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Platinum in PDB 5l4r: X-Ray Structure of the Adduct Between Thaumatin and Cisplatin

Protein crystallography data

The structure of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin, PDB code: 5l4r was solved by I.Russo Krauss, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.97 / 1.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.837, 57.837, 150.159, 90.00, 90.00, 90.00
R / Rfree (%) 11.2 / 15.4

Other elements in 5l4r:

The structure of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Platinum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Platinum atom in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin (pdb code 5l4r). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 15 binding sites of Platinum where determined in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin, PDB code: 5l4r:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 15 in 5l4r

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Platinum binding site 1 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt503

b:15.2
occ:0.88
PT1 A:73M503 0.0 15.2 0.9
N1 A:73M503 1.8 19.5 0.9
N A:ALA1 2.1 15.0 1.0
O2 A:73M503 2.1 19.2 0.9
CL1 A:73M503 2.3 21.4 0.9
CA A:ALA1 3.0 15.2 1.0
C A:ALA1 3.4 13.7 1.0
O A:HOH861 3.7 46.3 1.0
O A:VAL41 3.7 15.0 1.0
O A:ALA1 3.8 17.0 1.0
CG A:PRO43 3.8 17.4 1.0
O A:HOH757 3.9 15.2 1.0
O A:HOH700 4.0 19.2 1.0
CD A:PRO43 4.1 15.7 1.0
O A:HOH614 4.1 31.0 1.0
N A:THR2 4.3 13.2 1.0
O A:HOH924 4.3 59.6 1.0
CB A:ALA1 4.4 15.8 1.0
CL1 A:CPT510 4.5 21.6 0.2
O A:HOH685 4.5 22.6 1.0
N A:PRO43 4.6 15.6 1.0
O A:HOH654 4.8 29.8 0.8
C A:VAL41 4.9 13.3 1.0
CB A:PRO43 5.0 15.5 1.0

Platinum binding site 2 out of 15 in 5l4r

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Platinum binding site 2 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt504

b:16.5
occ:0.25
PT1 A:CPT504 0.0 16.5 0.2
CL1 A:CPT504 1.8 39.0 0.2
NZ A:LYS106 2.0 25.5 1.0
N2 A:CPT504 2.0 14.8 0.2
N1 A:CPT504 2.1 6.9 0.2
CL1 A:CPT504 2.2 20.0 0.2
O A:HOH704 2.5 8.8 0.3
O A:HOH836 2.8 17.8 0.3
PT1 A:CPT504 2.9 49.2 0.2
O A:HOH688 3.1 33.3 0.8
CE A:LYS106 3.5 27.9 1.0
CD A:LYS106 3.7 22.7 1.0
O A:HOH869 4.1 35.2 1.0
OG1 A:THR150 4.2 14.2 1.0
CG A:PRO83 4.2 17.9 1.0
PT1 A:CPT504 4.2 71.8 0.2
O A:HOH867 4.4 46.9 0.6
O A:HOH792 4.5 22.2 1.0
N1 A:CPT504 4.5 41.8 0.2
N2 A:CPT504 4.7 33.1 0.2
CD A:PRO83 4.7 15.2 1.0
O A:HOH601 4.8 76.5 0.8
O A:HOH1004 4.8 21.4 0.2

Platinum binding site 3 out of 15 in 5l4r

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Platinum binding site 3 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt504

b:49.2
occ:0.20
PT1 A:CPT504 0.0 49.2 0.2
CL1 A:CPT504 1.5 20.0 0.2
O A:HOH601 1.9 76.5 0.8
N2 A:CPT504 2.1 33.1 0.2
N1 A:CPT504 2.1 41.8 0.2
CL1 A:CPT504 2.3 39.0 0.2
NZ A:LYS106 2.6 25.5 1.0
O A:HOH867 2.7 46.9 0.6
O A:HOH603 2.8 36.2 0.8
PT1 A:CPT504 2.9 16.5 0.2
CE A:LYS106 3.1 27.9 1.0
CD A:LYS106 3.6 22.7 1.0
PT1 A:CPT504 4.0 71.8 0.2
O A:HOH851 4.1 36.9 1.0
N1 A:CPT504 4.3 6.9 0.2
CG A:LYS106 4.7 15.0 1.0
CG A:PRO83 4.7 17.9 1.0
O A:HOH946 4.8 27.1 0.5
N2 A:CPT504 4.8 14.8 0.2
CD A:PRO83 4.9 15.2 1.0
O A:HOH907 4.9 55.2 1.0
O A:HOH704 5.0 8.8 0.3

