Magnesium in PDB 1kjq: Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp, PDB code: 1kjq 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 / 1.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.350, 179.340, 75.620, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp (pdb code 1kjq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp, PDB code: 1kjq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg393 b:12.9 occ:1.00 O A:HOH841 1.7 14.2 1.0 O3B A:ADP1 1.8 13.3 1.0 O2A A:ADP1 1.8 14.2 1.0 OE2 A:GLU267 1.9 15.3 1.0 OE1 A:GLU279 1.9 14.6 1.0 O A:HOH485 1.9 14.8 1.0 CD A:GLU267 2.9 16.8 1.0 CD A:GLU279 3.0 12.7 1.0 PA A:ADP1 3.1 12.2 1.0 PB A:ADP1 3.1 15.7 1.0 OE1 A:GLU267 3.2 14.0 1.0 O3A A:ADP1 3.4 14.7 1.0 CG A:GLU279 3.7 9.9 1.0 O A:HOH691 3.8 37.5 1.0 O2B A:ADP1 3.9 21.9 1.0 O A:HOH785 3.9 59.7 1.0 O A:HOH479 4.0 14.9 1.0 OE2 A:GLU279 4.0 14.9 1.0 O1A A:ADP1 4.2 14.3 1.0 O5' A:ADP1 4.2 12.7 1.0 O A:HOH595 4.2 23.4 1.0 CG A:GLU267 4.2 11.4 1.0 O1B A:ADP1 4.2 17.0 1.0 C5' A:ADP1 4.3 14.8 1.0 NE2 A:HIS285 4.3 10.2 1.0 O A:HOH528 4.4 28.7 1.0 O3' A:ADP1 4.5 11.7 1.0 O A:HOH442 4.7 13.2 1.0 CB A:GLU267 4.8 8.9 1.0 CE1 A:HIS285 5.0 9.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:19.7 occ:1.00 O3B B:ADP397 1.7 24.4 1.0 O B:HOH767 1.7 20.9 1.0 OE1 B:GLU279 1.9 7.6 0.5 OE1 B:GLU267 1.9 12.1 0.5 O2A B:ADP397 2.0 23.7 1.0 O B:HOH470 2.1 21.4 1.0 CD B:GLU267 2.9 10.2 0.5 CD B:GLU279 2.9 3.9 0.5 PB B:ADP397 3.1 29.4 1.0 PA B:ADP397 3.2 26.1 1.0 OE2 B:GLU267 3.3 12.3 0.5 O3A B:ADP397 3.3 32.2 1.0 CG B:GLU279 3.8 7.7 0.5 O B:HOH728 3.8 27.1 1.0 O2B B:ADP397 3.8 34.0 1.0 OE2 B:GLU279 3.9 8.2 0.5 O B:HOH505 4.0 20.1 1.0 CG B:GLU267 4.2 13.2 0.5 C5' B:ADP397 4.2 19.0 1.0 O5' B:ADP397 4.2 33.4 1.0 O1B B:ADP397 4.2 29.2 1.0 CG B:GLU267 4.3 13.8 0.5 O1A B:ADP397 4.3 22.2 1.0 O B:HOH582 4.4 34.4 1.0 O3' B:ADP397 4.4 19.0 1.0 NE2 B:HIS285 4.4 20.1 1.0 OE2 B:GLU279 4.6 0.0 0.5 CD B:GLU267 4.8 49.6 0.5 C3' B:ADP397 4.9 16.1 1.0 CB B:GLU267 4.9 11.8 0.5 CB B:GLU267 5.0 12.8 0.5

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