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Platinum in PDB 4rte: The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (1:10 Ratio)

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

All present enzymatic activity of The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (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 Cisplatin (1:10 Ratio), PDB code: 4rte was solved by I.Russo Krauss, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.23 / 1.95
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 63.770, 63.770, 63.575, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 22.4

Other elements in 4rte:

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

Chlorine (Cl) 6 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 Cisplatin (1:10 Ratio) (pdb code 4rte). 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 Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (1:10 Ratio), PDB code: 4rte:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 4rte

Go back to Platinum Binding Sites List in 4rte
Platinum binding site 1 out of 4 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (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 Cisplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt501

b:48.1
occ:0.40
 PT1 A:CPT501 0.0 48.1 0.4
N1 A:CPT501 2.0 38.2 0.4
N2 A:CPT501 2.0 41.4 0.4
CL1 A:CPT501 2.3 36.3 0.4
ND1 A:HIS119 2.4 48.5 1.0
CL A:CL507 2.6 21.1 0.4
CG A:HIS119 3.1 42.1 1.0
CB A:HIS119 3.1 32.6 1.0
CA A:HIS119 3.4 25.9 1.0
CE1 A:HIS119 3.5 42.5 1.0
O A:HOH734 3.8 54.5 1.0
O A:HOH727 4.0 39.9 1.0
O A:HOH679 4.0 28.6 1.0
O A:VAL118 4.1 28.6 1.0
N A:PHE120 4.3 23.7 1.0
CD2 A:HIS119 4.3 44.2 1.0
C A:HIS119 4.4 25.4 1.0
O A:HOH757 4.5 55.0 1.0
O A:HOH633 4.5 39.9 1.0
O A:HOH676 4.5 41.0 1.0
NE2 A:HIS119 4.5 45.2 1.0
N A:HIS119 4.6 24.0 1.0
C A:VAL118 4.8 25.0 1.0
O A:PHE120 4.9 25.2 1.0
O A:HOH662 4.9 26.6 1.0

Platinum binding site 2 out of 4 in 4rte

Go back to Platinum Binding Sites List in 4rte
Platinum binding site 2 out of 4 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (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 Cisplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt502

b:46.9
occ:0.20
 PT1 A:CPT502 0.0 46.9 0.2
N1 A:CPT502 2.0 38.2 0.2
N2 A:CPT502 2.0 40.7 0.2
CL1 A:CPT502 2.3 22.4 0.2
NE2 A:HIS105 2.4 29.7 1.0
CE1 A:HIS105 3.2 26.4 1.0
CD2 A:HIS105 3.4 23.6 1.0
O A:HOH661 3.6 25.7 1.0
CG2 A:THR78 4.1 27.6 1.0
O A:HOH712 4.2 41.7 1.0
ND1 A:HIS105 4.4 26.3 1.0
CG A:HIS105 4.5 26.3 1.0
O A:HOH643 4.7 8.7 0.5

Platinum binding site 3 out of 4 in 4rte

Go back to Platinum Binding Sites List in 4rte
Platinum binding site 3 out of 4 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (1:10 Ratio)


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 Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt503

b:41.1
occ:0.60
 PT1 A:CPT503 0.0 41.1 0.6
PT1 A:CPT504 2.0 42.5 0.4
N1 A:CPT503 2.1 31.7 0.6
N2 A:CPT503 2.1 33.4 0.6
CL1 A:CPT503 2.4 31.8 0.6
SD A:MET29 2.6 21.4 0.6
SD A:MET29 2.8 28.8 0.4
CG A:MET29 3.4 20.7 0.6
CG A:MET29 3.5 26.4 0.4
CE A:MET29 3.7 20.4 0.6
CE2 A:TYR25 3.8 25.8 1.0
CD2 A:TYR25 4.1 22.8 1.0
OD2 A:ASP14 4.2 26.6 1.0
O A:HOH665 4.4 29.5 1.0
CE A:MET29 4.4 29.2 0.4
CZ A:TYR25 4.7 22.5 1.0
O A:HOH672 4.8 31.0 1.0
CB A:MET29 4.8 21.7 0.6
CB A:MET29 4.8 26.2 0.4
CG A:ASP14 4.9 25.3 1.0
OD1 A:ASP14 4.9 26.9 1.0

Platinum binding site 4 out of 4 in 4rte

Go back to Platinum Binding Sites List in 4rte
Platinum binding site 4 out of 4 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (1:10 Ratio)


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 Bovine Pancreatic Ribonuclease Incubated in the Presence of An Excess of Cisplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt504

b:42.5
occ:0.40
 SD A:MET29 1.7 21.4 0.6
PT1 A:CPT503 2.0 41.1 0.6
CL1 A:CPT503 2.4 31.8 0.6
SD A:MET29 2.6 28.8 0.4
CG A:MET29 2.9 20.7 0.6
CG A:MET29 3.0 26.4 0.4
CE A:MET29 3.3 20.4 0.6
N2 A:CPT503 3.5 33.4 0.6
CE A:MET29 3.6 29.2 0.4
CA A:MET29 3.8 24.6 0.4
CA A:MET29 3.8 21.6 0.6
OG A:SER32 3.8 32.2 1.0
CB A:MET29 3.8 21.7 0.6
N A:MET29 3.9 23.5 0.6
CB A:MET29 3.9 26.2 0.4
N A:MET29 3.9 25.3 0.4
N1 A:CPT503 4.0 31.7 0.6
C A:GLN28 4.2 25.4 1.0
O A:GLN28 4.5 23.8 1.0
CB A:GLN28 4.5 30.2 1.0
O A:HOH672 4.5 31.0 1.0
O A:HOH650 4.6 19.0 0.5
CB A:SER32 4.8 27.0 1.0
OE1 A:GLN28 4.9 48.6 1.0
O A:TYR25 5.0 21.3 1.0

Reference:

D.Picone, F.Donnarumma, G.Ferraro, I.Russo Krauss, A.Fagagnini, G.Gotte, A.Merlino. Platinated Oligomers of Bovine Pancreatic Ribonuclease: Structure and Stability. J.Inorg.Biochem. V. 146 37 2015.
ISSN: ISSN 0162-0134
PubMed: 25756333
DOI: 10.1016/J.JINORGBIO.2015.02.011
Page generated: Thu Oct 10 11:10:04 2024

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