Magnesium in PDB 1kji: Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp, PDB code: 1kji 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 (°)	62.200, 179.200, 76.200, 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-Amppcp also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp (pdb code 1kji). 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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp, PDB code: 1kji:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg393 b:28.6 occ:1.00 O A:HOH509 1.8 29.3 1.0 O2B A:ACP1 2.0 25.3 1.0 O3G A:ACP1 2.0 22.7 1.0 OE1 A:GLU279 2.4 23.9 1.0 OE2 A:GLU279 2.5 30.2 1.0 O A:HOH536 2.5 28.6 1.0 CD A:GLU279 2.7 37.2 1.0 PB A:ACP1 3.2 32.6 1.0 PG A:ACP1 3.2 34.6 1.0 C3B A:ACP1 3.6 41.1 1.0 O2G A:ACP1 3.8 38.1 1.0 O A:HOH501 3.8 31.0 1.0 MG A:MG394 3.9 30.5 1.0 NH1 A:ARG114 4.1 22.7 1.0 O1B A:ACP1 4.1 41.5 1.0 O A:SER159 4.1 98.8 1.0 CG A:GLU279 4.2 16.1 1.0 O2A A:ACP1 4.3 25.6 1.0 O A:HOH644 4.3 42.4 1.0 NH2 A:ARG114 4.3 35.0 1.0 O3A A:ACP1 4.4 28.9 1.0 OE1 A:GLU84 4.4 63.5 1.0 O A:HOH466 4.4 26.8 1.0 O1G A:ACP1 4.5 34.1 1.0 OE2 A:GLU84 4.5 35.3 1.0 CZ A:ARG114 4.6 22.8 1.0 CA A:SER160 4.7 86.6 1.0 PA A:ACP1 4.7 21.1 1.0 CD A:GLU84 4.8 56.8 1.0 O1A A:ACP1 4.8 23.0 1.0 O A:HOH739 4.9 33.9 1.0 CB A:SER160 4.9 97.3 1.0 CB A:GLU279 5.0 12.7 1.0 OE1 A:GLU267 5.0 35.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg394 b:30.5 occ:1.00 O2A A:ACP1 2.1 25.6 1.0 O2G A:ACP1 2.1 38.1 1.0 OE1 A:GLU279 2.1 23.9 1.0 O A:HOH465 2.2 21.5 1.0 OE1 A:GLU267 2.2 35.4 1.0 OE2 A:GLU267 2.4 30.9 1.0 CD A:GLU267 2.6 41.0 1.0 CD A:GLU279 3.2 37.2 1.0 PG A:ACP1 3.2 34.6 1.0 C3B A:ACP1 3.5 41.1 1.0 PA A:ACP1 3.5 21.1 1.0 O3G A:ACP1 3.8 22.7 1.0 O A:HOH563 3.8 33.3 1.0 CG A:GLU279 3.8 16.1 1.0 O2B A:ACP1 3.9 25.3 1.0 MG A:MG393 3.9 28.6 1.0 PB A:ACP1 4.0 32.6 1.0 O A:HOH501 4.0 31.0 1.0 O3A A:ACP1 4.1 28.9 1.0 O A:HOH592 4.1 42.2 1.0 CG A:GLU267 4.2 14.0 1.0 OE2 A:GLU279 4.2 30.2 1.0 O A:HOH516 4.2 25.6 1.0 O1A A:ACP1 4.3 23.0 1.0 O5' A:ACP1 4.4 24.1 1.0 O1G A:ACP1 4.4 34.1 1.0 C5' A:ACP1 4.5 25.1 1.0 O3' A:ACP1 4.5 20.8 1.0 NE2 A:HIS285 4.7 21.9 1.0 CB A:GLU267 4.9 13.9 1.0 O A:HOH536 5.0 28.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:39.4 occ:1.00 O B:HOH547 1.7 37.2 1.0 O2B B:ACP396 2.1 38.6 1.0 O3G B:ACP396 2.1 43.2 1.0 OE1 B:GLU279 2.1 29.6 1.0 OE2 B:GLU279 2.3 50.9 1.0 CD B:GLU279 2.5 33.5 1.0 O B:HOH470 2.8 41.3 1.0 PG B:ACP396 3.2 43.1 1.0 PB B:ACP396 3.3 39.3 1.0 O2G B:ACP396 3.5 62.3 1.0 C3B B:ACP396 3.7 98.3 1.0 MG B:MG394 3.8 55.8 1.0 O B:HOH526 3.9 35.9 1.0 CG B:GLU279 4.0 25.7 1.0 O2A B:ACP396 4.0 47.1 1.0 NH1 B:ARG114 4.1 30.4 1.0 NH2 B:ARG114 4.2 39.0 1.0 O3A B:ACP396 4.2 33.6 1.0 O B:HOH520 4.2 38.9 1.0 O B:SER159 4.3 0.0 1.0 O1B B:ACP396 4.4 54.0 1.0 OE2 B:GLU84 4.4 0.0 1.0 PA B:ACP396 4.4 36.1 1.0 CZ B:ARG114 4.5 68.9 1.0 O1G B:ACP396 4.5 54.0 1.0 O1A B:ACP396 4.5 39.6 1.0 O B:HOH557 4.6 34.0 1.0 OE1 B:GLU84 4.8 0.0 1.0 CB B:GLU279 4.8 22.0 1.0 CA B:SER160 4.8 87.9 1.0 OE1 B:GLU267 4.8 39.7 1.0 CB B:SER160 4.9 92.1 1.0 O B:HOH491 4.9 43.4 1.0 CD B:GLU84 5.0 52.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg394 b:55.8 occ:1.00 O2A B:ACP396 1.9 47.1 1.0 O2G B:ACP396 1.9 62.3 1.0 OE1 B:GLU279 2.3 29.6 1.0 OE2 B:GLU267 2.3 38.0 1.0 O B:HOH635 2.4 36.7 1.0 OE1 B:GLU267 2.8 39.7 1.0 CD B:GLU267 2.9 55.6 1.0 PA B:ACP396 3.2 36.1 1.0 PG B:ACP396 3.2 43.1 1.0 CD B:GLU279 3.2 33.5 1.0 O3A B:ACP396 3.6 33.6 1.0 C3B B:ACP396 3.7 98.3 1.0 MG B:MG393 3.8 39.4 1.0 CG B:GLU279 3.8 25.7 1.0 O3G B:ACP396 3.8 43.2 1.0 PB B:ACP396 3.9 39.3 1.0 O B:HOH503 3.9 34.9 1.0 O2B B:ACP396 4.0 38.6 1.0 O5' B:ACP396 4.0 52.8 1.0 C5' B:ACP396 4.1 23.8 1.0 O1A B:ACP396 4.2 39.6 1.0 OE2 B:GLU279 4.3 50.9 1.0 O B:HOH526 4.3 35.9 1.0 O1G B:ACP396 4.3 54.0 1.0 O3' B:ACP396 4.4 35.7 1.0 CG B:GLU267 4.4 24.4 1.0 C3' B:ACP396 4.8 41.2 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