Magnesium 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:

Chlorine	(Cl)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Escherichia Coli Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg and Amppnp, PDB code: 1eyz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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:Mg401 b:18.5 occ:1.00 O3G A:ANP400 1.9 16.7 1.0 O2B A:ANP400 2.0 15.8 1.0 O A:HOH1119 2.1 15.6 1.0 OE1 A:GLU279 2.2 15.6 1.0 OE2 A:GLU279 2.3 16.1 1.0 O A:HOH1131 2.3 23.1 1.0 CD A:GLU279 2.5 15.3 1.0 PG A:ANP400 3.2 18.0 1.0 PB A:ANP400 3.2 16.7 1.0 N3B A:ANP400 3.5 22.2 1.0 O2G A:ANP400 3.6 13.3 1.0 MG A:MG402 3.8 15.4 1.0 O A:HOH1229 3.8 20.0 1.0 O2A A:ANP400 3.9 15.8 1.0 O A:HOH1175 4.0 22.5 1.0 CG A:GLU279 4.0 9.4 1.0 NH1 A:ARG114 4.1 13.8 1.0 O A:HOH1824 4.2 49.4 1.0 O1B A:ANP400 4.2 21.6 1.0 O3A A:ANP400 4.3 13.5 1.0 O A:HOH1149 4.4 15.5 1.0 O A:SER159 4.4 38.3 1.0 NH2 A:ARG114 4.4 16.9 1.0 O1G A:ANP400 4.4 12.6 1.0 OE1 A:GLU84 4.5 28.7 1.0 PA A:ANP400 4.5 13.9 1.0 OE2 A:GLU84 4.5 24.4 1.0 O1A A:ANP400 4.6 13.6 1.0 CZ A:ARG114 4.7 11.7 1.0 CA A:SER160 4.7 30.1 1.0 OE1 A:GLU267 4.8 14.8 1.0 CB A:SER160 4.8 87.5 1.0 CB A:GLU279 4.9 8.6 1.0 CD A:GLU84 5.0 0.0 1.0

Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg 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 A:Mg402 b:15.4 occ:1.00 O2A A:ANP400 2.0 15.8 1.0 O2G A:ANP400 2.0 13.3 1.0 OE1 A:GLU279 2.1 15.6 1.0 OE2 A:GLU267 2.1 14.1 1.0 O A:HOH1113 2.2 15.1 1.0 OE1 A:GLU267 2.2 14.8 1.0 CD A:GLU267 2.5 10.2 1.0 CD A:GLU279 3.1 15.3 1.0 PG A:ANP400 3.2 18.0 1.0 PA A:ANP400 3.5 13.9 1.0 N3B A:ANP400 3.6 22.2 1.0 CG A:GLU279 3.7 9.4 1.0 O3G A:ANP400 3.7 16.7 1.0 MG A:MG401 3.8 18.5 1.0 CG A:GLU267 4.0 13.1 1.0 O2B A:ANP400 4.0 15.8 1.0 O A:HOH1143 4.2 26.3 1.0 O3A A:ANP400 4.2 13.5 1.0 OE2 A:GLU279 4.2 16.1 1.0 PB A:ANP400 4.2 16.7 1.0 O A:HOH1229 4.2 20.0 1.0 O1A A:ANP400 4.2 13.6 1.0 O A:HOH1331 4.3 41.2 1.0 O A:HOH1174 4.3 15.5 1.0 O5' A:ANP400 4.3 18.3 1.0 O3' A:ANP400 4.4 13.6 1.0 O1G A:ANP400 4.5 12.6 1.0 C5' A:ANP400 4.6 19.4 1.0 O A:HOH1131 4.6 23.1 1.0 O A:HOH1258 4.6 32.7 1.0 NE2 A:HIS285 4.8 17.4 1.0 CB A:GLU267 4.8 10.2 1.0

Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg403 b:29.6 occ:1.00 O A:HOH1143 2.1 26.3 1.0 O A:HOH1792 2.2 29.5 1.0 O A:HOH1794 2.3 30.6 1.0 O1G A:ANP400 2.3 12.6 1.0 OD2 A:ASP286 2.6 31.0 1.0 O A:HOH1258 3.0 32.7 1.0 CG A:ASP286 3.2 14.2 1.0 OD1 A:ASP286 3.3 14.8 1.0 PG A:ANP400 3.4 18.0 1.0 O2G A:ANP400 3.5 13.3 1.0 O A:HOH1394 3.6 38.0 1.0 O A:HOH1144 3.8 19.3 1.0 OG A:SER161 4.0 63.2 1.0 O A:HOH1175 4.2 22.5 1.0 O A:HOH1331 4.3 41.2 1.0 O3G A:ANP400 4.4 16.7 1.0 O A:HOH1173 4.5 23.6 1.0 CB A:ASP286 4.5 15.2 1.0 N3B A:ANP400 4.6 22.2 1.0 NH2 A:ARG363 4.6 23.8 1.0 CA A:SER161 4.8 26.4 1.0 O A:HOH1138 4.8 33.7 1.0 CB A:SER161 4.9 71.4 1.0 N A:SER161 4.9 27.6 1.0

Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg401 b:25.1 occ:1.00 O B:HOH1615 1.9 31.6 1.0 O2B B:ANP961 2.0 35.7 1.0 O3G B:ANP961 2.0 24.7 1.0 OE2 B:GLU279 2.2 22.4 1.0 OE1 B:GLU279 2.4 28.1 1.0 O B:HOH1885 2.5 32.5 1.0 CD B:GLU279 2.6 25.1 1.0 PB B:ANP961 3.3 37.8 1.0 PG B:ANP961 3.3 36.6 1.0 N3B B:ANP961 3.7 36.3 1.0 O B:HOH1626 3.8 49.8 1.0 OE1 B:GLU84 3.8 47.9 1.0 O B:HOH1542 3.8 27.1 1.0 NH2 B:ARG114 3.8 40.0 1.0 MG B:MG402 3.9 23.9 1.0 O2G B:ANP961 3.9 23.7 1.0 NH1 B:ARG114 4.1 25.6 1.0 O2A B:ANP961 4.1 33.2 1.0 CG B:GLU279 4.1 19.3 1.0 O3A B:ANP961 4.2 18.6 1.0 O B:HOH1661 4.2 34.6 1.0 O B:SER159 4.3 87.0 1.0 O1B B:ANP961 4.3 36.9 1.0 CZ B:ARG114 4.3 26.9 1.0 O1G B:ANP961 4.5 50.7 1.0 PA B:ANP961 4.6 27.9 1.0 O B:HOH1528 4.6 30.4 1.0 O1A B:ANP961 4.7 20.2 1.0 CA B:SER160 4.8 75.9 1.0 CD B:GLU84 4.9 21.3 1.0 CB B:SER160 4.9 41.5 1.0 O B:HOH1505 4.9 24.4 1.0 CB B:GLU279 4.9 13.3 1.0

Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg402 b:23.9 occ:1.00 O2G B:ANP961 1.8 23.7 1.0 O2A B:ANP961 2.0 33.2 1.0 OE1 B:GLU279 2.0 28.1 1.0 O B:HOH1473 2.0 21.5 1.0 OE2 B:GLU267 2.1 23.1 1.0 OE1 B:GLU267 2.4 24.2 1.0 CD B:GLU267 2.6 30.1 1.0 PG B:ANP961 3.0 36.6 1.0 CD B:GLU279 3.1 25.1 1.0 PA B:ANP961 3.4 27.9 1.0 O3G B:ANP961 3.4 24.7 1.0 N3B B:ANP961 3.5 36.3 1.0 CG B:GLU279 3.7 19.3 1.0 O B:HOH1542 3.8 27.1 1.0 MG B:MG401 3.9 25.1 1.0 O B:HOH2064 4.1 60.4 1.0 O3A B:ANP961 4.1 18.6 1.0 PB B:ANP961 4.1 37.8 1.0 O2B B:ANP961 4.1 35.7 1.0 CG B:GLU267 4.1 21.7 1.0 OE2 B:GLU279 4.2 22.4 1.0 O1G B:ANP961 4.2 50.7 1.0 O B:HOH1555 4.3 22.5 1.0 O5' B:ANP961 4.3 28.7 1.0 O1A B:ANP961 4.3 20.2 1.0 C5' B:ANP961 4.4 20.1 1.0 O3' B:ANP961 4.4 26.7 1.0 NE2 B:HIS285 4.8 16.5 1.0 C3' B:ANP961 4.8 29.8 1.0 O B:HOH1885 4.9 32.5 1.0 CB B:GLU267 4.9 14.7 1.0 O B:HOH1579 5.0 38.6 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