Magnesium in PDB 3av3: Crystal Structure of Glycinamide Ribonucleotide Transformylase 1 From Geobacillus Kaustophilus

All present enzymatic activity of Crystal Structure of Glycinamide Ribonucleotide Transformylase 1 From Geobacillus Kaustophilus:
2.1.2.2;

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase 1 From Geobacillus Kaustophilus, PDB code: 3av3 was solved by M.Kanagawa, S.Baba, N.Nakagawa, A.Ebihara, S.Kuramitsu, S.Yokoyama, G.Sampei, G.Kawai, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.77 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	51.861, 117.408, 67.251, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of Glycinamide Ribonucleotide Transformylase 1 From Geobacillus Kaustophilus (pdb code 3av3). 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 1 From Geobacillus Kaustophilus, PDB code: 3av3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase 1 From Geobacillus Kaustophilus


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 1 From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:37.5 occ:1.00 O A:HOH435 2.4 30.9 1.0 O A:HOH340 2.4 23.6 1.0 O A:HOH439 2.5 32.8 1.0 O A:HOH379 2.5 26.6 1.0 O A:HOH231 2.5 39.2 1.0 O A:HOH234 2.6 46.0 1.0 OE2 A:GLU71 4.1 16.9 1.0 O A:HOH310 4.1 20.5 1.0 O A:HOH438 4.3 23.6 1.0 O A:HOH228 4.3 38.7 1.0 O A:HOH317 4.6 22.9 1.0 OE1 A:GLU71 4.6 17.1 1.0 CD A:GLU71 4.8 15.6 1.0 OH A:TYR62 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase 1 From Geobacillus Kaustophilus


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 1 From Geobacillus Kaustophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg212 b:40.4 occ:1.00 O A:HOH480 2.5 28.3 1.0 O A:HOH357 2.5 31.8 1.0 O A:HOH351 2.5 30.0 1.0 O A:HOH457 2.5 30.3 1.0 O A:HOH477 4.3 31.0 1.0 O A:HOH467 4.4 41.3 1.0 OD1 A:ASP26 4.5 22.7 1.0 OD2 A:ASP26 4.6 23.2 1.0 O A:ARG24 4.7 24.1 1.0 O A:HOH421 4.8 45.0 1.0

G.Sampei, M.Kanagawa, S.Baba, T.Shimasaki, H.Taka, S.Mitsui, S.Fujiwara, Y.Yanagida, M.Kusano, S.Suzuki, K.Terao, H.Kawai, Y.Fukai, N.Nakagawa, A.Ebihara, S.Kuramitsu, S.Yokoyama, G.Kawai. Structures and Reaction Mechanisms of the Two Related Enzymes, Purn and Puru. J.Biochem. V. 154 569 2013.
ISSN: ISSN 0021-924X
PubMed: 24108189
DOI: 10.1093/JB/MVT090