Sodium in PDB 1kjj: Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S

The structure of Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S, PDB code: 1kjj 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 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.900, 179.300, 76.100, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S (pdb code 1kjj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S, PDB code: 1kjj:

Sodium binding site 1 out of 1 in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S


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 Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na395 b:35.8 occ:1.00 O A:PRO103 2.5 21.5 1.0 O A:HOH432 2.5 24.7 1.0 O A:VAL101 2.7 20.8 1.0 ND2 A:ASN100 2.8 65.7 1.0 O A:HOH443 3.2 25.3 1.0 C A:PRO103 3.4 19.8 1.0 O A:HOH415 3.5 23.1 1.0 CG A:ASN100 3.7 74.5 1.0 C A:VAL101 3.8 22.9 1.0 CA A:CYS104 4.0 16.6 1.0 OD1 A:ASN100 4.0 54.0 1.0 N A:CYS104 4.0 17.2 1.0 N A:VAL101 4.1 22.5 1.0 CB A:CYS104 4.2 20.2 1.0 O A:HOH695 4.2 49.1 1.0 O A:HOH558 4.3 28.3 1.0 O A:HOH717 4.3 46.4 1.0 CA A:PRO103 4.5 17.4 1.0 CA A:VAL102 4.6 17.2 1.0 OE1 A:GLU95 4.6 26.1 1.0 CA A:VAL101 4.6 20.1 1.0 N A:VAL102 4.6 20.1 1.0 C A:ASN100 4.6 29.0 1.0 CA A:ASN100 4.7 27.7 1.0 CB A:ASN100 4.7 31.5 1.0 CA A:GLY260 4.8 20.1 1.0 O A:HOH718 4.9 65.2 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