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Platinum in PDB 5nj7: The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1:
3.1.27.5;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1, PDB code: 5nj7 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.94 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.535, 32.855, 72.939, 90.00, 90.17, 90.00
R / Rfree (%) 18.7 / 25

Other elements in 5nj7:

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1 also contains other interesting chemical elements:

Arsenic (As) 4 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1 (pdb code 5nj7). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1, PDB code: 5nj7:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 5nj7

Go back to Platinum Binding Sites List in 5nj7
Platinum binding site 1 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:40.9
occ:0.60
 PT1 A:A6R201 0.0 40.9 0.6
N1 A:A6R201 2.0 47.8 0.6
N2 A:A6R201 2.0 35.8 0.6
NE2 A:HIS105 2.1 37.5 1.0
AS1 A:A6R201 2.3 54.4 0.6
C3 A:A6R201 2.8 41.6 0.6
C1 A:A6R201 2.8 51.4 0.6
O2 A:A6R201 3.0 46.6 0.6
CD2 A:HIS105 3.0 31.1 1.0
O1 A:A6R201 3.0 54.2 0.6
CE1 A:HIS105 3.1 31.6 1.0
O3 A:A6R201 3.5 57.1 0.6
O4 A:A6R201 3.6 58.4 0.6
CG A:HIS105 4.2 30.9 1.0
ND1 A:HIS105 4.2 32.6 1.0
C2 A:A6R201 4.2 47.7 0.6
C4 A:A6R201 4.3 40.5 0.6
CG2 A:THR78 4.6 33.2 1.0

Platinum binding site 2 out of 4 in 5nj7

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Platinum binding site 2 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:43.3
occ:0.75
 PT1 A:A6R202 0.0 43.3 0.8
N2 A:A6R202 2.0 44.4 0.8
N1 A:A6R202 2.0 38.1 0.8
ND1 A:HIS119 2.1 35.9 1.0
AS1 A:A6R202 2.2 58.1 0.8
C3 A:A6R202 2.8 51.0 0.8
C1 A:A6R202 2.9 44.4 0.8
O2 A:A6R202 2.9 51.5 0.8
CG A:HIS119 3.0 30.2 1.0
CE1 A:HIS119 3.1 37.4 1.0
O1 A:A6R202 3.1 45.8 0.8
CB A:HIS119 3.3 26.6 1.0
O4 A:A6R202 3.4 55.7 0.8
O A:HOH322 3.5 3.7 0.2
O3 A:A6R202 3.5 56.3 0.8
CA A:HIS119 3.8 24.8 1.0
O A:VAL118 4.1 28.5 1.0
O A:HOH311 4.2 30.2 1.0
CD2 A:HIS119 4.2 34.6 1.0
NE2 A:HIS119 4.2 37.4 1.0
C4 A:A6R202 4.3 54.1 0.8
C2 A:A6R202 4.3 41.7 0.8
C A:HIS119 4.8 22.6 1.0
N A:HIS119 4.8 24.0 1.0
O A:HOH313 4.9 31.1 1.0
N A:PHE120 4.9 22.4 1.0
C A:VAL118 4.9 24.4 1.0

Platinum binding site 3 out of 4 in 5nj7

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Platinum binding site 3 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:41.1
occ:0.60
 PT1 B:A6R201 0.0 41.1 0.6
N1 B:A6R201 2.0 34.1 0.6
N2 B:A6R201 2.0 43.7 0.6
ND1 B:HIS119 2.1 35.0 1.0
AS1 B:A6R201 2.3 54.7 0.6
C3 B:A6R201 2.8 49.4 0.6
C1 B:A6R201 2.9 39.8 0.6
O2 B:A6R201 2.9 48.9 0.6
O1 B:A6R201 3.0 41.3 0.6
CE1 B:HIS119 3.1 35.6 1.0
CG B:HIS119 3.1 31.2 1.0
O B:HOH326 3.2 3.2 0.4
CB B:HIS119 3.4 30.4 1.0
O3 B:A6R201 3.5 53.8 0.6
O4 B:A6R201 3.6 49.3 0.6
CA B:HIS119 3.8 25.8 1.0
O B:HOH351 4.1 26.6 1.0
O B:VAL118 4.2 22.6 1.0
NE2 B:HIS119 4.2 38.3 1.0
CD2 B:HIS119 4.2 38.4 1.0
C4 B:A6R201 4.3 49.4 0.6
C2 B:A6R201 4.3 41.5 0.6
O B:HOH365 4.3 30.0 1.0
O B:HOH338 4.4 36.5 1.0
N B:PHE120 4.6 25.0 1.0
O B:HOH330 4.6 31.7 1.0
C B:HIS119 4.7 25.4 1.0
N B:HIS119 4.9 24.4 1.0
C B:VAL118 5.0 22.6 1.0

Platinum binding site 4 out of 4 in 5nj7

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Platinum binding site 4 out of 4 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Arsenoplatin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:49.2
occ:0.70
 PT1 B:A6R202 0.0 49.2 0.7
N1 B:A6R202 2.0 41.6 0.7
N2 B:A6R202 2.0 38.6 0.7
NE2 B:HIS105 2.1 33.9 1.0
AS1 B:A6R202 2.3 66.6 0.7
C1 B:A6R202 2.8 53.0 0.7
C3 B:A6R202 2.8 52.8 0.7
O2 B:A6R202 3.0 60.6 0.7
O1 B:A6R202 3.0 51.8 0.7
CD2 B:HIS105 3.1 27.2 1.0
CE1 B:HIS105 3.1 28.2 1.0
O B:HOH323 3.1 37.2 1.0
O3 B:A6R202 3.5 59.0 0.7
O4 B:A6R202 3.6 66.6 0.7
ND1 B:HIS105 4.2 31.4 1.0
CG B:HIS105 4.2 27.3 1.0
O B:HOH345 4.2 41.0 1.0
C2 B:A6R202 4.3 45.5 0.7
C4 B:A6R202 4.3 49.8 0.7
CG2 B:THR78 4.4 22.0 1.0

Reference:

D.Miodragovic, A.Merlino, E.P.Swindell, A.Bogachkov, R.W.Ahn, S.Abuhadba, G.Ferraro, T.Marzo, A.P.Mazar, L.Messori, T.V.O'halloran. Arsenoplatin-1 Is A Dual Pharmacophore Anticancer Agent. J.Am.Chem.Soc. V. 141 6453 2019.
ISSN: ESSN 1520-5126
PubMed: 30943017
DOI: 10.1021/JACS.8B13681
Page generated: Thu Oct 10 11:39:54 2024

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