Chlorine in PDB 8r5v: Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide

The structure of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide, PDB code: 8r5v was solved by R.Dolot, K.Jastrzebska, P.Antonczyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.44 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.315, 32.709, 72.802, 90, 90.07, 90
R / Rfree (%)	16.4 / 23

The binding sites of Chlorine atom in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide (pdb code 8r5v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide, PDB code: 8r5v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:24.5 occ:1.00 CL1 A:TF4202 0.0 24.5 1.0 C1 A:TF4202 1.8 16.9 1.0 C A:TF4202 2.8 13.9 1.0 O A:TF4202 2.8 12.5 1.0 CL2 A:TF4202 3.0 18.5 1.0 O A:HOH322 3.2 32.6 1.0 CE A:LYS33 3.6 24.2 1.0 OE1 A:GLN37 3.7 19.1 1.0 O3' A:Y4I201 3.7 13.3 1.0 NE2 A:GLN37 3.8 17.4 1.0 NZ A:LYS33 3.8 29.6 1.0 O2 A:TF4202 3.9 11.1 1.0 O A:HOH382 3.9 31.1 1.0 CD A:GLN37 3.9 16.2 1.0 O A:HOH426 4.1 36.6 1.0 CD A:LYS33 4.3 20.6 1.0 O A:HOH352 4.7 14.9 1.0 C3' A:Y4I201 4.7 12.8 1.0 CG A:LYS33 4.8 17.1 1.0 O A:HOH324 4.8 31.9 1.0 NZ A:LYS67 4.9 16.9 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl202 b:18.5 occ:1.00 CL2 A:TF4202 0.0 18.5 1.0 C1 A:TF4202 1.8 16.9 1.0 C A:TF4202 2.7 13.9 1.0 CL1 A:TF4202 3.0 24.5 1.0 O2 A:TF4202 3.1 11.1 1.0 O A:HOH352 3.5 14.9 1.0 O A:TF4202 3.7 12.5 1.0 O A:VAL144 3.7 9.5 1.0 NE2 A:HIS38 3.7 8.4 1.0 CD A:GLN37 3.8 16.2 1.0 CA A:PHE34 3.8 9.8 1.0 CD2 A:HIS38 3.8 7.9 1.0 OE1 A:GLN37 3.8 19.1 1.0 CG A:GLN37 3.9 14.6 1.0 N A:PHE34 3.9 10.8 1.0 CB A:GLN37 4.0 12.0 1.0 O A:LYS33 4.1 11.5 1.0 CG A:LYS33 4.1 17.1 1.0 C A:LYS33 4.1 12.6 1.0 NE2 A:GLN37 4.3 17.4 1.0 CB A:PHE34 4.5 9.5 1.0 CD A:LYS33 4.6 20.6 1.0 C A:VAL144 4.6 9.1 1.0 CE A:LYS33 4.6 24.2 1.0 CD2 A:PHE34 4.7 8.4 1.0 CA A:HIS145 4.7 7.8 1.0 CB A:LYS33 4.7 15.6 1.0 C A:PHE34 4.9 10.3 1.0 CE1 A:HIS38 5.0 8.4 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:35.1 occ:0.55 CL1 B:TF4201 0.0 35.1 0.6 CL2 B:TF4201 0.9 8.2 0.5 C1 B:TF4201 1.5 7.6 0.5 C1 B:TF4201 1.8 30.2 0.6 CL1 B:TF4201 2.2 9.3 0.5 C B:TF4201 2.7 7.1 0.5 C B:TF4201 2.7 26.3 0.6 CL2 B:TF4201 2.9 36.0 0.6 O2 B:TF4201 2.9 6.5 0.5 O2 B:TF4201 3.1 21.8 0.6 O B:HOH348 3.6 23.8 1.0 O B:HOH482 3.6 27.4 1.0 O B:TF4201 3.6 20.3 0.6 O B:HOH402 3.7 27.8 1.0 O B:TF4201 3.8 6.1 0.5 O B:HOH338 3.8 20.5 1.0 O B:HOH472 3.8 46.0 1.0 O B:HOH345 3.9 23.9 1.0 O B:ASP147 4.2 9.1 1.0 O B:PHE146 4.3 8.3 1.0 CD1 