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Platinum in PDB 5na9: The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio)

Enzymatic activity of The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio)

All present enzymatic activity of The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio):
3.1.27.5;

Protein crystallography data

The structure of The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio), PDB code: 5na9 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) 55.57 / 2.07
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 64.168, 64.168, 64.271, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 24.4

Other elements in 5na9:

The structure of The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio) also contains other interesting chemical elements:

Caesium (Cs) 5 atoms
Chlorine (Cl) 9 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio) (pdb code 5na9). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio), PDB code: 5na9:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 5na9

Go back to Platinum Binding Sites List in 5na9
Platinum binding site 1 out of 2 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio)


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 Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:50.8
occ:0.25
 PT1 A:QPT201 0.0 50.8 0.2
N1 A:QPT201 2.0 35.7 0.2
N2 A:QPT201 2.0 41.4 0.2
O2 A:QPT201 2.2 36.8 0.2
PT1 A:QPT201 2.4 38.3 0.3
O2 A:QPT201 2.5 26.2 0.3
SD A:MET29 2.7 24.8 1.0
CG A:MET29 3.7 21.3 1.0
N1 A:QPT201 3.8 31.9 0.3
OD2 A:ASP14 3.8 17.6 1.0
CE2 A:TYR25 3.8 15.4 1.0
CE A:MET29 3.9 25.8 1.0
O A:HOH351 3.9 33.8 1.0
O A:HOH459 4.0 36.9 1.0
O A:HOH433 4.0 28.6 1.0
CD2 A:TYR25 4.2 15.2 1.0
CG A:ASP14 4.5 18.5 1.0
OG A:SER16 4.6 23.2 1.0
OD1 A:ASP14 4.6 16.2 1.0
CZ A:TYR25 4.6 15.0 1.0
O A:HOH385 5.0 29.6 1.0

Platinum binding site 2 out of 2 in 5na9

Go back to Platinum Binding Sites List in 5na9
Platinum binding site 2 out of 2 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio)


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 Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:38.3
occ:0.35
 PT1 A:QPT201 0.0 38.3 0.3
O2 A:QPT201 1.9 36.8 0.2
N1 A:QPT201 2.0 31.9 0.3
O2 A:QPT201 2.2 26.2 0.3
PT1 A:QPT201 2.4 50.8 0.2
SD A:MET29 2.6 24.8 1.0
CG A:MET29 3.3 21.3 1.0
CB A:GLN28 3.8 20.7 1.0
N2 A:QPT201 4.0 41.4 0.2
N A:MET29 4.0 18.7 1.0
N1 A:QPT201 4.0 35.7 0.2
O A:HOH459 4.1 36.9 1.0
OG A:SER32 4.1 22.0 1.0
C A:GLN28 4.1 18.0 1.0
CA A:MET29 4.2 17.2 1.0
OE1 A:GLN28 4.2 29.8 1.0
O A:HOH433 4.3 28.6 1.0
CE A:MET29 4.3 25.8 1.0
CB A:MET29 4.3 19.5 1.0
O A:GLN28 4.4 16.6 1.0
CA A:GLN28 4.7 19.1 1.0
O A:TYR25 4.8 14.2 1.0

Reference:

D.Picone, F.Donnarumma, G.Ferraro, G.Gotte, A.Fagagnini, G.Butera, M.Donadelli, A.Merlino. A Comparison Study on Rnase A Oligomerization Induced By Cisplatin, Carboplatin and Oxaliplatin. J. Inorg. Biochem. V. 173 105 2017.
ISSN: ISSN 1873-3344
PubMed: 28511060
DOI: 10.1016/J.JINORGBIO.2017.05.005
Page generated: Thu Oct 10 11:39:22 2024

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