Magnesium in PDB 1kjj: Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S

The structure of Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S, PDB code: 1kjj 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 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.900, 179.300, 76.100, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S also contains other interesting chemical elements:

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

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

Magnesium binding site 1 out of 4 in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S


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 Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg393 b:46.6 occ:1.00 O3G A:AGS1 1.7 61.8 1.0 O A:HOH736 1.9 40.1 1.0 O2B A:AGS1 2.0 36.2 1.0 O A:HOH627 2.5 37.2 1.0 OE1 A:GLU279 2.8 30.4 1.0 OE2 A:GLU279 2.9 32.1 1.0 PG A:AGS1 3.2 71.4 1.0 CD A:GLU279 3.2 42.4 1.0 PB A:AGS1 3.3 42.0 1.0 O A:HOH497 3.5 37.6 1.0 O3B A:AGS1 3.7 67.0 1.0 O A:SER159 3.9 88.5 1.0 O2G A:AGS1 3.9 64.3 1.0 OE1 A:GLU84 4.0 58.7 1.0 MG A:MG394 4.1 30.0 1.0 O A:HOH425 4.1 43.6 1.0 CA A:SER160 4.1 76.6 1.0 O1B A:AGS1 4.1 37.4 1.0 NH2 A:ARG114 4.3 35.0 1.0 NH1 A:ARG114 4.3 21.6 1.0 CB A:SER160 4.3 84.0 1.0 O2A A:AGS1 4.4 30.2 1.0 S1G A:AGS1 4.4 61.9 1.0 O3A A:AGS1 4.5 25.1 1.0 CG A:GLU279 4.6 18.7 1.0 CZ A:ARG114 4.7 25.2 1.0 O A:HOH481 4.7 28.6 1.0 C A:SER159 4.8 85.7 1.0 PA A:AGS1 4.8 22.8 1.0 N A:SER161 4.9 75.7 1.0 N A:SER160 4.9 79.8 1.0 O1A A:AGS1 5.0 22.9 1.0 CD A:GLU84 5.0 0.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S


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 Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg394 b:30.0 occ:1.00 O2G A:AGS1 1.8 64.3 1.0 O2A A:AGS1 2.0 30.2 1.0 O A:HOH467 2.1 21.2 1.0 OE1 A:GLU279 2.1 30.4 1.0 OE1 A:GLU267 2.1 38.2 1.0 OE2 A:GLU267 2.5 36.3 1.0 CD A:GLU267 2.6 51.5 1.0 PG A:AGS1 2.9 71.4 1.0 CD A:GLU279 3.2 42.4 1.0 PA A:AGS1 3.4 22.8 1.0 O3B A:AGS1 3.4 67.0 1.0 O3G A:AGS1 3.5 61.8 1.0 O A:HOH649 3.8 55.8 1.0 O2B A:AGS1 3.9 36.2 1.0 CG A:GLU279 3.9 18.7 1.0 O A:HOH461 3.9 21.8 1.0 PB A:AGS1 4.0 42.0 1.0 MG A:MG393 4.1 46.6 1.0 O3A A:AGS1 4.1 25.1 1.0 CG A:GLU267 4.2 20.0 1.0 O1A A:AGS1 4.2 22.9 1.0 O A:HOH425 4.2 43.6 1.0 OE2 A:GLU279 4.3 32.1 1.0 O5' A:AGS1 4.3 20.6 1.0 S1G A:AGS1 4.3 61.9 1.0 O3' A:AGS1 4.4 20.0 1.0 O A:HOH514 4.5 36.8 1.0 C5' A:AGS1 4.5 22.9 1.0 NE2 A:HIS285 4.8 21.8 1.0 C3' A:AGS1 4.9 18.8 1.0 O A:HOH627 4.9 37.2 1.0 CB A:GLU267 4.9 15.7 1.0 O A:HOH793 5.0 30.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S


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 Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:40.6 occ:1.00 O B:HOH626 1.7 64.7 1.0 OE1 B:GLU279 2.1 35.9 1.0 O2B B:AGS395 2.1 41.0 1.0 O3G B:AGS395 2.3 28.9 1.0 OE2 B:GLU279 2.3 37.3 1.0 CD B:GLU279 2.5 33.2 1.0 O B:HOH479 2.8 37.9 1.0 PG B:AGS395 3.3 60.0 1.0 PB B:AGS395 3.4 56.9 1.0 O2G B:AGS395 3.5 32.9 1.0 O3B B:AGS395 3.7 70.0 1.0 O B:HOH465 3.8 32.6 1.0 MG B:MG394 3.9 39.9 1.0 OE1 B:GLU84 3.9 66.5 1.0 CG B:GLU279 4.0 35.5 1.0 O2A B:AGS395 4.1 62.6 1.0 O3A B:AGS395 4.3 28.5 1.0 NH2 B:ARG114 4.3 40.0 1.0 NH1 B:ARG114 4.3 27.2 1.0 O1B B:AGS395 4.4 51.3 1.0 O B:SER159 4.5 85.4 1.0 PA B:AGS395 4.6 36.9 1.0 CZ B:ARG114 4.6 47.1 1.0 O B:HOH509 4.6 45.4 1.0 OE1 B:GLU267 4.7 37.1 1.0 CB B:GLU279 4.8 21.9 1.0 CA B:SER160 4.8 80.6 1.0 S1G B:AGS395 4.8 60.0 1.0 CB B:SER160 4.9 82.9 1.0 O1A B:AGS395 4.9 29.7 1.0 CD B:GLU84 5.0 71.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S


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 Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:39.9 occ:1.00 OE2 B:GLU267 1.8 51.2 1.0 O2A B:AGS395 1.9 62.6 1.0 O2G B:AGS395 2.0 32.9 1.0 OE1 B:GLU279 2.0 35.9 1.0 O B:HOH527 2.4 30.1 1.0 CD B:GLU267 2.6 79.9 1.0 OE1 B:GLU267 2.6 37.1 1.0 CD B:GLU279 2.9 33.2 1.0 PG B:AGS395 3.3 60.0 1.0 CG B:GLU279 3.3 35.5 1.0 PA B:AGS395 3.4 36.9 1.0 O B:HOH434 3.7 29.5 1.0 O3B B:AGS395 3.8 70.0 1.0 MG B:MG393 3.9 40.6 1.0 CG B:GLU267 4.0 17.0 1.0 O3G B:AGS395 4.0 28.9 1.0 OE2 B:GLU279 4.1 37.3 1.0 O B:HOH465 4.2 32.6 1.0 O3A B:AGS395 4.2 28.5 1.0 O5' B:AGS395 4.2 32.9 1.0 O1A B:AGS395 4.3 29.7 1.0 O2B B:AGS395 4.3 41.0 1.0 O3' B:AGS395 4.3 38.4 1.0 C5' B:AGS395 4.4 27.7 1.0 PB B:AGS395 4.4 56.9 1.0 CB B:GLU267 4.5 15.6 1.0 S1G B:AGS395 4.5 60.0 1.0 C3' B:AGS395 4.7 46.0 1.0 O B:HOH461 4.8 34.1 1.0 CB B:GLU279 4.9 21.9 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