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Platinum in PDB 7wok: Crystal Structure of Hsa Soaked with Cisplatin For One Week

Protein crystallography data

The structure of Crystal Structure of Hsa Soaked with Cisplatin For One Week, PDB code: 7wok was solved by S.L.Chen, C.Yuan, L.G.Jiang, Z.P.Luo, M.D.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.55 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.376, 180.518, 58.503, 90, 103.87, 90
R / Rfree (%) 20.7 / 24.4

Other elements in 7wok:

The structure of Crystal Structure of Hsa Soaked with Cisplatin For One Week also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Hsa Soaked with Cisplatin For One Week (pdb code 7wok). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 10 binding sites of Platinum where determined in the Crystal Structure of Hsa Soaked with Cisplatin For One Week, PDB code: 7wok:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 10 in 7wok

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Platinum binding site 1 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


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 Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt601

b:146.9
occ:0.61
PT1 A:CPT601 0.0 146.9 0.6
N2 A:CPT601 2.0 159.9 0.6
N1 A:CPT601 2.0 184.8 0.6
SD A:MET298 2.3 135.9 1.0
CG A:MET298 3.5 170.2 1.0
CE A:MET298 3.6 104.5 1.0
CB A:MET298 3.8 129.7 1.0
CD2 A:LEU302 4.2 147.1 1.0
O A:PRO299 4.7 189.8 1.0
O A:MET298 4.9 147.2 1.0

Platinum binding site 2 out of 10 in 7wok

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Platinum binding site 2 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


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 Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt602

b:139.1
occ:0.56
PT1 A:CPT602 0.0 139.1 0.6
N1 A:CPT602 2.0 88.6 0.6
SD A:MET329 2.1 108.4 1.0
N2 A:CPT602 2.1 111.1 0.6
CL1 A:CPT602 2.3 108.6 0.6
CG A:MET329 3.0 146.7 1.0
CB A:MET329 3.1 154.7 1.0
CE A:MET329 3.6 177.0 1.0
CA A:MET329 4.5 110.4 1.0
OE2 A:GLU333 4.7 185.8 1.0
CZ A:PHE309 4.8 131.8 1.0

Platinum binding site 3 out of 10 in 7wok

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Platinum binding site 3 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


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 Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt603

b:143.5
occ:0.59
PT1 A:CPT603 0.0 143.5 0.6
N1 A:CPT603 2.1 157.2 0.6
N2 A:CPT603 2.1 94.5 0.6
ND1 A:HIS105 2.2 160.2 1.0
CE1 A:HIS105 2.9 119.0 1.0
CG A:HIS105 3.4 161.7 1.0
CA A:HIS105 3.8 124.0 1.0
CB A:HIS105 4.0 114.8 1.0
O A:HIS105 4.0 108.4 1.0
NE2 A:HIS105 4.2 144.3 1.0
CD2 A:HIS105 4.4 132.6 1.0
C A:HIS105 4.4 139.8 1.0
O A:GLN104 4.7 133.5 1.0
N A:HIS105 5.0 98.4 1.0

Platinum binding site 4 out of 10 in 7wok

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Platinum binding site 4 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


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 Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt604

b:130.7
occ:0.36
PT1 A:CPT604 0.0 130.7 0.4
N1 A:CPT604 2.0 97.9 0.4
N2 A:CPT604 2.1 90.2 0.4
NE2 A:HIS288 2.1 128.6 1.0
CE1 A:HIS288 3.0 129.6 1.0
CD2 A:HIS288 3.1 99.5 1.0
OE1 A:GLU292 3.2 133.5 1.0
ND1 A:HIS288 4.1 97.9 1.0
CD A:GLU292 4.1 224.9 1.0
CG A:HIS288 4.2 118.3 1.0
OE2 A:GLU292 4.7 224.6 1.0
OE1 A:GLU188 4.8 108.1 1.0
CB A:GLU292 4.9 130.8 1.0

Platinum binding site 5 out of 10 in 7wok

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Platinum binding site 5 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


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 Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt605

b:140.8
occ:0.40
PT1 A:CPT605 0.0 140.8 0.4
NE2 A:HIS247 2.0 173.4 1.0
N2 A:CPT605 2.0 146.7 0.4
N1 A:CPT605 2.0 87.9 0.4
CE1 A:HIS247 2.7 150.8 1.0
CD2 A:HIS247 3.1 128.7 1.0
ND1 A:HIS247 3.9 132.0 1.0
CG A:HIS247 4.1 136.4 1.0
OE1 A:GLU100 4.3 135.0 1.0
OE2 A:GLU100 4.4 214.2 1.0
CD A:GLU100 4.7 95.0 1.0
CA A:GLN204 4.7 77.5 1.0
CG A:GLN204 4.8 113.3 1.0

