Chlorine in PDB 3h30: Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole

All present enzymatic activity of Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole:
2.7.11.1;

The structure of Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole, PDB code: 3h30 was solved by K.Niefind, J.Raaf, O.-G.Issinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.56
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	71.506, 71.506, 125.789, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole (pdb code 3h30). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 38 binding sites of Chlorine where determined in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole, PDB code: 3h30:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


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 the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl336 b:94.3 occ:1.00 CL2 A:RFZ336 0.0 94.3 1.0 C4 A:RFZ336 1.7 91.3 1.0 C5 A:RFZ336 2.7 90.9 1.0 C3 A:RFZ336 2.7 91.3 1.0 CL1 A:RFZ336 3.2 95.0 1.0 CE A:MET163 3.6 25.1 1.0 O A:VAL116 3.7 26.7 1.0 CG1 A:VAL66 3.9 21.0 1.0 C6 A:RFZ336 4.0 90.7 1.0 C2 A:RFZ336 4.0 90.0 1.0 O A:ASN117 4.3 29.3 1.0 CG2 A:VAL66 4.3 23.0 1.0 CD1 A:LEU45 4.3 26.9 1.0 C A:VAL116 4.4 30.1 1.0 CB A:VAL116 4.5 28.4 1.0 CG A:MET163 4.5 19.6 1.0 C7 A:RFZ336 4.5 90.2 1.0 CA A:ASN118 4.6 31.5 1.0 SD A:MET163 4.6 25.3 1.0 CB A:VAL66 4.7 19.3 1.0 OD1 A:ASN118 4.7 38.1 1.0 C A:ASN117 4.7 31.9 1.0 CG1 A:VAL53 4.7 21.2 1.0 CG1 A:VAL116 4.8 28.2 1.0 N A:ASN118 4.9 31.0 1.0 O2' A:RFZ336 4.9 93.6 1.0 CA A:VAL116 5.0 28.2 1.0

Chlorine binding site 2 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


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 the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl336 b:95.0 occ:1.00 CL1 A:RFZ336 0.0 95.0 1.0 C3 A:RFZ336 1.7 91.3 1.0 C2 A:RFZ336 2.7 90.0 1.0 C4 A:RFZ336 2.7 91.3 1.0 CL2 A:RFZ336 3.2 94.3 1.0 CG2 A:ILE174 4.0 12.9 1.0 C7 A:RFZ336 4.0 90.2 1.0 C5 A:RFZ336 4.0 90.9 1.0 CG1 A:VAL66 4.1 21.0 1.0 CD1 A:ILE95 4.3 26.1 1.0 CD1 A:ILE174 4.4 12.9 1.0 CL A:CL339 4.5 26.5 1.0 C6 A:RFZ336 4.5 90.7 1.0 CG1 A:ILE95 4.6 24.6 1.0 CB A:ILE174 4.6 12.6 1.0 CG A:MET163 4.8 19.6 1.0 CB A:VAL66 4.8 19.3 1.0 CG1 A:VAL53 4.9 21.2 1.0 CD2 A:PHE113 4.9 17.6 1.0

Chlorine binding site 3 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


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 the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl337 b:44.0 occ:1.00 CL2 A:RFZ337 0.0 44.0 1.0 C4 A:RFZ337 1.7 37.4 1.0 C3 A:RFZ337 2.7 39.3 1.0 C5 A:RFZ337 2.7 38.3 1.0 CL1 A:RFZ337 3.0 45.5 1.0 CG2 A:VAL101 3.2 25.6 1.0 CB A:TYR39 3.7 20.6 1.0 C2 A:RFZ337 4.0 37.8 1.0 C6 A:RFZ337 4.0 33.7 1.0 O A:GLN36 4.0 31.9 1.0 CD2 A:TYR39 4.3 22.7 1.0 CG1 A:VAL67 4.4 22.2 1.0 CG A:TYR39 4.4 19.7 1.0 CD2 A:LEU41 4.4 18.6 1.0 CB A:VAL101 4.5 27.0 1.0 C7 A:RFZ337 4.5 37.2 1.0 CA A:GLN36 4.5 32.7 1.0 O A:TYR39 4.6 23.5 1.0 CB A:GLN36 4.7 34.0 1.0 CB A:ALA110 4.7 25.6 1.0 C A:GLN36 4.7 30.0 1.0 CG2 A:VAL67 4.8 15.7 1.0 CA A:TYR39 4.8 23.6 1.0 C A:TYR39 4.8 20.4 1.0

