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Chlorine 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:

Platinum (Pt) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4rte

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Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl501

b:36.3
occ:0.40
 CL1 A:CPT501 0.0 36.3 0.4
CL A:CL507 1.0 21.1 0.4
PT1 A:CPT501 2.3 48.1 0.4
O A:HOH757 2.6 55.0 1.0
O A:HOH633 2.9 39.9 1.0
N1 A:CPT501 3.1 38.2 0.4
N A:PHE120 3.2 23.7 1.0
NE2 A:HIS12 3.3 21.2 1.0
ND1 A:HIS119 3.4 48.5 1.0
O A:HOH679 3.6 28.6 1.0
O A:HOH727 3.6 39.9 1.0
O A:PHE120 3.6 25.2 1.0
CA A:HIS119 3.8 25.9 1.0
CG A:HIS119 4.0 42.1 1.0
C A:HIS119 4.0 25.4 1.0
CB A:PHE120 4.1 24.6 1.0
CE1 A:HIS119 4.1 42.5 1.0
CA A:PHE120 4.1 26.8 1.0
CD2 A:HIS12 4.2 19.8 1.0
CE1 A:HIS12 4.2 20.3 1.0
CB A:HIS119 4.3 32.6 1.0
C A:PHE120 4.3 29.4 1.0
NE2 A:GLN11 4.3 29.1 1.0
N2 A:CPT501 4.4 41.4 0.4
NE2 A:HIS119 5.0 45.2 1.0
CD2 A:HIS119 5.0 44.2 1.0

Chlorine binding site 2 out of 6 in 4rte

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Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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:Cl502

b:22.4
occ:0.20
 CL1 A:CPT502 0.0 22.4 0.2
PT1 A:CPT502 2.3 46.9 0.2
CE1 A:HIS105 3.0 26.4 1.0
N1 A:CPT502 3.1 38.2 0.2
NE2 A:HIS105 3.2 29.7 1.0
O A:TYR76 3.9 22.3 1.0
O A:HOH661 4.2 25.7 1.0
ND1 A:HIS105 4.3 26.3 1.0
CG2 A:THR78 4.4 27.6 1.0
N2 A:CPT502 4.4 40.7 0.2
CD2 A:HIS105 4.5 23.6 1.0
N A:THR78 4.6 21.2 1.0
CA A:SER77 4.7 19.8 1.0
O A:HOH643 4.8 8.7 0.5
C A:SER77 4.9 19.6 1.0
C A:TYR76 5.0 20.2 1.0

Chlorine binding site 3 out of 6 in 4rte

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Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl 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:Cl503

b:31.8
occ:0.60
 CL1 A:CPT503 0.0 31.8 0.6
PT1 A:CPT503 2.4 41.1 0.6
PT1 A:CPT504 2.4 42.5 0.4
OE1 A:GLN28 3.0 48.6 1.0
N1 A:CPT503 3.1 31.7 0.6
CG A:MET29 3.4 26.4 0.4
CB A:GLN28 3.4 30.2 1.0
CG A:MET29 3.4 20.7 0.6
SD A:MET29 3.5 21.4 0.6
O A:TYR25 3.8 21.3 1.0
SD A:MET29 3.9 28.8 0.4
CD A:GLN28 4.0 46.3 1.0
CD2 A:TYR25 4.0 22.8 1.0
N A:MET29 4.0 23.5 0.6
N A:MET29 4.0 25.3 0.4
CA A:TYR25 4.2 22.3 1.0
CG A:GLN28 4.3 36.5 1.0
C A:GLN28 4.4 25.4 1.0
CE2 A:TYR25 4.4 25.8 1.0
N2 A:CPT503 4.5 33.4 0.6
CA A:GLN28 4.5 26.7 1.0
C A:TYR25 4.5 21.9 1.0
CB A:MET29 4.5 26.2 0.4
CB A:MET29 4.6 21.7 0.6
CA A:MET29 4.6 24.6 0.4
CG A:TYR25 4.6 21.9 1.0
CA A:MET29 4.6 21.6 0.6
CB A:TYR25 4.9 20.1 1.0

