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Caesium 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:

Platinum (Pt) 2 atoms
Chlorine (Cl) 9 atoms

Caesium Binding Sites:

The binding sites of Caesium 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 Caesium atom.
In total 5 binding sites of Caesium 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 Caesium binding site number: 1; 2; 3; 4; 5;

Caesium binding site 1 out of 5 in 5na9

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Caesium binding site 1 out of 5 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 Caesium with other atoms in the Cs 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:Cs202

b:20.4
occ:0.30
 O A:HIS48 3.0 14.5 1.0
OE1 A:GLU49 3.3 10.6 1.0
OE2 A:GLU49 3.6 10.3 1.0
O A:HOH337 3.7 22.5 1.0
CD A:GLU49 3.7 11.9 1.0
O A:HOH431 4.1 34.4 1.0
C A:HIS48 4.2 12.6 1.0
O A:SER18 4.2 20.9 1.0
CB A:SER80 4.4 16.0 1.0
CA A:SER18 4.5 26.7 1.0
O A:HOH304 4.5 22.2 1.0
CB A:SER18 4.7 26.5 1.0
CA A:GLU49 4.7 12.1 1.0
C A:SER18 4.8 25.4 1.0
CG A:GLU49 4.9 11.3 1.0
N A:GLU49 4.9 12.1 1.0
CB A:HIS48 4.9 15.8 1.0
O A:HOH346 5.0 9.2 1.0

Caesium binding site 2 out of 5 in 5na9

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Caesium binding site 2 out of 5 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 Caesium with other atoms in the Cs 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:Cs203

b:51.2
occ:0.60
 O A:HOH340 2.3 24.2 1.0
O A:THR70 3.2 25.3 1.0
OH A:TYR73 3.3 20.4 1.0
OD1 A:ASN62 3.4 20.1 1.0
O A:HOH477 3.8 42.0 1.0
CG A:ASN62 3.8 20.5 1.0
ND2 A:ASN62 3.8 22.6 1.0
CZ A:TYR73 4.4 19.2 1.0
C A:THR70 4.4 27.6 1.0
OG1 A:THR70 4.5 31.9 1.0
OH A:TYR115 4.8 17.9 1.0
O A:HOH368 4.8 28.8 1.0
CB A:ASN62 4.8 18.9 1.0
CA A:ASN71 4.9 21.7 1.0
CB A:THR70 5.0 33.5 1.0
O A:HOH464 5.0 32.8 1.0

Caesium binding site 3 out of 5 in 5na9

Go back to Caesium Binding Sites List in 5na9
Caesium binding site 3 out of 5 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 Caesium with other atoms in the Cs binding site number 3 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:Cs204

b:20.3
occ:0.30
 CS A:CS204 0.0 20.3 0.3
O A:SER32 2.9 18.0 1.0
CS A:CS204 3.6 10.9 0.3
C A:SER32 3.8 19.3 1.0
OD1 A:ASN34 3.9 24.9 1.0
CA A:SER32 4.1 19.1 1.0
ND2 A:ASN34 4.1 23.9 1.0
CG A:ASN34 4.3 23.4 1.0
O A:LYS31 4.7 17.1 1.0
CB A:SER32 4.7 20.5 1.0
O A:HOH454 4.8 25.7 1.0

Caesium binding site 4 out of 5 in 5na9

Go back to Caesium Binding Sites List in 5na9
Caesium binding site 4 out of 5 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 Caesium with other atoms in the Cs binding site number 4 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:Cs204

b:10.9
occ:0.30
 CS A:CS204 0.0 10.9 0.3
OD1 A:ASN34 3.1 24.9 1.0
O A:LYS31 3.2 17.1 1.0
CS A:CS204 3.6 20.3 0.3
O A:HOH454 3.8 25.7 1.0
O A:HOH482 3.9 46.1 1.0
C A:LYS31 4.2 18.5 1.0
O A:HOH357 4.2 21.2 1.0
CG A:ASN34 4.3 23.4 1.0
CG A:LYS31 4.4 25.7 1.0
CA A:SER32 4.6 19.1 1.0
O A:SER32 4.8 18.0 1.0
N A:SER32 4.8 18.3 1.0
C A:SER32 4.9 19.3 1.0
ND2 A:ASN34 5.0 23.9 1.0

Caesium binding site 5 out of 5 in 5na9

Go back to Caesium Binding Sites List in 5na9
Caesium binding site 5 out of 5 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 Caesium with other atoms in the Cs binding site number 5 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:Cs205

b:20.9
occ:0.50
 OG A:SER23 3.1 18.1 1.0
OD1 A:ASN24 3.2 18.9 1.0
O A:HOH347 3.3 19.8 1.0
O A:HOH463 3.5 24.8 1.0
O A:HOH429 3.6 13.3 1.0
O A:HOH408 3.7 36.0 1.0
CB A:SER23 3.7 21.9 1.0
O A:SER23 3.9 17.1 1.0
CG A:ASN24 4.0 19.6 1.0
C A:SER23 4.2 18.2 1.0
O A:HOH499 4.3 28.0 1.0
ND2 A:ASN24 4.4 21.2 1.0
N A:ASN24 4.6 16.5 1.0
CA A:SER23 4.6 20.3 1.0
O A:HOH376 4.9 11.7 1.0
CA A:ASN24 4.9 17.2 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: Tue Jul 30 20:44:52 2024

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