Magnesium in PDB 5a2z: Crystal Structure of Mtpap in Complex with Gtp

The structure of Crystal Structure of Mtpap in Complex with Gtp, PDB code: 5a2z was solved by M.Lapkouski, B.M.Hallberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.67 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.746, 94.364, 192.014, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 29.5

The binding sites of Magnesium atom in the Crystal Structure of Mtpap in Complex with Gtp (pdb code 5a2z). 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 Mtpap in Complex with Gtp, PDB code: 5a2z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mtpap in Complex with Gtp


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 Mtpap in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1529 b:67.8 occ:1.00 OD2 A:ASP239 2.5 42.7 1.0 O2A A:GTP1528 2.8 78.3 1.0 O A:ASP237 2.9 33.9 1.0 O2B A:GTP1528 2.9 76.1 1.0 OG A:SER226 3.1 34.7 1.0 O3G A:GTP1528 3.1 82.8 1.0 O A:HOH2002 3.3 48.1 1.0 CG A:ASP239 3.4 40.5 1.0 C A:ASP237 3.5 33.9 1.0 CB A:ASP237 3.5 35.9 1.0 O A:HOH2005 3.8 30.0 1.0 CA A:ASP237 3.8 34.0 1.0 OD1 A:ASP239 3.8 41.7 1.0 N A:ASP237 3.8 34.1 1.0 PA A:GTP1528 3.9 76.4 1.0 PB A:GTP1528 4.1 80.0 1.0 O A:HOH2006 4.1 41.2 1.0 O5' A:GTP1528 4.1 75.7 1.0 O3A A:GTP1528 4.3 78.9 1.0 PG A:GTP1528 4.4 82.6 1.0 CB A:SER226 4.4 33.6 1.0 O3B A:GTP1528 4.4 82.2 1.0 N A:VAL238 4.5 33.7 1.0 N A:ASP239 4.5 36.5 1.0 SG A:CYS236 4.6 33.0 1.0 CB A:CYS236 4.6 31.7 1.0 CB A:ASP239 4.6 38.6 1.0 C A:CYS236 4.7 32.6 1.0 N A:SER226 4.7 32.2 1.0 CG A:ASP237 4.8 37.2 1.0 CA A:VAL238 4.9 33.7 1.0 O1G A:GTP1528 4.9 83.5 1.0 C A:VAL238 5.0 34.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mtpap in Complex with Gtp


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 Mtpap in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1529 b:32.9 occ:1.00 OD2 B:ASP239 2.4 27.2 1.0 O2B B:GTP1528 2.7 67.7 1.0 OG B:SER226 2.7 36.2 1.0 O1G B:GTP1528 2.8 64.5 1.0 O B:ASP237 3.0 31.9 1.0 O B:HOH2003 3.2 28.3 1.0 O2A B:GTP1528 3.3 67.7 1.0 CG B:ASP239 3.4 29.0 1.0 C B:ASP237 3.7 32.2 1.0 CB B:ASP237 3.8 35.3 1.0 PB B:GTP1528 3.9 68.6 1.0 PG B:GTP1528 3.9 66.2 1.0 CB B:SER226 4.0 34.5 1.0 OD1 B:ASP239 4.0 28.4 1.0 O B:HOH2008 4.0 35.7 1.0 O3B B:GTP1528 4.0 67.5 1.0 CA B:ASP237 4.1 34.1 1.0 N B:ASP237 4.1 33.6 1.0 N B:SER226 4.1 32.9 1.0 O B:HOH2009 4.2 39.4 1.0 O3G B:GTP1528 4.4 67.5 1.0 N B:ASP239 4.5 29.2 1.0 PA B:GTP1528 4.5 68.1 1.0 O3A B:GTP1528 4.5 69.5 1.0 SG B:CYS236 4.5 30.5 1.0 CA B:SER226 4.6 34.1 1.0 CB B:ASP239 4.6 29.9 1.0 N B:VAL238 4.6 30.9 1.0 N B:SER227 4.7 34.0 1.0 CB B:CYS236 4.7 31.9 1.0 C B:CYS236 4.8 33.4 1.0 OG B:SER227 4.9 32.4 1.0 CA B:VAL238 5.0 29.6 1.0

M.Lapkouski, B.M.Hallberg. Structure of Mitochondrial Poly(A) Rna Polymerase Reveals the Structural Basis For Dimerization, Atp Selectivity and the SPAX4 Disease Phenotype. Nucleic Acids Res. V. 43 9065 2015.
ISSN: ISSN 0305-1048
PubMed: 26319014
DOI: 10.1093/NAR/GKV861