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Chlorine 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
Platinum (Pt) 2 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 Carboplatin (1:10 Ratio) (pdb code 5na9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5na9

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Chlorine binding site 1 out of 9 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 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 Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:23.6
occ:1.00
 O A:HOH481 2.9 37.9 1.0
ND2 A:ASN34 3.0 23.9 1.0
CD A:ARG10 3.5 14.2 1.0
CB A:ASN34 3.9 20.6 1.0
CG A:ASN34 3.9 23.4 1.0
NE A:ARG10 4.0 14.0 1.0
CZ A:ARG10 4.4 15.4 1.0
NH1 A:ARG10 4.4 16.0 1.0
O A:HOH320 4.7 45.1 1.0
O A:ARG33 4.8 18.7 1.0
CG A:ARG10 4.8 13.2 1.0

Chlorine binding site 2 out of 9 in 5na9

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Chlorine binding site 2 out of 9 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 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 Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:21.4
occ:1.00
 OG1 A:THR3 3.0 15.7 1.0
CB A:THR3 3.9 16.3 1.0
CB A:ALA5 4.0 12.7 1.0
CG2 A:THR3 4.0 17.3 1.0
N A:ALA6 4.2 11.8 1.0
CB A:ALA6 4.3 12.2 1.0
O A:HOH500 4.3 16.7 1.0
CA A:ALA6 4.7 12.0 1.0
C A:ALA5 4.8 11.7 1.0
CA A:ALA5 4.9 12.3 1.0

Chlorine binding site 3 out of 9 in 5na9

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Chlorine binding site 3 out of 9 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 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 Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:23.5
occ:1.00
 O A:SER15 3.3 25.5 1.0
O A:HOH492 3.5 10.4 1.0
O A:HOH444 3.7 47.9 1.0
O A:HOH460 4.0 31.0 1.0
O A:HOH412 4.0 35.6 1.0
C A:SER15 4.3 23.1 1.0
CA A:SER16 4.8 24.6 1.0
CB A:SER15 4.9 18.5 1.0

Chlorine binding site 4 out of 9 in 5na9

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Chlorine binding site 4 out of 9 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 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 Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl209

b:20.2
occ:1.00
 NH1 A:ARG39 2.5 47.0 1.0
O A:HOH356 2.8 36.0 1.0
O A:ARG39 3.2 27.7 1.0
O A:LEU35 3.3 20.7 1.0
CZ A:ARG39 3.6 44.1 1.0
CD A:ARG39 3.7 50.5 1.0
CG A:ARG39 3.8 47.4 1.0
C A:ARG39 3.9 29.0 1.0
N A:ARG39 4.0 39.0 1.0
C A:LEU35 4.1 21.8 1.0
NE A:ARG39 4.1 51.3 1.0
N A:LYS41 4.1 20.1 1.0
CA A:ARG39 4.3 34.6 1.0
CB A:ARG39 4.4 38.2 1.0
CB A:LYS41 4.4 17.7 1.0
N A:LYS37 4.4 38.6 1.0
CA A:LYS41 4.5 17.9 1.0
N A:ASP38 4.6 41.5 1.0
C A:CYS40 4.7 22.6 1.0
N A:THR36 4.7 26.7 1.0
NH2 A:ARG39 4.7 47.8 1.0
CA A:THR36 4.8 29.6 1.0
CA A:LEU35 4.8 21.4 1.0
N A:CYS40 4.8 24.7 1.0
C A:THR36 4.9 36.4 1.0

Chlorine binding site 5 out of 9 in 5na9

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Chlorine binding site 5 out of 9 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 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 Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl210

b:41.8
occ:1.00
 O A:SER90 2.5 27.3 1.0
NZ A:LYS91 2.8 43.3 0.5
O A:HOH416 2.9 24.6 1.0
O A:HOH386 3.0 52.6 1.0
O A:THR87 3.3 25.1 1.0
O A:GLY88 3.3 37.4 1.0
C A:SER90 3.6 31.6 1.0
O A:HOH451 3.8 42.0 1.0
N A:SER90 3.8 33.9 1.0
C A:GLY88 3.8 35.3 1.0
CB A:SER90 3.9 25.9 1.0
CA A:SER90 4.0 30.9 1.0
CE A:LYS91 4.0 44.7 0.5
CA A:GLY88 4.2 31.3 1.0
CD A:LYS91 4.4 43.4 0.5
C A:THR87 4.4 26.6 1.0
OE2 A:GLU86 4.5 22.5 1.0
C A:SER89 4.6 39.6 1.0
N A:SER89 4.7 36.8 1.0
OG A:SER90 4.7 23.7 1.0
N A:LYS91 4.7 33.8 0.5
N A:LYS91 4.7 33.6 0.5
N A:GLY88 4.8 28.5 1.0
O A:HOH341 4.8 59.6 1.0
O A:HOH406 4.9 42.8 1.0

