Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg, Amppnp, and Gar, PDB code: 1ez1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg401 b:15.3 occ:1.00 O3G A:ANP400 1.9 15.3 1.0 O2B A:ANP400 2.1 9.7 1.0 O A:HOH1164 2.1 13.1 1.0 O A:HOH1251 2.2 13.2 1.0 OE1 A:GLU279 2.2 11.5 1.0 OE2 A:GLU279 2.3 13.5 1.0 CD A:GLU279 2.6 10.6 1.0 PG A:ANP400 3.2 15.1 1.0 PB A:ANP400 3.3 12.8 1.0 OG A:SER160 3.4 55.0 1.0 N3B A:ANP400 3.5 15.8 1.0 O2G A:ANP400 3.6 17.4 1.0 MG A:MG402 3.9 11.4 1.0 O A:HOH1216 3.9 34.1 1.0 O2A A:ANP400 4.0 17.9 1.0 CG A:GLU279 4.0 9.1 1.0 O A:HOH1515 4.1 27.8 1.0 NH1 A:ARG114 4.1 12.7 1.0 O3A A:ANP400 4.3 14.0 1.0 NH2 A:ARG114 4.3 11.6 1.0 O1B A:ANP400 4.3 11.3 1.0 O A:HOH1172 4.3 10.0 1.0 OE2 A:GLU84 4.3 23.9 1.0 O A:SER159 4.4 39.9 1.0 O1G A:ANP400 4.5 13.9 1.0 OE1 A:GLU84 4.5 44.0 1.0 PA A:ANP400 4.5 12.9 1.0 CZ A:ARG114 4.6 11.3 1.0 CB A:SER160 4.7 43.0 1.0 CB A:GLU279 4.7 11.2 1.0 OE1 A:GLU267 4.8 13.3 1.0 O1A A:ANP400 4.8 13.1 1.0 CA A:SER160 4.8 90.2 1.0 CD A:GLU84 4.9 0.0 1.0

Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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 A:Mg402 b:11.4 occ:1.00 O2A A:ANP400 2.0 17.9 1.0 O2G A:ANP400 2.0 17.4 1.0 OE2 A:GLU267 2.0 13.2 1.0 OE1 A:GLU279 2.1 11.5 1.0 OE1 A:GLU267 2.1 13.3 1.0 O A:HOH1106 2.2 9.8 1.0 CD A:GLU267 2.4 12.5 1.0 CD A:GLU279 3.1 10.6 1.0 PG A:ANP400 3.2 15.1 1.0 PA A:ANP400 3.4 12.9 1.0 N3B A:ANP400 3.6 15.8 1.0 CG A:GLU279 3.7 9.1 1.0 O3G A:ANP400 3.8 15.3 1.0 MG A:MG401 3.9 15.3 1.0 CG A:GLU267 3.9 9.9 1.0 O2B A:ANP400 4.0 9.7 1.0 O3A A:ANP400 4.1 14.0 1.0 O A:HOH1197 4.1 16.2 1.0 O A:HOH1216 4.1 34.1 1.0 PB A:ANP400 4.2 12.8 1.0 OE2 A:GLU279 4.2 13.5 1.0 O1A A:ANP400 4.3 13.1 1.0 O A:HOH1253 4.3 27.6 1.0 O5' A:ANP400 4.3 12.8 1.0 O A:HOH1141 4.4 13.0 1.0 C5' A:ANP400 4.4 11.2 1.0 O3' A:ANP400 4.5 12.9 1.0 O1G A:ANP400 4.5 13.9 1.0 NE2 A:HIS285 4.6 15.4 1.0 CB A:GLU267 4.7 7.6 1.0 O A:HOH1251 4.8 13.2 1.0 C3' A:ANP400 4.9 10.5 1.0

Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg401 b:65.9 occ:1.00 O3G B:ANP1003 2.4 49.3 1.0 OE2 B:GLU279 2.6 37.6 1.0 O B:HOH1616 2.6 48.7 1.0 OE1 B:GLU279 3.1 52.2 1.0 CD B:GLU279 3.2 33.8 1.0 O2B B:ANP1003 3.3 75.7 1.0 O B:HOH1446 3.8 34.9 1.0 PG B:ANP1003 4.0 71.9 1.0 OE1 B:GLU84 4.0 47.9 1.0 O2G B:ANP1003 4.4 79.3 1.0 MG B:MG402 4.5 65.0 1.0 CG B:GLU279 4.5 53.9 1.0 PB B:ANP1003 4.6 94.3 1.0 OE1 B:GLU267 4.6 69.1 1.0 N3B B:ANP1003 4.7 0.0 1.0 CD B:GLU84 4.8 0.0 1.0 O1G B:ANP1003 4.9 93.1 1.0

Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg402 b:65.0 occ:1.00 O2A B:ANP1003 2.0 0.0 1.0 OE1 B:GLU279 2.0 52.2 1.0 O2G B:ANP1003 2.0 79.3 1.0 OE2 B:GLU267 2.3 65.1 1.0 O B:HOH2183 2.3 39.9 1.0 OE1 B:GLU267 2.5 69.1 1.0 CD B:GLU267 2.7 0.0 1.0 CD B:GLU279 3.1 33.8 1.0 PG B:ANP1003 3.2 71.9 1.0 PA B:ANP1003 3.5 74.7 1.0 O3G B:ANP1003 3.6 49.3 1.0 N3B B:ANP1003 3.8 0.0 1.0 CG B:GLU279 3.9 53.9 1.0 C5' B:ANP1003 4.1 31.2 1.0 OE2 B:GLU279 4.2 37.6 1.0 O3' B:ANP1003 4.2 45.8 1.0 O1A B:ANP1003 4.2 41.9 1.0 CG B:GLU267 4.2 26.9 1.0 O3A B:ANP1003 4.2 59.6 1.0 O5' B:ANP1003 4.3 71.1 1.0 O B:HOH1996 4.4 41.2 1.0 O B:HOH1329 4.4 24.4 1.0 PB B:ANP1003 4.4 94.3 1.0 O1G B:ANP1003 4.4 93.1 1.0 O2B B:ANP1003 4.5 75.7 1.0 C3' B:ANP1003 4.5 31.9 1.0 MG B:MG401 4.5 65.9 1.0 O B:HOH1469 4.6 47.5 1.0 NE2 B:HIS285 4.8 23.8 1.0 C4' B:ANP1003 4.8 0.0 1.0 O B:HOH1324 5.0 35.9 1.0 CB B:GLU267 5.0 13.6 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