Platinum binding site 6 out of 10 in 7wok

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Platinum binding site 6 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt601

b:151.1
occ:0.62
PT1 B:CPT601 0.0 151.1 0.6
N2 B:CPT601 2.0 91.0 0.6
N1 B:CPT601 2.1 176.5 0.6
SD B:MET298 2.2 150.2 1.0
CG B:MET298 3.2 197.2 1.0
CB B:MET298 3.5 196.7 1.0
CE B:MET298 3.7 170.6 1.0
O B:PRO299 3.7 100.1 1.0
O B:MET298 4.3 145.3 1.0
C B:MET298 4.4 126.0 1.0
CA B:MET298 4.6 183.8 1.0
C B:PRO299 4.8 146.1 1.0
CD1 B:LEU302 4.9 142.1 1.0
N B:PRO299 5.0 156.6 1.0

Platinum binding site 7 out of 10 in 7wok

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Platinum binding site 7 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Crystal Structure of Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt602

b:139.5
occ:0.67
PT1 B:CPT602 0.0 139.5 0.7
N1 B:CPT602 2.0 120.5 0.7
N2 B:CPT602 2.1 92.4 0.7
SD B:MET329 2.3 107.4 1.0
CL1 B:CPT602 2.3 132.0 0.7
CG B:MET329 3.0 146.4 1.0
CB B:MET329 3.3 113.1 1.0
CE B:MET329 3.9 136.3 1.0
OE2 B:GLU333 4.4 126.8 1.0
CA B:MET329 4.5 100.4 1.0

Platinum binding site 8 out of 10 in 7wok

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Platinum binding site 8 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of Crystal Structure of Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt603

b:142.2
occ:0.48
PT1 B:CPT603 0.0 142.2 0.5
ND1 B:HIS105 1.9 213.2 1.0
N1 B:CPT603 2.0 108.1 0.5
N2 B:CPT603 2.1 161.2 0.5
CE1 B:HIS105 2.8 154.7 1.0
CG B:HIS105 2.9 244.9 1.0
CB B:HIS105 3.3 186.2 1.0
CA B:HIS105 3.4 133.9 1.0
NE2 B:HIS105 4.0 168.8 1.0
CD2 B:HIS105 4.0 207.3 1.0
O B:HIS105 4.2 93.3 1.0
C B:HIS105 4.3 85.8 1.0
N B:HIS105 4.4 141.6 1.0
O B:GLN104 4.9 112.9 1.0

Platinum binding site 9 out of 10 in 7wok

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Platinum binding site 9 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of Crystal Structure of Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt604

b:128.2
occ:0.34
PT1 B:CPT604 0.0 128.2 0.3
NE2 B:HIS288 2.0 119.1 1.0
N2 B:CPT604 2.0 119.2 0.3
N1 B:CPT604 2.1 104.3 0.3
CD2 B:HIS288 2.9 101.6 1.0
CE1 B:HIS288 3.0 111.4 1.0
CG B:GLU292 3.5 137.5 1.0
CD B:GLU292 4.0 172.2 1.0
CG B:HIS288 4.1 89.0 1.0
ND1 B:HIS288 4.1 91.1 1.0
OE1 B:GLU292 4.2 191.8 1.0
CB B:GLU292 4.2 133.4 1.0
OE2 B:GLU292 4.7 147.1 1.0
OE1 B:GLU188 4.8 108.1 1.0

Platinum binding site 10 out of 10 in 7wok

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Platinum binding site 10 out of 10 in the Crystal Structure of Hsa Soaked with Cisplatin For One Week


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of Crystal Structure of Hsa Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt605

b:121.6
occ:0.25
NE2 B:HIS67 1.9 147.3 1.0
OD2 B:ASP249 1.9 102.3 1.0
ND1 B:HIS247 2.0 120.2 1.0
O B:HOH701 2.1 50.2 1.0
OD1 B:ASP249 2.1 160.4 1.0
CG B:ASP249 2.2 165.3 1.0
CE1 B:HIS247 2.4 95.2 1.0
CE1 B:HIS67 2.6 133.2 1.0
CD2 B:HIS67 3.1 176.1 1.0
CG B:HIS247 3.1 162.2 1.0
NE2 B:HIS247 3.5 130.7 1.0
CB B:ASP249 3.6 106.8 1.0
ND1 B:HIS67 3.8 115.8 1.0
CD2 B:HIS247 3.9 115.1 1.0
CB B:HIS247 3.9 185.4 1.0
CG B:HIS67 4.1 174.0 1.0
N B:ASP249 4.2 90.0 1.0
CA B:ASP249 4.4 97.9 1.0
O B:HIS247 4.5 164.6 1.0
C B:HIS247 4.6 128.9 1.0
ND2 B:ASN99 4.8 173.5 1.0
CA B:HIS247 4.9 102.3 1.0
C B:GLY248 5.0 103.1 1.0

Reference:

S.L.Chen, C.Yuan, L.G.Jiang, Z.P.Luo, M.D.Huang. Crystallographic Analysis of Interaction Between Cisplatin and Human Serum Albumin: Effect of Fatty Acid. Int.J.Biol.Macromol. V. 216 172 2022.
ISSN: ISSN 0141-8130
PubMed: 35788007
DOI: 10.1016/J.IJBIOMAC.2022.06.181
Page generated: Fri Apr 7 19:48:34 2023

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