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Platinum in PDB 6ffk: Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach

Enzymatic activity of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach

All present enzymatic activity of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach:
1.15.1.1;

Protein crystallography data

The structure of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach, PDB code: 6ffk was solved by V.Calderone, C.Nativi, F.Cantini, L.Di Cesare Mannelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.46 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.850, 35.370, 114.590, 90.00, 112.26, 90.00
R / Rfree (%) 22.6 / 25.6

Other elements in 6ffk:

The structure of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach (pdb code 6ffk). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach, PDB code: 6ffk:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 6ffk

Go back to Platinum Binding Sites List in 6ffk
Platinum binding site 1 out of 4 in the Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:69.1
occ:0.40
PT8 A:D7Z201 0.0 69.1 0.4
N1 A:D7Z201 2.0 68.3 0.4
N2 A:D7Z201 2.0 69.2 0.4
SG A:CYS111 2.3 54.3 1.0
CL1 A:D7Z201 2.4 70.4 0.4
C1 A:D7Z201 2.8 68.7 0.4
C2 A:D7Z201 2.8 69.0 0.4
CB A:CYS111 3.1 50.7 1.0
PT8 B:D7Z201 4.2 0.3 0.3
C6 A:D7Z201 4.2 68.6 0.4
C3 A:D7Z201 4.2 68.9 0.4
C1 B:D7Z201 4.4 0.1 0.3
CB A:ILE113 4.5 48.0 1.0
N2 B:D7Z201 4.5 0.2 0.3
N1 B:D7Z201 4.5 0.2 0.3
CA A:CYS111 4.5 48.9 1.0
O A:LEU106 4.6 60.3 1.0
CA A:SER107 4.7 60.6 1.0
O A:ILE113 4.7 43.8 1.0
C A:CYS111 4.9 49.4 1.0
CL1 B:D7Z201 5.0 0.2 0.3

Platinum binding site 2 out of 4 in 6ffk

Go back to Platinum Binding Sites List in 6ffk
Platinum binding site 2 out of 4 in the Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:0.3
occ:0.30
PT8 B:D7Z201 0.0 0.3 0.3
N1 B:D7Z201 2.0 0.2 0.3
N2 B:D7Z201 2.0 0.2 0.3
SG B:CYS111 2.4 54.1 1.0
CL1 B:D7Z201 2.4 0.2 0.3
C1 B:D7Z201 2.8 0.1 0.3
C2 B:D7Z201 2.8 0.1 0.3
CB B:CYS111 3.4 51.5 1.0
PT8 A:D7Z201 4.2 69.1 0.4
C6 B:D7Z201 4.2 0.0 0.3
C3 B:D7Z201 4.2 0.1 0.3
N1 A:D7Z201 4.5 68.3 0.4
C1 A:D7Z201 4.5 68.7 0.4
CB B:ILE113 4.6 45.6 1.0
N2 A:D7Z201 4.6 69.2 0.4
O B:LEU106 4.6 55.2 1.0
O B:ILE113 4.6 44.1 1.0
CA B:SER107 4.7 54.7 1.0
CA B:CYS111 4.8 51.2 1.0
CL1 A:D7Z201 4.9 70.4 0.4

Platinum binding site 3 out of 4 in 6ffk

Go back to Platinum Binding Sites List in 6ffk
Platinum binding site 3 out of 4 in the Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt201

b:65.4
occ:0.30
PT8 D:D7Z201 0.0 65.4 0.3
N1 D:D7Z201 2.0 65.2 0.3
N2 D:D7Z201 2.0 65.6 0.3
SG D:CYS111 2.3 54.4 1.0
CL1 D:D7Z201 2.4 63.7 0.3
C1 D:D7Z201 2.8 65.5 0.3
C2 D:D7Z201 2.8 65.8 0.3
CB D:CYS111 3.2 51.3 1.0
C6 D:D7Z201 4.2 65.8 0.3
C3 D:D7Z201 4.2 66.2 0.3
CB D:ILE113 4.3 49.0 1.0
N2 F:D7Z201 4.5 70.8 0.2
PT8 F:D7Z201 4.5 71.3 0.2
O D:ILE113 4.5 45.5 1.0
C1 F:D7Z201 4.6 70.8 0.2
CA D:CYS111 4.6 49.3 1.0
O D:LEU106 4.7 59.8 1.0
N1 F:D7Z201 4.8 71.0 0.2
CA D:SER107 4.8 58.7 1.0
CG2 D:ILE113 4.9 50.1 1.0
CD1 D:ILE113 5.0 58.3 1.0
C D:CYS111 5.0 49.4 1.0
N D:ILE113 5.0 44.8 1.0

Platinum binding site 4 out of 4 in 6ffk

Go back to Platinum Binding Sites List in 6ffk
Platinum binding site 4 out of 4 in the Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Human Apo-SOD1 Bound to PTCL2(1R,2R-1,4-Dach within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Pt201

b:71.3
occ:0.20
PT8 F:D7Z201 0.0 71.3 0.2
N2 F:D7Z201 2.0 70.8 0.2
N1 F:D7Z201 2.0 71.0 0.2
SG F:CYS111 2.3 57.1 1.0
CL1 F:D7Z201 2.4 70.7 0.2
C2 F:D7Z201 2.8 70.7 0.2
C1 F:D7Z201 2.8 70.8 0.2
CB F:CYS111 3.2 54.2 1.0
C6 F:D7Z201 4.2 70.7 0.2
C3 F:D7Z201 4.3 70.8 0.2
CB F:ILE113 4.5 51.4 1.0
PT8 D:D7Z201 4.5 65.4 0.3
CA F:SER107 4.5 56.1 1.0
O F:ILE113 4.6 50.4 1.0
O F:LEU106 4.6 54.2 1.0
CA F:CYS111 4.6 53.1 1.0
N2 D:D7Z201 4.7 65.6 0.3
C1 D:D7Z201 4.7 65.5 0.3
O F:GLY108 4.9 66.8 1.0
N1 D:D7Z201 4.9 65.2 0.3
N F:GLY108 4.9 62.6 1.0
C F:SER107 4.9 61.7 1.0
CG2 F:ILE113 5.0 51.7 1.0

Reference:

F.Cantini, V.Calderone, L.Di Cesare Mannelli, M.Korsak, L.Gonnelli, O.Francesconi, C.Ghelardini, L.Banci, C.Nativi. Interaction of Half Oxa-/Halfcis-Platin Complex with Human Superoxide Dismutase and Induced Reduction of Neurotoxicity. Acs Med Chem Lett V. 9 1094 2018.
ISSN: ISSN 1948-5875
PubMed: 30429951
DOI: 10.1021/ACSMEDCHEMLETT.8B00199
Page generated: Wed Dec 16 02:05:35 2020

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