Chlorine binding site 4 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


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 the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl337 b:45.5 occ:1.00 CL1 A:RFZ337 0.0 45.5 1.0 C3 A:RFZ337 1.7 39.3 1.0 C4 A:RFZ337 2.7 37.4 1.0 CB A:ALA110 2.7 25.6 1.0 C2 A:RFZ337 2.7 37.8 1.0 CL2 A:RFZ337 3.0 44.0 1.0 CG1 A:ILE69 3.6 22.8 1.0 CD1 A:ILE69 3.7 25.1 1.0 CG1 A:VAL67 3.8 22.2 1.0 C5 A:RFZ337 4.0 38.3 1.0 C7 A:RFZ337 4.0 37.2 1.0 CG2 A:VAL101 4.0 25.6 1.0 CA A:ALA110 4.2 26.1 1.0 CA A:ASP103 4.3 36.2 1.0 OD1 A:ASP103 4.4 35.8 1.0 C6 A:RFZ337 4.5 33.7 1.0 O A:LYS102 4.5 30.7 1.0 N A:ASP103 4.7 32.2 1.0 CD A:PRO104 4.7 37.2 1.0 C A:LYS102 4.7 32.4 1.0 CB A:ILE69 4.8 24.5 1.0 CB A:ASP103 4.8 35.5 1.0 CG2 A:ILE69 4.9 26.1 1.0 N A:ALA110 4.9 23.7 1.0

Chlorine binding site 5 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


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 the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl338 b:11.6 occ:1.00 ND1 A:HIS148 3.0 11.7 1.0 O A:HOH390 3.1 13.2 1.0 N A:ALA315 3.3 13.5 1.0 O A:HOH384 3.3 7.6 1.0 CG2 A:VAL11 3.7 18.9 1.0 CB A:ALA315 3.7 17.8 1.0 CB A:HIS148 3.8 12.0 1.0 CG A:HIS148 3.8 11.0 1.0 CB A:THR314 4.0 14.3 1.0 CE1 A:HIS148 4.1 10.3 1.0 CA A:ALA315 4.1 14.5 1.0 CE2 A:TYR12 4.1 14.6 1.0 CA A:THR314 4.2 13.0 1.0 C A:THR314 4.2 14.3 1.0 CD2 A:TYR12 4.2 12.3 1.0 OD1 A:ASP145 4.6 12.8 1.0 CB A:TYR211 4.7 11.9 1.0 CB A:VAL11 4.8 20.4 1.0 CG2 A:THR314 4.8 16.3 1.0 N A:ARG316 5.0 15.6 1.0

Chlorine binding site 6 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


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 the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl339 b:26.5 occ:1.00 NZ A:LYS68 3.1 33.0 1.0 O A:HOH429 3.1 15.8 1.0 N A:ASP175 3.2 15.3 1.0 O A:HOH541 3.6 22.8 1.0 CA A:ASP175 3.8 15.8 1.0 CB A:ILE174 3.8 12.6 1.0 CE A:LYS68 3.8 29.3 1.0 CD A:LYS68 3.9 27.5 1.0 CZ A:PHE113 4.2 18.8 1.0 C A:ILE174 4.2 12.9 1.0 CE2 A:PHE113 4.2 19.8 1.0 C2 A:RFZ336 4.3 90.0 1.0 CA A:ILE174 4.3 12.5 1.0 CL1 A:RFZ336 4.5 95.0 1.0 CG2 A:ILE174 4.5 12.9 1.0 CD1 A:ILE174 4.6 12.9 1.0 CG1 A:ILE174 4.7 14.1 1.0 CB A:ASP175 4.7 13.2 1.0 N A:TRP176 4.7 14.8 1.0 OD1 A:ASP175 4.8 31.6 1.0 CG2 A:ILE95 4.8 20.1 1.0 C A:ASP175 4.9 14.5 1.0 CE1 A:PHE113 4.9 19.2 1.0 C3 A:RFZ336 4.9 91.3 1.0 OE2 A:GLU81 5.0 24.0 1.0 CD2 A:PHE113 5.0 17.6 1.0

