Chlorine in PDB 2yzr: Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii

The structure of Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii, PDB code: 2yzr was solved by M.Manzoku, A.Ebihara, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.30 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.054, 170.797, 173.334, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.5

The binding sites of Chlorine atom in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii (pdb code 2yzr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii, PDB code: 2yzr:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:16.7 occ:1.00 O C:HOH548 3.1 21.8 1.0 O C:HOH551 3.2 14.4 1.0 NZ C:LYS186 3.3 24.7 1.0 N A:GLU211 3.3 15.1 1.0 CE C:LYS186 3.7 21.9 1.0 CA C:GLY183 3.7 8.0 1.0 CG A:GLU211 3.8 22.1 1.0 CA A:LEU210 3.8 16.1 1.0 CD2 C:TYR182 3.8 11.1 1.0 O A:HOH589 3.9 28.4 1.0 C A:LEU210 4.0 15.5 1.0 N C:GLY183 4.1 10.3 1.0 CD2 A:LEU210 4.1 12.8 1.0 CB A:GLU211 4.2 17.4 1.0 CB A:LEU210 4.3 13.7 1.0 CA A:GLU211 4.3 16.0 1.0 CE2 C:TYR182 4.4 12.9 1.0 OE1 A:GLU211 4.5 22.5 1.0 CD A:GLU211 4.5 26.0 1.0 C C:TYR182 4.7 10.6 1.0 CD C:LYS186 4.7 20.6 1.0 O C:GLU179 4.7 14.7 1.0 O A:VAL209 4.8 16.8 1.0 CG A:LEU210 4.9 12.5 1.0 CG C:TYR182 4.9 12.9 1.0 O C:TYR182 4.9 11.2 1.0

Chlorine binding site 2 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:15.7 occ:1.00 O A:HOH529 3.1 11.5 1.0 N C:GLU211 3.2 16.4 1.0 NZ A:LYS186 3.3 29.5 1.0 CG C:GLU211 3.6 23.2 1.0 CA C:LEU210 3.7 17.3 1.0 CE A:LYS186 3.7 26.5 1.0 O C:HOH613 3.8 37.7 1.0 CA A:GLY183 3.8 11.5 1.0 C C:LEU210 3.9 17.6 1.0 CD2 A:TYR182 4.0 11.7 1.0 CD2 C:LEU210 4.0 17.4 1.0 CB C:LEU210 4.1 16.7 1.0 N A:GLY183 4.2 13.2 1.0 CB C:GLU211 4.2 18.9 1.0 CA C:GLU211 4.3 17.7 1.0 OE2 C:GLU211 4.5 28.0 1.0 CE2 A:TYR182 4.5 13.3 1.0 CD C:GLU211 4.5 27.1 1.0 O C:VAL209 4.7 16.9 1.0 CD A:LYS186 4.7 23.2 1.0 O A:GLU179 4.7 13.5 1.0 C A:TYR182 4.8 13.4 1.0 CG C:LEU210 4.8 19.4 1.0 N C:LEU210 4.9 17.5 1.0 N C:ASN212 4.9 14.9 1.0 O A:TYR182 5.0 13.8 1.0

Chlorine binding site 3 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:22.1 occ:1.00 NH1 A:ARG137 3.1 13.2 1.0 NE A:ARG136 3.2 12.1 1.0 NH2 A:ARG136 3.2 10.4 1.0 NH2 A:ARG137 3.5 13.3 1.0 CZ A:ARG136 3.6 12.4 1.0 CZ A:ARG137 3.8 16.3 1.0 NH2 A:ARG191 3.8 50.4 1.0 CG A:GLU133 4.1 18.8 1.0 CZ A:ARG191 4.1 49.8 1.0 NH1 A:ARG191 4.3 50.4 1.0 CD A:ARG136 4.3 8.0 1.0 CD A:GLU133 4.6 24.8 1.0 CA A:GLU133 4.6 12.4 1.0 CB A:GLU133 4.6 14.3 1.0 OE1 A:GLU133 4.8 27.0 1.0 NE A:ARG191 4.8 46.6 1.0 CE1 A:HIS114 4.9 17.3 1.0 CB A:ARG136 4.9 7.5 1.0 O A:HOH566 4.9 20.0 1.0 NH1 A:ARG136 4.9 11.4 1.0

Chlorine binding site 4 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:23.3 occ:1.00 N A:LEU241 3.3 14.1 1.0 OD1 A:ASN245 3.4 23.0 1.0 CG A:LEU241 3.7 15.3 1.0 CB A:ARG240 3.8 15.6 1.0 CB A:LEU241 3.8 14.1 1.0 CB A:ASN245 3.9 16.1 1.0 NE A:ARG240 4.0 21.4 1.0 NH1 A:ARG240 4.1 17.4 1.0 CG A:ASN245 4.1 18.9 1.0 CA A:ARG240 4.1 15.2 1.0 CZ A:ARG240 4.1 21.6 1.0 CA A:LEU241 4.1 14.6 1.0 CD1 A:LEU241 4.2 12.5 1.0 C A:ARG240 4.2 14.9 1.0 CD1 A:ILE170 4.6 17.2 1.0 O A:LEU241 4.8 16.8 1.0 CD A:ARG240 4.8 19.7 1.0 CG A:ARG240 4.8 18.6 1.0 NH2 A:ARG240 4.9 18.2 1.0 C A:LEU241 5.0 15.9 1.0

