Chlorine binding site 7 out of 12 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl211

b:32.7
occ:1.00
PT B:PT201 2.6 20.4 0.3
CL B:CL210 3.4 33.5 1.0
OD1 B:ASN99 3.5 46.3 1.0
CD B:ARG100 3.6 17.2 1.0
CG B:ARG100 3.7 18.8 1.0
CL B:CL209 3.8 35.4 1.0
CA B:ALA96 3.8 10.6 1.0
CB B:ASN99 4.0 19.9 1.0
CG B:ASN99 4.1 32.9 1.0
CB B:ALA96 4.1 11.8 1.0
O B:ALA96 4.1 13.3 1.0
C B:ALA96 4.5 12.9 1.0
O B:HOH301 4.5 39.3 1.0
N B:ALA96 4.9 13.4 1.0
O B:HOH345 5.0 22.9 1.0

Chlorine binding site 8 out of 12 in 5v6i

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Chlorine binding site 8 out of 12 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl212

b:30.8
occ:1.00
PT B:PT201 2.6 20.4 0.3
CL B:CL209 3.5 35.4 1.0
CL B:CL210 3.6 33.5 1.0
O B:HOH349 4.1 37.1 1.0
NH2 B:ARG100 4.5 27.2 1.0

Chlorine binding site 9 out of 12 in 5v6i

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Chlorine binding site 9 out of 12 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl213

b:53.8
occ:1.00
PT B:PT202 2.6 43.8 0.2
N B:CYS24 2.9 17.9 1.0
O B:HOH308 3.4 34.6 1.0
CA B:SER23 3.4 17.3 1.0
C B:SER23 3.6 18.0 1.0
CB B:SER23 3.8 23.9 1.0
CA B:CYS24 4.0 16.4 1.0
O B:CYS24 4.0 22.1 1.0
CB B:CYS24 4.0 20.5 1.0
PT B:PT202 4.0 51.4 0.2
OG B:SER23 4.2 29.8 1.0
O B:LEU22 4.2 26.5 1.0
SG B:CYS24 4.4 23.6 1.0
OD2 B:ASP26 4.4 66.3 1.0
C B:CYS24 4.5 22.9 1.0
N B:SER23 4.6 16.4 1.0
O B:SER23 4.9 13.0 1.0
C B:LEU22 4.9 25.8 1.0

Chlorine binding site 10 out of 12 in 5v6i

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Chlorine binding site 10 out of 12 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 Chlorine with other atoms in the Cl binding site number 10 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:Cl214

b:63.6
occ:1.00
PT B:PT204 2.8 37.5 0.3
CL B:CL215 3.8 44.3 1.0
CL B:CL205 3.9 62.2 1.0
CE2 B:PHE74 4.1 19.2 1.0
CD1 B:LEU116 4.2 23.9 1.0
CD2 B:PHE74 4.4 12.4 1.0
CG2 B:THR76 4.6 12.3 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 Oct 28 13:05:51 2020

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