Chlorine binding site 6 out of 9 in 5na9

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Chlorine binding site 6 out of 9 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 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 Carboplatin (1:10 Ratio) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl211

b:33.7
occ:1.00
 O A:ASN113 2.9 20.5 1.0
O A:HOH380 3.6 50.5 1.0
ND2 A:ASN113 3.7 41.9 1.0
C A:ASN113 3.9 22.8 1.0
CB A:ASN113 4.1 29.5 1.0
CG A:ASN113 4.1 35.8 1.0
CA A:ASN113 4.6 23.0 1.0
N A:PRO114 4.8 21.1 1.0
OD1 A:ASN113 4.9 40.6 1.0
CD A:PRO114 5.0 21.2 1.0

Chlorine binding site 7 out of 9 in 5na9

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Chlorine binding site 7 out of 9 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl212

b:35.2
occ:1.00
 O A:THR36 2.7 32.7 1.0
O A:HOH327 3.1 40.0 1.0
O A:HOH388 3.2 47.1 1.0
OG1 A:THR36 3.5 26.3 1.0
CE1 A:TYR92 3.5 40.9 1.0
O A:PRO93 3.7 33.1 1.0
O A:HOH313 3.7 21.5 1.0
C A:THR36 3.8 36.4 1.0
CB A:THR36 3.9 28.8 1.0
CD1 A:TYR92 4.0 39.1 1.0
O A:HOH482 4.1 46.1 1.0
C A:PRO93 4.3 35.6 1.0
CA A:PRO93 4.3 37.4 1.0
CB A:PRO93 4.4 40.1 1.0
SG A:CYS95 4.5 23.0 1.0
CA A:THR36 4.5 29.6 1.0
O A:LYS37 4.5 45.6 1.0
CZ A:TYR92 4.5 41.5 1.0
OH A:TYR92 4.8 43.9 1.0
N A:LYS37 4.8 38.6 1.0
CA A:LYS37 5.0 43.3 1.0
C A:LYS37 5.0 41.6 1.0

Chlorine binding site 8 out of 9 in 5na9

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Chlorine binding site 8 out of 9 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl213

b:34.8
occ:1.00
 O A:HOH355 2.4 32.9 1.0
O A:PHE120 2.9 18.4 1.0
CL A:CL214 3.5 18.7 1.0
O A:HOH427 3.5 15.3 1.0
O A:HOH462 3.7 30.1 1.0
C A:PHE120 4.0 19.1 1.0
CB A:PHE120 4.4 16.1 1.0
CA A:PHE120 4.6 16.4 1.0
N A:PHE120 4.7 15.9 1.0
CE1 A:HIS12 4.7 13.0 1.0
NE2 A:HIS12 4.8 12.2 1.0
O A:HOH465 4.9 42.1 1.0
NZ A:LYS41 4.9 20.0 1.0

Chlorine binding site 9 out of 9 in 5na9

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Chlorine binding site 9 out of 9 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 Chlorine with other atoms in the Cl binding site number 9 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:Cl214

b:18.7
occ:1.00
 N A:THR45 3.2 14.6 1.0
CE1 A:HIS12 3.3 13.0 1.0
CL A:CL213 3.5 34.8 1.0
OG1 A:THR45 3.6 15.4 1.0
CA A:ASN44 3.6 14.7 1.0
CB A:THR45 3.8 14.6 1.0
CD1 A:PHE120 3.9 16.1 1.0
C A:ASN44 3.9 14.9 1.0
ND1 A:HIS12 4.0 13.8 1.0
CA A:THR45 4.1 14.8 1.0
CB A:PHE120 4.2 16.1 1.0
OD1 A:ASN44 4.2 16.2 1.0
CG A:PHE120 4.3 15.1 1.0
O A:VAL43 4.3 16.1 1.0
NE2 A:HIS12 4.3 12.2 1.0
N A:ASN44 4.4 14.5 1.0
O A:HOH355 4.4 32.9 1.0
NZ A:LYS41 4.4 20.0 1.0
C A:VAL43 4.6 15.3 1.0
O A:PHE120 4.6 18.4 1.0
CG A:ASN44 4.6 15.2 1.0
O A:THR45 4.7 13.6 1.0
CE1 A:PHE120 4.7 15.8 1.0
CB A:ASN44 4.7 15.5 1.0
CG1 A:VAL43 4.9 17.9 1.0
C A:THR45 5.0 14.4 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: Fri Jul 26 13:20:08 2024

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