Platinum binding site 4 out of 15 in 5l4r

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Platinum binding site 4 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt504

b:71.8
occ:0.20
PT1 A:CPT504 0.0 71.8 0.2
O A:HOH867 2.3 46.9 0.6
N1 A:CPT504 2.6 57.2 0.2
NZ A:LYS106 2.8 25.5 1.0
CE A:LYS106 2.9 27.9 1.0
O A:HOH876 3.3 34.4 1.0
O A:HOH991 3.7 43.8 1.0
O A:HOH971 3.8 35.1 1.0
N2 A:CPT504 3.8 33.1 0.2
O A:HOH668 3.8 27.8 1.0
PT1 A:CPT504 4.0 49.2 0.2
PT1 A:CPT504 4.2 16.5 0.2
O A:HOH601 4.4 76.5 0.8
CD A:LYS106 4.4 22.7 1.0
O A:HOH792 4.5 22.2 1.0
N2 A:CPT504 4.6 14.8 0.2
O A:HOH850 4.7 30.0 0.5
O A:HOH704 4.8 8.8 0.3
O A:HOH869 4.8 35.2 1.0
CL1 A:CPT504 4.9 20.0 0.2
O A:HOH946 4.9 27.1 0.5
O A:HOH900 4.9 34.1 1.0

Platinum binding site 5 out of 15 in 5l4r

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Platinum binding site 5 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt505

b:20.9
occ:0.25
PT1 A:73M505 0.0 20.9 0.2
N1 A:73M505 2.0 23.4 0.2
N2 A:73M505 2.0 22.0 0.2
OE2 A:GLU168 2.1 22.5 1.0
O2 A:73M505 2.1 11.7 0.2
O A:HOH602 2.5 49.4 0.7
CD A:GLU168 2.9 31.3 1.0
OE1 A:GLU168 3.0 31.6 1.0
O A:HOH615 3.5 55.3 1.0
O A:HOH683 4.0 44.1 1.0
CG A:GLU168 4.4 18.5 1.0

Platinum binding site 6 out of 15 in 5l4r

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Platinum binding site 6 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt506

b:29.3
occ:0.20
PT1 A:CPT506 0.0 29.3 0.2
CL2 A:CPT506 0.7 12.5 0.2
PT1 A:CPT506 1.6 44.4 0.2
N1 A:CPT506 2.1 26.1 0.2
CL1 A:CPT506 2.3 54.6 0.2
CL2 A:CPT506 2.3 38.2 0.2
NZ A:LYS49 2.6 18.4 1.0
CL1 A:CPT506 2.6 41.8 0.2
O A:HOH850 2.8 30.0 0.5
O A:HOH946 2.9 27.1 0.5
CE A:LYS49 3.0 18.4 1.0
O A:HOH900 3.1 34.1 1.0
N1 A:CPT506 3.7 21.2 0.2
OE2 A:GLU89 3.9 14.4 1.0
O A:HOH720 4.2 32.2 1.0
O A:HOH634 4.2 13.9 0.5
O A:HOH677 4.3 10.2 0.5
N1 A:CPT504 4.5 57.2 0.2
CD A:LYS49 4.5 16.8 1.0
O A:HOH963 4.8 31.5 0.4
O A:HOH904 4.8 58.3 1.0
O A:HOH876 5.0 34.4 1.0

