Sodium in PDB 1ez1: Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg, Amppnp, and Gar

The structure of Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg, Amppnp, and Gar, PDB code: 1ez1 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 (°)	61.800, 179.400, 75.300, 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, Amppnp, and Gar also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg, Amppnp, and Gar (pdb code 1ez1). 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, Amppnp, and Gar, PDB code: 1ez1:
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, Amppnp, and Gar


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, Amppnp, and Gar within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:13.6 occ:1.00 O A:HOH1670 2.3 38.3 1.0 O A:VAL101 2.4 9.7 1.0 O A:PRO103 2.4 14.8 1.0 ND2 A:ASN100 2.6 83.9 1.0 O A:HOH1189 2.7 21.0 1.0 O A:HOH1183 3.1 10.7 1.0 C A:PRO103 3.2 18.1 1.0 C A:VAL101 3.4 5.5 1.0 CG A:ASN100 3.4 46.0 1.0 OD1 A:ASN100 3.7 33.8 1.0 N A:VAL101 3.8 17.2 1.0 N A:CYS104 3.9 17.8 1.0 CA A:CYS104 3.9 9.3 1.0 N A:VAL102 4.2 12.1 1.0 CA A:PRO103 4.2 12.8 1.0 CA A:VAL101 4.2 17.3 1.0 CA A:VAL102 4.3 10.7 1.0 O A:HOH1227 4.3 24.7 1.0 CB A:CYS104 4.3 10.2 1.0 O A:HOH1287 4.3 32.9 1.0 O A:HOH1962 4.4 35.1 1.0 C A:ASN100 4.5 16.8 1.0 CB A:ASN100 4.6 19.7 1.0 CA A:ASN100 4.7 18.8 1.0 OE1 A:GLU95 4.7 23.3 1.0 CG2 A:VAL102 4.9 7.6 1.0

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


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, Amppnp, and Gar within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1002 b:18.9 occ:1.00 O B:VAL101 2.4 23.1 1.0 OD1 B:ASN100 2.4 69.0 1.0 O B:HOH1930 2.5 48.2 1.0 O B:PRO103 2.5 15.4 1.0 O B:HOH1453 2.8 23.7 1.0 O B:HOH1148 3.3 15.3 1.0 C B:VAL101 3.4 15.3 1.0 C B:PRO103 3.4 17.1 1.0 CG B:ASN100 3.7 24.7 1.0 N B:VAL101 3.8 15.6 1.0 O B:HOH1356 4.0 22.9 1.0 CA B:CYS104 4.0 12.2 1.0 N B:CYS104 4.0 10.9 1.0 O B:HOH1330 4.1 26.3 1.0 N B:VAL102 4.2 11.9 1.0 CA B:VAL101 4.2 15.9 1.0 CA B:VAL102 4.3 14.4 1.0 CA B:PRO103 4.4 15.0 1.0 CB B:CYS104 4.4 15.4 1.0 C B:ASN100 4.4 33.6 1.0 ND2 B:ASN100 4.4 38.8 1.0 CA B:ASN100 4.6 17.9 1.0 OE1 B:GLU95 4.6 21.0 1.0 O B:HOH2216 4.7 61.6 1.0 CB B:ASN100 4.7 20.6 1.0 O B:HOH1932 4.8 65.0 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