Magnesium in PDB 4kaz: Crystal Structure of Rnase T in Complex with A Y Structured Dna

The structure of Crystal Structure of Rnase T in Complex with A Y Structured Dna, PDB code: 4kaz was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.77 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.675, 90.580, 46.621, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.8

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Y Structured Dna (pdb code 4kaz). 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 Rnase T in Complex with A Y Structured Dna, PDB code: 4kaz:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Rnase T in Complex with A Y Structured 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 Rnase T in Complex with A Y Structured Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:34.0 occ:1.00 OP1 B:DC20 2.1 17.9 1.0 OD2 A:ASP186 2.3 49.6 1.0 OE1 A:GLU25 2.4 41.5 1.0 O A:HOH429 2.5 36.6 1.0 CG A:ASP186 3.0 48.3 1.0 CD A:GLU25 3.3 32.0 1.0 OE2 A:GLU25 3.4 24.3 1.0 P B:DC20 3.4 19.2 1.0 CA A:HIS181 3.6 54.9 1.0 OD1 A:ASP186 3.6 51.7 1.0 OD2 A:ASP23 3.8 28.4 1.0 CB A:ASP186 4.0 26.3 1.0 OP2 B:DC20 4.0 23.6 1.0 OD1 A:ASP23 4.0 25.1 1.0 N A:HIS181 4.0 48.9 1.0 MG B:MG101 4.0 22.4 1.0 C A:HIS181 4.1 39.8 1.0 N A:SER182 4.2 44.5 1.0 O A:HOH409 4.2 20.4 1.0 O5' B:DC20 4.3 16.5 1.0 CG A:ASP23 4.3 20.9 1.0 O3' B:DC19 4.5 14.2 1.0 ND1 A:HIS181 4.5 64.0 1.0 CB A:HIS181 4.6 56.7 1.0 C5' B:DC20 4.7 16.7 1.0 CG A:GLU25 4.7 23.0 1.0 O A:SER182 4.7 28.1 1.0 C A:SER182 4.8 32.9 1.0 O B:HOH208 4.9 30.1 1.0 O A:VAL24 4.9 15.8 1.0 O A:HIS181 5.0 44.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rnase T in Complex with A Y Structured 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 Rnase T in Complex with A Y Structured Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:22.4 occ:1.00 O A:HOH409 2.2 20.4 1.0 OD1 A:ASP23 2.3 25.1 1.0 O A:HOH410 2.3 15.5 1.0 O3' B:DC19 2.4 14.2 1.0 O A:HOH419 2.4 17.4 1.0 OP1 B:DC20 2.7 17.9 1.0 P B:DC20 3.2 19.2 1.0 CG A:ASP23 3.5 20.9 1.0 C3' B:DC19 3.6 14.7 1.0 OD2 A:ASP186 3.8 49.6 1.0 C4' B:DC19 3.9 17.3 1.0 C2' B:DC19 4.0 17.6 1.0 O A:HOH440 4.0 17.1 1.0 MG A:MG301 4.0 34.0 1.0 OD2 A:ASP125 4.1 19.2 1.0 O A:HOH407 4.1 17.5 1.0 OD2 A:ASP23 4.2 28.4 1.0 C5' B:DC20 4.2 16.7 1.0 O5' B:DC20 4.2 16.5 1.0 OP2 B:DC20 4.3 23.6 1.0 O A:VAL24 4.4 15.8 1.0 OD1 A:ASP125 4.5 14.2 1.0 CB A:ASP23 4.6 11.3 1.0 O A:HIS120 4.6 12.2 1.0 CG A:ASP125 4.7 14.2 1.0 O B:HOH208 4.8 30.1 1.0 C5' B:DC19 4.8 10.4 1.0 CG A:ASP186 4.9 48.3 1.0 O4' B:DC19 5.0 17.0 1.0

Y.Y.Hsiao, W.H.Fang, C.C.Lee, Y.P.Chen, H.S.Yuan. Structural Insights Into Dna Repair By Rnase T--An Exonuclease Processing 3' End of Structured Dna in Repair Pathways. Plos Biol. V. 12 01803 2014.
ISSN: ISSN 1544-9173
PubMed: 24594808
DOI: 10.1371/JOURNAL.PBIO.1001803