Sodium in PDB 1kj9: Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp, PDB code: 1kj9 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 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.300, 179.500, 75.700, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp (pdb code 1kj9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp, PDB code: 1kj9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na396 b:24.7 occ:1.00 O A:HOH779 2.3 16.3 1.0 O A:ALA53 2.4 10.9 1.0 O B:HOH649 2.4 20.4 1.0 O B:HOH465 2.4 21.4 1.0 O B:HOH647 2.5 28.1 1.0 O A:HOH483 2.7 21.0 1.0 O B:HOH648 3.3 37.3 1.0 O B:ALA53 3.4 13.0 1.0 C A:ALA53 3.6 16.4 1.0 O A:HOH426 3.8 15.7 1.0 O A:HIS54 4.1 11.7 1.0 O B:HIS51 4.2 10.4 1.0 CA A:HIS54 4.2 7.6 1.0 N A:ALA53 4.3 12.7 1.0 C A:HIS54 4.3 9.4 1.0 O B:HOH443 4.3 16.8 1.0 N A:HIS54 4.4 8.9 1.0 O A:HIS51 4.5 8.8 1.0 CA A:ALA53 4.5 9.6 1.0 C B:ALA53 4.6 13.8 1.0 O A:MET50 4.6 11.1 1.0 O B:HIS54 4.6 17.1 1.0 C4 A:MPO400 4.8 14.3 1.0 C A:VAL52 4.9 17.8 1.0 O B:HOH517 4.9 20.0 1.0 O B:MET50 4.9 11.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na397 b:27.6 occ:1.00 ND2 A:ASN100 2.5 26.0 1.0 O A:PRO103 2.5 15.2 1.0 O A:HOH438 2.5 15.6 1.0 O A:VAL101 2.5 13.5 1.0 O A:HOH863 3.2 66.7 1.0 O A:HOH456 3.3 11.8 1.0 C A:PRO103 3.4 14.3 1.0 CG A:ASN100 3.5 62.1 1.0 C A:VAL101 3.6 14.7 1.0 O A:HOH927 3.7 27.7 1.0 N A:VAL101 3.9 14.1 1.0 CA A:CYS104 3.9 11.3 1.0 N A:CYS104 4.0 10.9 1.0 OD1 A:ASN100 4.1 28.8 1.0 O A:HOH539 4.1 21.0 1.0 CB A:CYS104 4.2 11.4 1.0 O A:HOH659 4.3 31.8 1.0 O A:HOH589 4.3 22.1 1.0 O A:HOH862 4.3 69.1 1.0 CA A:VAL101 4.4 11.8 1.0 C A:ASN100 4.4 19.6 1.0 N A:VAL102 4.4 13.6 1.0 CA A:VAL102 4.4 10.3 1.0 CA A:PRO103 4.5 13.3 1.0 OE1 A:GLU95 4.5 16.4 1.0 CA A:ASN100 4.5 13.1 1.0 CB A:ASN100 4.6 13.3 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