Atomistry » Chlorine » PDB 5n6t-5ncv » 5na9
Atomistry »
  Chlorine »
    PDB 5n6t-5ncv »
      5na9 »

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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Go back to Chlorine Binding Sites List in 5na9
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy