Magnesium in PDB 4ygi: Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna

All present enzymatic activity of Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna:
2.1.1.43;

The structure of Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna, PDB code: 4ygi was solved by E.Rajakumara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.96 / 2.60
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.980, 76.980, 72.111, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 28.3

The binding sites of Magnesium atom in the Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna (pdb code 4ygi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna, PDB code: 4ygi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna


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 SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:69.2 occ:1.00 OE2 A:GLU500 3.2 67.0 1.0 OE1 A:GLU500 3.6 55.2 1.0 CD A:GLU500 3.8 58.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna


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 SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:80.2 occ:1.00 O3' B:DT10 3.1 67.6 1.0 O B:HOH201 3.2 68.3 1.0 C3' B:DT10 4.1 75.2 1.0 C1' B:DT10 4.3 73.1 1.0 C4' B:DT10 4.3 72.6 1.0 O4' B:DT10 4.5 74.3 1.0 C2' B:DT10 4.6 68.0 1.0 O2 B:DT10 4.9 64.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna


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 SUVH5 Sra Bound to Fully Hydroxymethylated Cg Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:72.2 occ:1.00 O6 B:DG9 3.4 57.8 1.0 O B:HOH203 3.6 64.8 1.0 N7 B:DG9 3.6 60.8 1.0 N7 B:DA8 4.0 59.9 1.0 C6 B:DG9 4.2 56.8 1.0 C5 B:DG9 4.3 56.6 1.0 C8 B:DA8 4.4 58.9 1.0 O4 B:DT10 4.6 58.8 1.0 C5 B:DA8 4.6 51.4 1.0 O B:HOH205 4.7 79.9 1.0 C8 B:DG9 4.8 58.4 1.0

E.Rajakumara, N.K.Nakarakanti, M.A.Nivya, M.Satish. Mechanistic Insights Into the Recognition of 5-Methylcytosine Oxidation Derivatives By the SUVH5 Sra Domain Sci Rep V. 6 20161 2016.
ISSN: ESSN 2045-2322
PubMed: 26841909
DOI: 10.1038/SREP20161