B:PHE146 4.6 9.2 1.0 C B:ASP147 4.8 9.6 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:9.3 occ:0.45 CL1 B:TF4201 0.0 9.3 0.5 C1 B:TF4201 1.1 30.2 0.6 CL2 B:TF4201 1.8 36.0 0.6 C1 B:TF4201 1.8 7.6 0.5 CL1 B:TF4201 2.2 35.1 0.6 O B:HOH472 2.5 46.0 1.0 C B:TF4201 2.6 26.3 0.6 C B:TF4201 2.7 7.1 0.5 CL2 B:TF4201 3.0 8.2 0.5 O2 B:TF4201 3.3 21.8 0.6 O B:TF4201 3.3 6.1 0.5 O B:TF4201 3.3 20.3 0.6 O B:VAL69 3.3 8.9 1.0 O2 B:TF4201 3.4 6.5 0.5 O B:HOH384 3.7 23.8 1.0 O B:HOH482 3.8 27.4 1.0 CG1 B:VAL69 3.9 10.5 1.0 C B:VAL69 4.0 9.0 1.0 CB B:VAL69 4.1 9.7 1.0 O B:HOH338 4.1 20.5 1.0 NZ B:LYS67 4.3 19.6 1.0 O B:HOH348 4.3 23.8 1.0 O B:HOH380 4.3 24.4 1.0 N B:ASN70 4.6 9.0 1.0 CA B:VAL69 4.7 9.1 1.0 CA B:ASN70 4.7 9.3 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:36.0 occ:0.55 CL2 B:TF4201 0.0 36.0 0.6 CL1 B:TF4201 1.8 9.3 0.5 C1 B:TF4201 1.8 30.2 0.6 C1 B:TF4201 1.8 7.6 0.5 O B:HOH380 2.6 24.4 1.0 C B:TF4201 2.7 7.1 0.5 C B:TF4201 2.7 26.3 0.6 O B:TF4201 2.7 6.1 0.5 O B:TF4201 2.8 20.3 0.6 O B:HOH338 2.9 20.5 1.0 CL1 B:TF4201 2.9 35.1 0.6 NZ B:LYS67 3.2 19.6 1.0 CL2 B:TF4201 3.5 8.2 0.5 O B:HOH472 3.5 46.0 1.0 O B:HOH482 3.5 27.4 1.0 O B:VAL69 3.7 8.9 1.0 O2 B:TF4201 3.8 6.5 0.5 O2 B:TF4201 3.9 21.8 0.6 O B:HOH384 4.1 23.8 1.0 CE1 B:HIS38 4.2 10.1 1.0 CE B:LYS67 4.3 17.5 1.0 OD1 B:ASN70 4.6 10.5 1.0 C B:VAL69 4.6 9.0 1.0 NE2 B:HIS38 4.6 9.5 1.0 CA B:ASN70 4.7 9.3 1.0 O B:PHE146 4.8 8.3 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Bovine Pancreatic Ribonuclease A in Complex with [Sp-Ps]-Mu-Dt Dinucleotide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:8.2 occ:0.45 CL2 B:TF4201 0.0 8.2 0.5 CL1 B:TF4201 0.9 35.1 0.6 C1 B:TF4201 1.8 7.6 0.5 C1 B:TF4201 2.3 30.2 0.6 C B:TF4201 2.6 7.1 0.5 O2 B:TF4201 2.7 6.5 0.5 C B:TF4201 2.8 26.3 0.6 CL1 B:TF4201 3.0 9.3 0.5 O2 B:TF4201 3.1 21.8 0.6 O B:HOH348 3.5 23.8 1.0 CL2 B:TF4201 3.5 36.0 0.6 O B:HOH345 3.5 23.9 1.0 O B:ASP147 3.5 9.1 1.0 O B:TF4201 3.6 20.3 0.6 O B:HOH402 3.7 27.8 1.0 O B:TF4201 3.8 6.1 0.5 O B:PHE146 3.8 8.3 1.0 CD1 B:PHE146 3.9 9.2 1.0 O B:HOH338 4.0 20.5 1.0 C B:ASP147 4.0 9.6 1.0 O B:HOH482 4.1 27.4 1.0 CE1 B:PHE146 4.3 9.0 1.0 N B:ALA148 4.4 9.3 1.0 CA B:ALA148 4.5 10.0 1.0 O B:HOH404 4.5 16.7 1.0 C B:PHE146 4.6 7.8 1.0 O B:HOH472 4.7 46.0 1.0 CA B:ASP147 4.9 8.9 1.0 CG B:PHE146 5.0 8.4 1.0

K.Jastrzebska, P.Antonczyk, R.Dolot. Synthesis of P-Stereodefined Morpholino Dinucleoside-3',6'-Thiophosphoramidates Using Unexpected Activator. To Be Published.