Magnesium in PDB 1kj9: Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp, PDB code: 1kj9 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 / 1.60
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 Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp (pdb code 1kj9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp, PDB code: 1kj9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg393 b:11.6 occ:1.00 O3G A:ATP1 1.9 9.9 1.0 O A:HOH417 2.0 13.7 1.0 O1 A:EDO403 2.1 16.0 1.0 O2B A:ATP1 2.1 11.8 1.0 OE2 A:GLU279 2.2 12.9 1.0 OE1 A:GLU279 2.2 10.8 1.0 CD A:GLU279 2.5 11.7 1.0 C1 A:EDO403 3.1 17.4 1.0 PG A:ATP1 3.1 13.1 1.0 PB A:ATP1 3.3 13.2 1.0 O3B A:ATP1 3.5 15.4 1.0 O2G A:ATP1 3.6 9.6 1.0 C2 A:EDO403 3.7 13.3 1.0 MG A:MG394 3.8 10.8 1.0 O A:HOH434 4.0 13.2 1.0 CG A:GLU279 4.0 9.1 1.0 O2A A:ATP1 4.2 12.2 1.0 NH1 A:ARG114 4.2 11.3 1.0 OE1 A:GLU84 4.3 18.8 1.0 O1B A:ATP1 4.3 14.1 1.0 OE2 A:GLU84 4.3 17.1 1.0 O A:SER159 4.3 21.2 1.0 O3A A:ATP1 4.3 13.3 1.0 O2 A:EDO403 4.4 21.5 1.0 O A:HOH459 4.4 14.7 1.0 O1G A:ATP1 4.4 14.6 1.0 NH2 A:ARG114 4.5 11.7 1.0 PA A:ATP1 4.6 12.0 1.0 CD A:GLU84 4.7 30.1 1.0 CZ A:ARG114 4.8 13.5 1.0 CA A:SER160 4.8 14.7 1.0 O1A A:ATP1 4.8 12.3 1.0 OE1 A:GLU267 4.8 16.9 1.0 CB A:GLU279 4.8 8.3 1.0 CB A:SER160 4.9 23.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg394 b:10.8 occ:1.00 O2A A:ATP1 2.0 12.2 1.0 OE1 A:GLU279 2.0 10.8 1.0 O2G A:ATP1 2.0 9.6 1.0 O A:HOH419 2.1 11.3 1.0 OE2 A:GLU267 2.1 9.7 1.0 OE1 A:GLU267 2.2 16.9 1.0 CD A:GLU267 2.5 9.4 1.0 CD A:GLU279 3.0 11.7 1.0 PG A:ATP1 3.2 13.1 1.0 PA A:ATP1 3.5 12.0 1.0 O3B A:ATP1 3.5 15.4 1.0 CG A:GLU279 3.7 9.1 1.0 O3G A:ATP1 3.8 9.9 1.0 MG A:MG393 3.8 11.6 1.0 CG A:GLU267 4.0 11.9 1.0 C2 A:EDO403 4.1 13.3 1.0 O2B A:ATP1 4.1 11.8 1.0 OE2 A:GLU279 4.1 12.9 1.0 O3A A:ATP1 4.1 13.3 1.0 O A:HOH474 4.2 19.2 1.0 PB A:ATP1 4.2 13.2 1.0 O A:HOH455 4.2 13.9 1.0 O A:HOH509 4.2 20.3 1.0 O1A A:ATP1 4.3 12.3 1.0 O5' A:ATP1 4.4 13.3 1.0 O3' A:ATP1 4.4 11.5 1.0 O1G A:ATP1 4.5 14.6 1.0 C5' A:ATP1 4.5 12.9 1.0 O A:HOH576 4.6 31.6 1.0 C1 A:EDO403 4.6 17.4 1.0 NE2 A:HIS285 4.7 10.0 1.0 CB A:GLU267 4.7 11.4 1.0 O1 A:EDO403 4.8 16.0 1.0 C3' A:ATP1 5.0 12.5 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg395 b:18.2 occ:1.00 O A:HOH478 2.1 16.4 1.0 OD2 A:ASP286 2.1 15.9 1.0 O A:HOH549 2.2 21.1 1.0 O A:HOH474 2.2 19.2 