Chlorine in PDB 1kjq: Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp, PDB code: 1kjq was solved by J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.350, 179.340, 75.620, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp (pdb code 1kjq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp, PDB code: 1kjq:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl395 b:19.4 occ:1.00 NH2 A:ARG119 3.2 14.4 1.0 N A:PHE134 3.2 10.4 1.0 O A:HOH466 3.4 14.3 1.0 CD2 A:PHE134 3.5 13.7 1.0 CA A:ARG133 3.6 8.9 1.0 O A:HOH661 3.6 30.4 1.0 C A:ARG133 3.9 10.8 1.0 CZ A:ARG119 4.0 10.3 1.0 NH1 A:ARG119 4.1 11.2 1.0 CB A:PHE134 4.2 10.1 1.0 CA A:PHE134 4.3 9.5 1.0 CG A:PHE134 4.3 11.4 1.0 CB A:ARG133 4.3 9.4 1.0 O A:TYR132 4.4 11.0 1.0 CE2 A:PHE134 4.4 15.0 1.0 CG A:ARG133 4.4 8.4 1.0 N A:ARG133 4.6 8.9 1.0 CD1 A:TYR132 4.6 10.3 1.0 O A:PHE134 4.6 13.4 1.0 CE1 A:TYR132 4.8 9.8 1.0 C A:TYR132 4.8 10.4 1.0 O A:HOH499 4.9 20.6 1.0 C A:PHE134 5.0 11.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl396 b:18.0 occ:1.00 O A:HOH468 2.8 14.4 1.0 NH1 A:ARG43 3.0 16.8 1.0 O A:HOH447 3.1 14.2 1.0 NH2 A:ARG43 3.7 13.5 1.0 CZ A:ARG43 3.8 14.2 1.0 N A:ASN60 3.9 12.5 1.0 C1 A:EDO403 4.0 25.8 1.0 CA A:ILE59 4.2 9.2 1.0 C A:ILE59 4.3 12.1 1.0 C2 A:EDO403 4.4 24.7 1.0 CB A:ASN60 4.4 13.9 1.0 O A:HOH571 4.6 21.0 1.0 CA A:ASN60 4.7 10.9 1.0 O A:HOH572 4.8 16.7 1.0 O A:HOH492 4.8 16.1 1.0 O A:VAL58 4.9 10.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl395 b:21.8 occ:1.00 O B:HOH644 2.7 32.5 1.0 O B:HOH488 2.7 17.7 1.0 N B:PHE217 3.1 8.8 1.0 CD2 B:HIS216 3.6 13.8 1.0 CA B:HIS216 3.6 8.0 1.0 CD1 B:PHE217 3.7 14.4 1.0 C B:HIS216 3.9 8.7 1.0 O B:PHE217 4.0 11.3 1.0 CB B:HIS216 4.0 8.8 1.0 CG B:HIS216 4.1 10.8 1.0 CA B:PHE217 4.1 10.6 1.0 CB B:PHE217 4.1 9.7 1.0 O B:HOH795 4.2 40.3 1.0 CG B:PHE217 4.4 9.6 1.0 C B:PHE217 4.5 9.1 1.0 CE1 B:PHE217 4.6 15.0 1.0 O B:VAL215 4.7 9.5 1.0 O B:HOH679 4.7 14.9 0.3 NE2 B:HIS216 4.8 12.2 1.0 O B:HOH679 4.8 15.7 0.3 O B:HOH430 4.8 12.0 1.0 N B:HIS216 4.9 8.0 1.0 O B:HOH460 4.9 19.4 1.0 O B:HOH559 5.0 26.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl396 b:23.1 occ:1.00 O A:HOH415 2.8 9.2 1.0 N B:GLY354 2.8 7.2 1.0 O B:HOH410 3.1 9.7 1.0 CA B:GLY354 3.2 7.5 1.0 O B:HOH405 3.3 9.5 1.0 CE2 B:PHE337 3.5 8.3 1.0 OG1 A:THR6 3.7 9.2 1.0 N B:PHE353 3.8 8.2 1.0 C B:LEU352 3.8 7.4 1.0 CB B:LEU352 3.8 8.1 1.0 CG2 A:THR6 3.9 8.8 1.0 C B:PHE353 3.9 8.3 1.0 CZ B:PHE337 3.9 8.2 1.0 C B:GLY354 4.1 9.7 1.0 O B:LEU352 4.1 8.5 1.0 CB A:THR6 4.2 9.9 1.0 N B:LYS355 4.2 8.7 1.0 CA A:GLY35 4.3 7.7 1.0 CA B:LEU352 4.3 7.3 1.0 CA A:THR6 4.3 7.8 1.0 CA B:PHE353 4.3 8.4 1.0 CD2 B:PHE337 4.5 6.8 1.0 O B:LEU364 4.6 7.8 1.0 O A:GLY5 4.7 8.4 1.0 O A:LEU34 4.8 8.0 1.0 O A:GLY35 4.9 7.8 1.0 O B:PHE353 5.0 8.8 1.0

J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden. Purt-Encoded Glycinamide Ribonucleotide Transformylase. Accommodation of Adenosine Nucleotide Analogs Within the Active Site. J.Biol.Chem. V. 277 23898 2002.
ISSN: ISSN 0021-9258
PubMed: 11953435
DOI: 10.1074/JBC.M202251200