Chlorine binding site 5 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:18.0 occ:1.00 NE B:ARG136 3.1 8.5 1.0 NH1 B:ARG137 3.2 10.3 1.0 NH2 B:ARG136 3.2 10.2 1.0 NH2 B:ARG137 3.6 9.5 1.0 CZ B:ARG136 3.6 11.1 1.0 CG B:GLU133 3.7 20.3 1.0 CZ B:ARG137 3.8 13.7 1.0 NH1 B:ARG191 4.1 46.4 1.0 CD B:ARG136 4.2 8.3 1.0 CG B:ARG191 4.5 33.9 1.0 CD B:GLU133 4.6 24.9 1.0 CA B:GLU133 4.6 15.0 1.0 CB B:GLU133 4.6 16.0 1.0 NH1 B:ARG136 4.9 8.2 1.0 CB B:ARG136 4.9 8.8 1.0 OE2 B:GLU133 4.9 26.5 1.0 CZ B:ARG191 4.9 45.5 1.0 O B:HOH578 5.0 24.8 1.0

Chlorine binding site 6 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl505 b:16.6 occ:1.00 N B:GLU211 3.2 15.5 1.0 CG B:GLU211 3.7 21.5 1.0 CA B:LEU210 3.8 14.7 1.0 C B:LEU210 4.0 15.9 1.0 CB B:GLU211 4.1 16.1 1.0 CD2 B:LEU210 4.1 14.1 1.0 CA B:GLU211 4.2 15.7 1.0 CB B:LEU210 4.2 13.0 1.0 CD B:GLU211 4.5 26.6 1.0 OE1 B:GLU211 4.5 27.5 1.0 O B:VAL209 4.8 15.9 1.0 CG B:LEU210 4.9 14.8 1.0 N B:ASN212 4.9 13.9 1.0

Chlorine binding site 7 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl509 b:26.6 occ:1.00 N B:LEU241 3.3 13.9 1.0 OD1 B:ASN245 3.5 22.3 1.0 CG B:LEU241 3.7 15.6 1.0 CB B:ARG240 3.7 15.8 1.0 CB B:LEU241 3.8 14.0 1.0 CB B:ASN245 4.0 16.7 1.0 NH1 B:ARG240 4.0 19.8 1.0 CA B:ARG240 4.1 15.8 1.0 NE B:ARG240 4.1 24.1 1.0 CZ B:ARG240 4.1 21.9 1.0 CA B:LEU241 4.1 15.3 1.0 C B:ARG240 4.2 14.1 1.0 CG B:ASN245 4.2 16.8 1.0 CD1 B:LEU241 4.2 12.6 1.0 CD1 B:ILE170 4.7 12.9 1.0 O B:LEU241 4.7 16.0 1.0 NH2 B:ARG240 4.8 19.1 1.0 CG B:ARG240 4.8 18.8 1.0 CD B:ARG240 4.9 20.5 1.0 C B:LEU241 5.0 15.4 1.0 CD2 B:LEU241 5.0 12.0 1.0

Chlorine binding site 8 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl504 b:19.3 occ:1.00 NH1 C:ARG137 3.0 8.9 1.0 NE C:ARG136 3.1 12.7 1.0 NH2 C:ARG136 3.2 14.3 1.0 CZ C:ARG136 3.6 14.2 1.0 NH2 C:ARG137 3.7 13.5 1.0 CZ C:ARG137 3.8 14.1 1.0 CG C:GLU133 3.9 19.4 1.0 NH1 C:ARG191 4.1 46.2 1.0 CD C:ARG136 4.2 10.2 1.0 CZ C:ARG191 4.5 45.4 1.0 CA C:GLU133 4.6 13.4 1.0 CD C:GLU133 4.7 23.2 1.0 CB C:GLU133 4.7 14.4 1.0 NE C:ARG191 4.7 42.9 1.0 CE1 C:HIS114 4.9 15.3 1.0 NH1 C:ARG136 4.9 10.5 1.0 CB C:ARG136 5.0 11.4 1.0 O C:HOH549 5.0 18.2 1.0

Chlorine binding site 9 out of 9 in the Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii


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 Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl508 b:23.4 occ:1.00 OD1 C:ASN245 3.3 23.4 1.0 N C:LEU241 3.3 14.9 1.0 CB C:ARG240 3.7 17.1 1.0 CG C:LEU241 3.8 14.8 1.0 CB C:LEU241 3.9 13.4 1.0 CB C:ASN245 3.9 17.2 1.0 CG C:ASN245 4.0 19.4 1.0 NE C:ARG240 4.1 23.9 1.0 CA C:ARG240 4.1 16.0 1.0 NH1 C:ARG240 4.1 20.5 1.0 CZ C:ARG240 4.1 23.0 1.0 C C:ARG240 4.2 14.8 1.0 CA C:LEU241 4.2 15.0 1.0 CD1 C:LEU241 4.2 11.0 1.0 CD1 C:ILE170 4.6 14.6 1.0 CG C:ARG240 4.8 19.4 1.0 CD C:ARG240 4.8 20.8 1.0 NH2 C:ARG240 4.8 19.1 1.0 O C:LEU241 4.8 15.7 1.0 O C:HOH604 4.9 25.1 1.0

M.Manzoku, A.Ebihara, L.Chen, Z.-Q.Fu, J.Chrzas, B.-C.Wang, S.Yokoyama, S.Kuramitsu. Crystal Structure of Pyridoxine Biosynthesis Protein From Methanocaldococcus Jannaschii To Be Published.