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Arsenic 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:

Platinum (Pt) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic 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 Arsenic atom.
In total 4 binding sites of Arsenic 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 Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 5nj7

Go back to Arsenic Binding Sites List in 5nj7
Arsenic 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 Arsenic with other atoms in the As 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:As201

b:54.4
occ:0.60
AS1 A:A6R201 0.0 54.4 0.6
O3 A:A6R201 1.7 57.1 0.6
O4 A:A6R201 1.7 58.4 0.6
O2 A:A6R201 2.0 46.6 0.6
O1 A:A6R201 2.0 54.2 0.6
PT1 A:A6R201 2.3 40.9 0.6
C3 A:A6R201 2.9 41.6 0.6
C1 A:A6R201 2.9 51.4 0.6
N1 A:A6R201 3.0 47.8 0.6
N2 A:A6R201 3.1 35.8 0.6
C4 A:A6R201 4.3 40.5 0.6
C2 A:A6R201 4.3 47.7 0.6
NE2 A:HIS105 4.4 37.5 1.0

Arsenic binding site 2 out of 4 in 5nj7

Go back to Arsenic Binding Sites List in 5nj7
Arsenic 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 Arsenic with other atoms in the As 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:As202

b:58.1
occ:0.75
AS1 A:A6R202 0.0 58.1 0.8
O3 A:A6R202 1.7 56.3 0.8
O4 A:A6R202 1.7 55.7 0.8
O2 A:A6R202 2.0 51.5 0.8
O1 A:A6R202 2.0 45.8 0.8
PT1 A:A6R202 2.2 43.3 0.8
C1 A:A6R202 2.8 44.4 0.8
N1 A:A6R202 2.9 38.1 0.8
C3 A:A6R202 2.9 51.0 0.8
N2 A:A6R202 3.0 44.4 0.8
O A:HOH311 3.9 30.2 1.0
O A:HOH313 3.9 31.1 1.0
NZ A:LYS7 4.0 49.7 1.0
C2 A:A6R202 4.2 41.7 0.8
C4 A:A6R202 4.3 54.1 0.8
CE A:LYS7 4.3 43.2 1.0
ND1 A:HIS119 4.3 35.9 1.0
O A:HOH322 4.3 3.7 0.2
O A:VAL118 4.5 28.5 1.0
NE2 A:GLN11 4.7 35.0 1.0
CD A:LYS7 4.8 39.9 1.0

Arsenic binding site 3 out of 4 in 5nj7

Go back to Arsenic Binding Sites List in 5nj7
Arsenic 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 Arsenic with other atoms in the As 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:As201

b:54.7
occ:0.60
AS1 B:A6R201 0.0 54.7 0.6
O3 B:A6R201 1.7 53.8 0.6
O4 B:A6R201 1.7 49.3 0.6
O2 B:A6R201 2.0 48.9 0.6
O1 B:A6R201 2.0 41.3 0.6
PT1 B:A6R201 2.3 41.1 0.6
C1 B:A6R201 2.9 39.8 0.6
C3 B:A6R201 2.9 49.4 0.6
N1 B:A6R201 3.0 34.1 0.6
N2 B:A6R201 3.1 43.7 0.6
O B:HOH351 3.9 26.6 1.0
O B:HOH330 3.9 31.7 1.0
O B:HOH326 4.0 3.2 0.4
CE B:LYS7 4.3 35.1 1.0
C2 B:A6R201 4.3 41.5 0.6
C4 B:A6R201 4.3 49.4 0.6
ND1 B:HIS119 4.4 35.0 1.0
NE2 B:GLN11 4.5 32.4 1.0
NZ B:LYS7 4.6 37.7 1.0
CD B:LYS7 4.6 30.8 1.0
O B:VAL118 4.8 22.6 1.0

Arsenic binding site 4 out of 4 in 5nj7

Go back to Arsenic Binding Sites List in 5nj7
Arsenic 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 Arsenic with other atoms in the As 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:As202

b:66.6
occ:0.70
AS1 B:A6R202 0.0 66.6 0.7
O3 B:A6R202 1.7 59.0 0.7
O4 B:A6R202 1.7 66.6 0.7
O2 B:A6R202 2.0 60.6 0.7
O1 B:A6R202 2.0 51.8 0.7
PT1 B:A6R202 2.3 49.2 0.7
C1 B:A6R202 2.9 53.0 0.7
C3 B:A6R202 2.9 52.8 0.7
N1 B:A6R202 3.1 41.6 0.7
N2 B:A6R202 3.1 38.6 0.7
O B:HOH323 3.4 37.2 1.0
C4 B:A6R202 4.3 49.8 0.7
C2 B:A6R202 4.3 45.5 0.7
NE2 B:HIS105 4.4 33.9 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: Tue Oct 27 16:55:51 2020

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