Chlorine binding site 4 out of 6 in 4rte

Go back to Chlorine Binding Sites List in 4rte
Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl 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:Cl505

b:33.4
occ:1.00
 OG1 A:THR3 2.9 21.9 1.0
O A:HOH677 3.3 25.3 1.0
CB A:THR3 3.9 22.1 1.0
CB A:ALA5 4.0 22.8 1.0
O A:HOH686 4.0 27.9 1.0
CG2 A:THR3 4.0 23.0 1.0
N A:ALA6 4.1 18.7 1.0
CB A:ALA6 4.3 19.2 1.0
CA A:ALA6 4.7 19.2 1.0
C A:ALA5 4.8 22.0 1.0
O A:HOH678 4.8 24.9 1.0
CA A:ALA5 4.9 20.9 1.0

Chlorine binding site 5 out of 6 in 4rte

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Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl506

b:25.8
occ:1.00
 N A:THR45 3.3 21.5 1.0
O A:HOH633 3.4 39.9 1.0
CE1 A:HIS12 3.5 20.3 1.0
CA A:ASN44 3.6 23.1 1.0
OG1 A:THR45 3.7 23.7 1.0
C A:ASN44 3.9 23.1 1.0
O A:HOH757 3.9 55.0 1.0
CD1 A:PHE120 4.0 23.3 1.0
CB A:THR45 4.0 22.2 1.0
ND1 A:HIS12 4.2 20.3 1.0
O A:VAL43 4.2 21.4 1.0
OD1 A:ASN44 4.2 22.6 1.0
CA A:THR45 4.2 21.4 1.0
N A:ASN44 4.3 22.4 1.0
NE2 A:HIS12 4.4 21.2 1.0
CB A:PHE120 4.4 24.6 1.0
CG A:PHE120 4.4 24.3 1.0
NZ A:LYS41 4.5 36.9 1.0
C A:VAL43 4.5 23.9 1.0
CG1 A:VAL43 4.6 26.9 1.0
O A:PHE120 4.7 25.2 1.0
CB A:ASN44 4.7 22.5 1.0
CG A:ASN44 4.7 22.8 1.0
CE1 A:PHE120 4.7 23.6 1.0
O A:THR45 4.9 20.9 1.0

Chlorine binding site 6 out of 6 in 4rte

Go back to Chlorine Binding Sites List in 4rte
Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl507

b:21.1
occ:0.40
 CL1 A:CPT501 1.0 36.3 0.4
PT1 A:CPT501 2.6 48.1 0.4
O A:HOH679 2.7 28.6 1.0
N1 A:CPT501 2.8 38.2 0.4
NE2 A:HIS12 2.9 21.2 1.0
O A:HOH757 2.9 55.0 1.0
N A:PHE120 3.2 23.7 1.0
CD2 A:HIS12 3.6 19.8 1.0
CA A:HIS119 3.6 25.9 1.0
O A:HOH727 3.7 39.9 1.0
O A:HOH633 3.7 39.9 1.0
NE2 A:GLN11 3.8 29.1 1.0
C A:HIS119 3.9 25.4 1.0
ND1 A:HIS119 3.9 48.5 1.0
CE1 A:HIS12 4.0 20.3 1.0
CB A:PHE120 4.1 24.6 1.0
CA A:PHE120 4.1 26.8 1.0
O A:PHE120 4.2 25.2 1.0
CB A:HIS119 4.3 32.6 1.0
CG A:HIS119 4.4 42.1 1.0
O A:VAL118 4.5 28.6 1.0
N2 A:CPT501 4.5 41.4 0.4
C A:PHE120 4.7 29.4 1.0
N A:HIS119 4.7 24.0 1.0
CD2 A:PHE8 4.8 20.4 1.0
CG A:HIS12 4.8 20.7 1.0
CE1 A:HIS119 4.8 42.5 1.0
ND1 A:HIS12 5.0 20.3 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: Fri Jul 26 01:34:49 2024

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