Sodium in PDB 1eyz: Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp

The structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp, PDB code: 1eyz was solved by J.B.Thoden, S.Firestine, A.Nixon, 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 (°)	62.300, 179.500, 75.700, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

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

Sodium binding site 1 out of 2 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na961 b:21.6 occ:1.00 O A:VAL101 2.4 12.0 1.0 ND2 A:ASN100 2.5 49.6 1.0 O A:PRO103 2.5 20.0 1.0 O A:HOH1162 2.6 22.6 1.0 O A:HOH1963 2.7 66.4 1.0 O A:HOH1155 3.0 18.5 1.0 C A:PRO103 3.2 17.4 1.0 C A:VAL101 3.4 14.1 1.0 CG A:ASN100 3.6 47.7 1.0 N A:VAL101 3.8 15.8 1.0 N A:CYS104 3.8 18.1 1.0 CA A:CYS104 3.9 12.4 1.0 O A:HOH1265 4.2 21.7 1.0 OD1 A:ASN100 4.2 30.6 1.0 CA A:VAL102 4.2 13.1 1.0 CB A:CYS104 4.2 12.8 1.0 N A:VAL102 4.2 15.6 1.0 CA A:PRO103 4.3 12.6 1.0 CA A:VAL101 4.3 13.2 1.0 O A:HOH1185 4.3 26.8 1.0 C A:ASN100 4.4 20.5 1.0 OE1 A:GLU95 4.5 18.3 1.0 CA A:ASN100 4.6 18.0 1.0 O A:HOH1262 4.6 37.5 1.0 CB A:ASN100 4.7 16.7 1.0 CG2 A:VAL102 4.9 10.8 1.0 O A:HOH2083 4.9 51.9 1.0

Sodium binding site 2 out of 2 in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na960 b:37.5 occ:1.00 O B:HOH1563 2.4 28.7 1.0 O A:HOH1288 2.5 21.4 1.0 O B:ALA53 2.6 18.3 1.0 O B:HOH2078 2.6 36.5 1.0 O A:ALA53 2.7 15.2 1.0 O B:HIS51 3.2 15.5 1.0 C A:ALA53 3.6 17.6 1.0 C B:ALA53 3.8 19.8 1.0 O A:HOH1293 3.9 27.4 1.0 N A:ALA53 3.9 15.8 1.0 O A:HIS51 4.0 14.8 1.0 C B:HIS51 4.0 21.1 1.0 N B:ALA53 4.0 10.9 1.0 O B:HOH1464 4.2 19.2 1.0 O B:MET50 4.2 18.6 1.0 C A:VAL52 4.2 23.1 1.0 C B:VAL52 4.3 14.7 1.0 CA A:ALA53 4.4 12.0 1.0 CA B:VAL52 4.4 19.9 1.0 O B:HOH1512 4.4 44.5 1.0 N A:HIS54 4.5 13.0 1.0 CA A:VAL52 4.5 11.0 1.0 CA A:HIS54 4.5 7.0 1.0 N B:VAL52 4.5 16.6 1.0 CA B:ALA53 4.6 7.4 1.0 O A:HOH1118 4.7 16.8 1.0 C A:HIS51 4.7 11.1 1.0 O A:HIS54 4.8 14.3 1.0 O A:VAL52 4.8 16.0 1.0 N B:HIS54 4.8 16.9 1.0 O B:HIS54 4.9 20.8 1.0 C A:HIS54 4.9 9.3 1.0 O A:MET50 4.9 13.2 1.0 N A:VAL52 4.9 12.6 1.0 O B:HOH1746 5.0 24.5 1.0 CA B:HIS54 5.0 12.3 1.0 CA B:HIS51 5.0 6.1 1.0

J.B.Thoden, S.Firestine, A.Nixon, S.J.Benkovic, H.M.Holden. Molecular Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase. Biochemistry V. 39 8791 2000.
ISSN: ISSN 0006-2960
PubMed: 10913290
DOI: 10.1021/BI000926J