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Platinum in PDB 7woj: Crystal Structure of Hsa-Myr Complex Soaked with Cisplatin For One Week

Protein crystallography data

The structure of Crystal Structure of Hsa-Myr Complex Soaked with Cisplatin For One Week, PDB code: 7woj 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) 43.41 / 2.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.91, 36.69, 90.01, 90, 105.41, 90
R / Rfree (%) 25.8 / 28.4

Other elements in 7woj:

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

Chlorine (Cl) 3 atoms

Platinum Binding Sites:

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

Platinum binding site 1 out of 9 in 7woj

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Platinum binding site 1 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt601

b:155.9
occ:0.92
PT1 A:CPT601 0.0 155.9 0.9
NE2 A:HIS338 1.8 102.3 1.0
N2 A:CPT601 2.0 99.6 0.9
N1 A:CPT601 2.1 161.6 0.9
CL1 A:CPT601 2.3 126.9 0.9
CE1 A:HIS338 2.6 94.0 1.0
CD2 A:HIS338 3.0 102.6 1.0
ND1 A:HIS338 3.8 100.3 1.0
CG A:HIS338 4.0 96.3 1.0
OH A:TYR341 4.4 90.7 1.0
CE1 A:TYR334 4.7 78.7 1.0
OH A:TYR334 4.9 86.7 1.0

Platinum binding site 2 out of 9 in 7woj

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Platinum binding site 2 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt602

b:131.0
occ:0.75
PT1 A:CPT602 0.0 131.0 0.8
N1 A:CPT602 2.0 86.5 0.8
N2 A:CPT602 2.1 100.5 0.8
SD A:MET329 2.1 82.6 1.0
CL1 A:CPT602 2.3 85.2 0.8
CG A:MET329 3.0 104.4 1.0
CB A:MET329 3.5 100.6 1.0
CE A:MET329 3.7 107.1 1.0
OE2 A:GLU333 4.5 137.1 1.0
CA A:MET329 4.7 81.4 1.0
CD2 A:PHE228 4.9 125.8 1.0
CB A:PHE228 5.0 95.4 1.0

Platinum binding site 3 out of 9 in 7woj

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Platinum binding site 3 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt603

b:101.3
occ:0.65
PT1 A:CPT603 0.0 101.3 0.7
N1 A:CPT603 2.0 58.9 0.7
N2 A:CPT603 2.1 57.8 0.7
SD A:MET548 2.2 83.3 1.0
CG A:MET548 2.8 98.8 1.0
CB A:MET548 3.1 114.1 1.0
CE A:MET548 3.6 105.6 1.0
C5 A:MYR613 4.0 92.0 1.0
C6 A:MYR613 4.4 89.1 1.0
CA A:MET548 4.5 105.5 1.0
C4 A:MYR613 4.5 93.7 1.0
CB A:ASN405 4.8 61.6 1.0
ND2 A:ASN405 4.8 85.9 1.0
CG A:ASN405 4.9 67.3 1.0
C2 A:MYR613 4.9 111.0 1.0
C A:MET548 5.0 109.3 1.0

Platinum binding site 4 out of 9 in 7woj

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Platinum binding site 4 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt604

b:113.7
occ:0.60
PT1 A:CPT604 0.0 113.7 0.6
N1 A:CPT604 2.0 97.8 0.6
N2 A:CPT604 2.0 90.1 0.6
ND1 A:HIS128 2.1 114.3 1.0
CL1 A:CPT604 2.4 101.8 0.6
CG A:HIS128 3.1 110.5 1.0
CE1 A:HIS128 3.2 103.6 1.0
CB A:HIS128 3.3 99.1 1.0
CA A:HIS128 3.4 84.3 1.0
O A:HIS128 4.2 80.8 1.0
CD2 A:HIS128 4.2 130.5 1.0
NE2 A:HIS128 4.3 108.4 1.0
C A:HIS128 4.3 77.0 1.0
N A:HIS128 4.4 78.2 1.0
O A:PHE127 4.4 87.4 1.0
C A:PHE127 4.8 77.2 1.0