Platinum binding site 7 out of 15 in 5l4r

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Platinum binding site 7 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt506

b:44.4
occ:0.20
PT1 A:CPT506 0.0 44.4 0.2
PT1 A:CPT506 1.6 29.3 0.2
CL2 A:CPT506 1.9 38.2 0.2
N1 A:CPT506 2.1 21.2 0.2
CL2 A:CPT506 2.3 12.5 0.2
CL1 A:CPT506 2.3 41.8 0.2
NZ A:LYS49 2.4 18.4 1.0
O A:HOH720 3.0 32.2 1.0
CL1 A:CPT506 3.2 54.6 0.2
CE A:LYS49 3.3 18.4 1.0
N1 A:CPT506 3.3 26.1 0.2
O A:HOH707 4.0 20.1 1.0
O A:HOH850 4.0 30.0 0.5
OE2 A:GLU89 4.2 14.4 1.0
O A:HOH946 4.4 27.1 0.5
O A:HOH900 4.7 34.1 1.0
CD A:LYS49 4.7 16.8 1.0
O A:HOH732 4.8 62.4 1.0
O1 A:GOL514 4.9 31.0 0.6
CD A:GLU89 5.0 12.3 1.0

Platinum binding site 8 out of 15 in 5l4r

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Platinum binding site 8 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt507

b:39.6
occ:0.30
PT1 A:CPT507 0.0 39.6 0.3
N2 A:CPT507 2.1 29.6 0.3
N1 A:CPT507 2.1 32.5 0.3
NZ A:LYS97 2.2 44.0 1.0
CL1 A:CPT507 2.3 39.5 0.3
O A:HOH874 2.4 38.7 0.7
O A:HOH972 2.5 43.9 0.7
CE A:LYS97 2.6 42.2 1.0
O A:HOH984 3.0 47.4 0.7
CD A:LYS97 3.4 30.6 1.0
PT1 A:CPT507 3.5 83.6 0.1
O A:HOH694 4.3 46.6 1.0
CG2 A:THR192 4.4 20.2 1.0
O A:HOH669 4.5 53.9 1.0
CG A:LYS97 4.5 25.8 1.0

Platinum binding site 9 out of 15 in 5l4r

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Platinum binding site 9 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt507

b:83.6
occ:0.15
PT1 A:CPT507 0.0 83.6 0.1
NZ A:LYS97 2.5 44.0 1.0
CE A:LYS97 3.3 42.2 1.0
N2 A:CPT507 3.3 29.6 0.3
O A:HOH881 3.4 69.0 1.0
PT1 A:CPT507 3.5 39.6 0.3
O A:HOH669 3.7 53.9 1.0
O4 A:TLA501 4.2 21.6 0.5
O41 A:TLA501 4.4 17.7 0.5
O A:HOH858 4.4 37.9 0.8
C4 A:TLA501 4.6 22.1 0.5
CD A:LYS97 4.8 30.6 1.0
O A:HOH874 4.8 38.7 0.7
O A:HOH807 4.8 50.1 1.0
CL1 A:CPT507 4.9 39.5 0.3

Platinum binding site 10 out of 15 in 5l4r

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Platinum binding site 10 out of 15 in the X-Ray Structure of the Adduct Between Thaumatin and Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of X-Ray Structure of the Adduct Between Thaumatin and Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt508

b:50.3
occ:0.22
PT1 A:CPT508 0.0 50.3 0.2
N1 A:CPT508 2.1 27.2 0.2
N2 A:CPT508 2.1 45.1 0.2
NZ A:LYS137 2.2 45.7 1.0
CL1 A:CPT508 2.4 60.0 0.2
CE A:LYS137 3.0 39.0 1.0
O A:HOH886 4.3 44.9 1.0
CD A:LYS137 4.5 23.7 1.0
O A:HOH977 4.6 48.2 1.0
O A:HOH911 4.9 39.9 1.0

Reference:

I.Russo Krauss, G.Ferraro, A.Merlino. Cisplatin-Protein Interactions: Unexpected Drug Binding to N-Terminal Amine and Lysine Side Chains. Inorg.Chem. V. 55 7814 2016.
ISSN: ISSN 0020-1669
PubMed: 27482735
DOI: 10.1021/ACS.INORGCHEM.6B01234
Page generated: Wed Dec 16 02:05:21 2020

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