1.0 O A:HOH482 2.2 19.9 1.0 O1G A:ATP1 2.2 14.6 1.0 CG A:ASP286 3.1 18.1 1.0 PG A:ATP1 3.4 13.1 1.0 OD1 A:ASP286 3.4 12.4 1.0 O2G A:ATP1 3.5 9.6 1.0 O A:HOH435 4.0 13.8 1.0 O A:HOH509 4.1 20.3 1.0 O A:HOH434 4.2 13.2 1.0 O A:HOH451 4.3 21.7 1.0 OD1 A:ASP229 4.3 27.6 1.0 NH2 A:ARG363 4.3 16.4 1.0 O3G A:ATP1 4.4 9.9 1.0 OG A:SER161 4.4 24.0 1.0 CB A:ASP286 4.4 10.2 1.0 O A:HOH576 4.4 31.6 1.0 O3B A:ATP1 4.5 15.4 1.0 N A:SER161 4.5 14.1 1.0 CA A:SER161 4.6 21.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:25.3 occ:1.00 O B:HOH502 1.7 22.5 1.0 O3G B:ATP395 2.0 25.3 1.0 O2B B:ATP395 2.1 29.1 1.0 O B:HOH447 2.2 23.3 1.0 OE2 B:GLU279 2.3 21.4 1.0 OE1 B:GLU279 2.4 24.9 1.0 CD B:GLU279 2.6 23.8 1.0 PG B:ATP395 3.2 29.8 1.0 PB B:ATP395 3.3 35.4 1.0 O3B B:ATP395 3.6 34.7 1.0 O B:HOH684 3.6 47.9 1.0 O2G B:ATP395 3.7 19.7 1.0 O B:HOH473 4.0 23.1 1.0 MG B:MG394 4.0 19.8 1.0 OE2 B:GLU84 4.1 45.3 1.0 CG B:GLU279 4.1 17.0 1.0 NH2 B:ARG114 4.1 34.9 1.0 NH1 B:ARG114 4.2 25.9 1.0 O2A B:ATP395 4.2 31.8 1.0 O3A B:ATP395 4.3 18.5 1.0 O B:SER159 4.3 42.6 1.0 O1B B:ATP395 4.3 35.9 1.0 O B:HOH489 4.4 33.4 1.0 O B:HOH504 4.4 30.6 1.0 O1G B:ATP395 4.5 38.5 1.0 CZ B:ARG114 4.5 32.6 1.0 PA B:ATP395 4.7 28.6 1.0 O1A B:ATP395 4.8 25.4 1.0 CA B:SER160 4.9 46.2 1.0 CB B:GLU279 4.9 15.2 1.0 O B:HOH529 4.9 30.3 1.0 CB B:SER160 4.9 39.8 1.0 OE1 B:GLU267 5.0 19.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase Complexed with Mg-Atp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:19.8 occ:1.00 O2G B:ATP395 1.9 19.7 1.0 O2A B:ATP395 2.0 31.8 1.0 OE2 B:GLU267 2.1 19.7 1.0 OE1 B:GLU279 2.1 24.9 1.0 O B:HOH557 2.1 21.6 1.0 OE1 B:GLU267 2.3 19.8 1.0 CD B:GLU267 2.5 21.0 1.0 CD B:GLU279 3.1 23.8 1.0 PG B:ATP395 3.2 29.8 1.0 PA B:ATP395 3.5 28.6 1.0 O3B B:ATP395 3.7 34.7 1.0 CG B:GLU279 3.8 17.0 1.0 O3G B:ATP395 3.9 25.3 1.0 O B:HOH473 3.9 23.1 1.0 CG B:GLU267 4.0 11.1 1.0 MG B:MG393 4.0 25.3 1.0 O3A B:ATP395 4.1 18.5 1.0 OE2 B:GLU279 4.2 21.4 1.0 PB B:ATP395 4.2 35.4 1.0 O B:HOH476 4.3 20.0 1.0 C5' B:ATP395 4.3 33.0 1.0 O B:HOH522 4.3 37.2 1.0 O2B B:ATP395 4.3 29.1 1.0 O3' B:ATP395 4.3 33.5 1.0 O5' B:ATP395 4.3 27.1 1.0 O1A B:ATP395 4.3 25.4 1.0 O1G B:ATP395 4.4 38.5 1.0 C3' B:ATP395 4.7 27.2 1.0 NE2 B:HIS285 4.7 16.9 1.0 CB B:GLU267 4.8 13.5 1.0 O B:HOH447 4.9 23.3 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