Chlorine binding site 7 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl340 b:21.5 occ:1.00 N A:HIS160 3.2 15.3 1.0 CB A:HIS160 3.5 21.5 1.0 CD A:PRO159 3.6 14.4 1.0 CD2 A:HIS160 3.7 30.6 1.0 N A:PRO159 3.7 13.4 1.0 CG A:HIS160 3.7 28.1 1.0 CB A:LYS158 3.8 13.3 1.0 CD A:LYS158 3.8 18.5 1.0 CG A:LYS158 3.8 15.4 1.0 CB A:PRO159 3.9 16.4 1.0 CA A:HIS160 3.9 16.7 1.0 CD A:LYS122 4.0 28.1 1.0 CG A:PRO159 4.1 18.4 1.0 C A:PRO159 4.1 12.1 1.0 CA A:PRO159 4.2 16.3 1.0 NZ A:LYS122 4.2 34.5 1.0 CE2 A:PHE197 4.3 20.2 1.0 C A:LYS158 4.3 14.4 1.0 CE A:LYS158 4.4 19.3 1.0 O A:HOH476 4.5 22.6 1.0 CE A:LYS122 4.5 30.6 1.0 CZ A:PHE197 4.6 17.4 1.0 CA A:LYS158 4.6 12.1 1.0 CG A:LYS122 4.8 22.2 1.0 NE2 A:HIS160 4.8 33.5 1.0 ND1 A:HIS160 4.9 26.7 1.0 NZ A:LYS158 4.9 19.8 1.0

Chlorine binding site 8 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl341 b:39.9 occ:1.00 CL A:CL342 3.2 23.9 1.0 NH1 A:ARG80 3.2 28.8 1.0 NH2 A:ARG155 3.3 16.9 1.0 NZ A:LYS77 3.5 39.6 1.0 CE A:LYS77 3.7 41.3 1.0 NH2 A:ARG80 3.8 26.9 1.0 ND2 A:ASN189 3.9 24.1 1.0 CZ A:ARG80 4.0 29.9 1.0 CZ A:ARG155 4.2 15.0 1.0 CB A:ASN189 4.3 27.8 1.0 CG A:ASN189 4.3 31.5 1.0 NH1 A:ARG155 4.4 17.4 1.0 O A:HOH469 4.5 18.8 1.0 CD A:LYS77 4.7 38.2 1.0 CG1 A:VAL192 4.8 18.6 1.0 CD2 A:LEU178 4.9 23.8 1.0

Chlorine binding site 9 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl342 b:23.9 occ:1.00 O A:HOH553 2.8 19.1 1.0 CL A:CL341 3.2 39.9 1.0 NH1 A:ARG155 3.3 17.4 1.0 OE1 A:GLU180 3.6 25.8 1.0 NH2 A:ARG155 3.7 16.9 1.0 N A:ASN189 3.9 25.4 1.0 CB A:ASN189 3.9 27.8 1.0 CD1 A:TYR188 4.0 16.9 1.0 CZ A:ARG155 4.0 15.0 1.0 NH1 A:ARG80 4.1 28.8 1.0 CG A:GLU180 4.3 26.2 1.0 CD A:GLU180 4.4 22.6 1.0 CA A:ASN189 4.5 27.2 1.0 CA A:TYR188 4.6 22.3 1.0 CB A:TYR188 4.6 21.0 1.0 CG A:TYR188 4.8 21.6 1.0 C A:TYR188 4.8 23.5 1.0 CE1 A:TYR188 4.8 19.4 1.0 CB A:GLU180 4.9 18.3 1.0 ND2 A:ASN189 4.9 24.1 1.0 CG A:ASN189 5.0 31.5 1.0

Chlorine binding site 10 out of 38 in the Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of the Catalytic Subunit of Human Protein Kinase CK2 with 5,6-Dichloro-1-Beta-D-Ribofuranosylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl343 b:23.5 occ:1.00 O A:HOH565 2.9 20.1 1.0 O A:HOH401 3.1 10.1 1.0 O A:HOH432 3.6 15.3 1.0 CZ3 A:TRP24 4.0 20.4 1.0 CE3 A:TRP24 4.1 21.0 1.0 CE2 A:TYR26 4.4 26.1 1.0 NE2 A:HIS183 4.4 18.0 1.0 O A:TRP24 4.5 18.9 1.0 CD2 A:HIS183 4.6 19.5 1.0 CZ A:TYR26 4.9 18.0 1.0 CD2 A:TYR26 4.9 23.0 1.0 OH A:TYR26 4.9 26.9 1.0 NE2 A:GLN186 4.9 23.5 1.0

J.Raaf, E.Brunstein, O.-G.Issinger, K.Niefind. The CK2ALPHA/CK2BETA Interface of Human Protein Kinase CK2 Harbors A Binding Pocket For Small Molecules Chem.Biol. V. 15 111 2008.
ISSN: ISSN 1074-5521
PubMed: 18291315
DOI: 10.1016/J.CHEMBIOL.2007.12.012