Platinum binding site 5 out of 9 in 7woj

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Platinum binding site 5 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt605

b:121.7
occ:0.55
PT1 A:CPT605 0.0 121.7 0.6
NE2 A:HIS440 1.9 88.5 1.0
N2 A:CPT605 2.0 72.2 0.6
N1 A:CPT605 2.1 77.0 0.6
NZ A:LYS436 2.3 141.3 1.0
CE1 A:HIS440 2.8 94.5 1.0
CD2 A:HIS440 3.0 77.1 1.0
CE A:LYS436 3.3 110.2 1.0
ND1 A:HIS440 3.9 90.3 1.0
CD A:LYS436 4.1 97.7 1.0
CG A:HIS440 4.1 72.6 1.0
SG A:CYS448 4.4 78.4 1.0
CG A:LYS436 4.6 78.9 1.0
CE2 A:TYR452 4.9 101.7 1.0
OH A:TYR452 5.0 123.6 1.0

Platinum binding site 6 out of 9 in 7woj

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Platinum binding site 6 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt606

b:110.8
occ:0.44
PT1 A:CPT606 0.0 110.8 0.4
NE2 A:HIS146 1.9 94.1 1.0
N2 A:CPT606 2.0 56.2 0.4
N1 A:CPT606 2.1 65.6 0.4
CE1 A:HIS146 2.5 94.8 1.0
CD2 A:HIS146 3.2 70.9 1.0
ND1 A:HIS146 3.7 83.5 1.0
CG A:HIS146 4.1 75.7 1.0
NH1 A:ARG114 4.9 142.1 1.0
CB A:ARG145 5.0 71.1 1.0

Platinum binding site 7 out of 9 in 7woj

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Platinum binding site 7 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt607

b:97.3
occ:0.35
PT1 A:CPT607 0.0 97.3 0.3
N1 A:CPT607 1.8 56.0 0.3
N2 A:CPT607 2.0 58.2 0.3
ND1 A:HIS247 2.3 126.1 1.0
CE1 A:HIS247 3.0 119.8 1.0
CG A:HIS247 3.5 122.5 1.0
CA A:HIS247 3.5 118.0 1.0
CB A:HIS247 4.1 116.4 1.0
O A:HIS247 4.2 123.5 1.0
NE2 A:HIS247 4.3 127.5 1.0
N A:HIS247 4.4 93.7 1.0
C A:HIS247 4.4 128.8 1.0
CD2 A:HIS247 4.5 123.8 1.0
O A:CYS246 4.7 83.9 1.0
C A:CYS246 4.8 92.4 1.0

Platinum binding site 8 out of 9 in 7woj

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Platinum binding site 8 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt608

b:88.1
occ:0.32
PT1 A:CPT608 0.0 88.1 0.3
N1 A:CPT608 2.1 51.6 0.3
N2 A:CPT608 2.1 52.4 0.3
SD A:MET298 2.1 91.4 1.0
CG A:MET298 2.8 117.2 1.0
CE A:MET298 3.2 95.3 1.0
CB A:MET298 4.2 135.0 1.0
O A:ARG337 4.7 86.7 1.0

Platinum binding site 9 out of 9 in 7woj

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Platinum binding site 9 out of 9 in the Crystal Structure of Hsa-Myr Complex 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-Myr Complex Soaked with Cisplatin For One Week within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt609

b:86.7
occ:0.29
PT1 A:CPT609 0.0 86.7 0.3
ND1 A:HIS105 1.8 99.0 1.0
N1 A:CPT609 2.0 48.4 0.3
N2 A:CPT609 2.1 48.9 0.3
CE1 A:HIS105 2.7 101.8 1.0
CG A:HIS105 2.9 101.9 1.0
CB A:HIS105 3.3 112.8 1.0
CA A:HIS105 3.5 99.8 1.0
NE2 A:HIS105 3.8 108.4 1.0
CB A:GLU86 3.8 107.1 1.0
CD2 A:HIS105 3.9 94.9 1.0
O A:GLN104 4.2 113.0 1.0
N A:HIS105 4.4 89.2 1.0
N A:MET87 4.5 139.7 1.0
C A:GLU86 4.5 135.6 1.0
C A:HIS105 4.6 87.9 1.0
C A:GLN104 4.6 110.5 1.0
O A:HIS105 4.6 125.8 1.0
CA A:GLU86 4.8 129.7 1.0
CA A:MET87 4.9 131.3 1.0
O A:GLU86 4.9 139.3 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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