Sodium in PDB 3g0r: Complex of MTH0212 and An 8BP Dsdna with Distorted Ends

All present enzymatic activity of Complex of MTH0212 and An 8BP Dsdna with Distorted Ends:
3.1.11.2;

The structure of Complex of MTH0212 and An 8BP Dsdna with Distorted Ends, PDB code: 3g0r was solved by K.Lakomek, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.751, 80.760, 105.211, 90.00, 94.03, 90.00
R / Rfree (%)	17.8 / 24.3

The binding sites of Sodium atom in the Complex of MTH0212 and An 8BP Dsdna with Distorted Ends (pdb code 3g0r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Complex of MTH0212 and An 8BP Dsdna with Distorted Ends, PDB code: 3g0r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Complex of MTH0212 and An 8BP Dsdna with Distorted Ends


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of MTH0212 and An 8BP Dsdna with Distorted Ends within 5.0Å range: probe atom residue distance (Å) B Occ G:Na14 b:14.5 occ:1.00 O6 G:DG6 2.6 27.1 1.0 O4 K:DU6 2.9 22.1 1.0 O6 K:DG5 2.9 19.2 1.0 N4 G:DC5 3.0 19.3 1.0 O G:HOH16 3.0 24.4 1.0 O K:HOH12 3.4 19.7 1.0 C4 G:DC5 3.6 18.7 1.0 C6 G:DG6 3.7 25.9 1.0 C6 K:DG5 3.7 17.5 1.0 C4 K:DU6 3.8 20.3 1.0 N3 K:DU6 4.0 19.2 1.0 N4 G:DC7 4.0 26.8 1.0 O G:HOH18 4.0 38.4 1.0 N7 G:DG6 4.1 26.5 1.0 N3 G:DC5 4.1 19.5 1.0 N7 K:DG5 4.1 18.4 1.0 C5 K:DG5 4.2 17.7 1.0 C5 G:DC5 4.2 19.4 1.0 C5 G:DG6 4.3 25.8 1.0 NA G:NA15 4.4 12.5 1.0 O6 K:DG7 4.5 25.6 1.0 O4 K:DT4 4.7 28.7 1.0 N1 K:DG5 4.7 18.9 1.0 O K:HOH191 4.7 21.4 1.0 O G:HOH103 4.8 30.8 1.0 N1 G:DG6 4.8 24.8 1.0 C4 K:DT4 4.9 27.9 1.0

Sodium binding site 2 out of 2 in the Complex of MTH0212 and An 8BP Dsdna with Distorted Ends


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complex of MTH0212 and An 8BP Dsdna with Distorted Ends within 5.0Å range: probe atom residue distance (Å) B Occ G:Na15 b:12.5 occ:1.00 O6 K:DG7 2.7 25.6 1.0 O6 G:DG4 2.9 20.6 1.0 N4 G:DC5 2.9 19.3 1.0 O4 K:DU6 3.1 22.1 1.0 O K:HOH18 3.2 15.0 1.0 O G:HOH25 3.3 31.0 1.0 C4 K:DU6 3.6 20.3 1.0 C6 G:DG4 3.6 19.2 1.0 C6 K:DG7 3.8 24.5 1.0 O G:HOH18 3.8 38.4 1.0 C4 G:DC5 3.9 18.7 1.0 N3 G:DC5 4.0 19.5 1.0 N4 K:DC8 4.1 20.7 1.0 N7 G:DG4 4.1 19.7 1.0 C5 G:DG4 4.1 18.5 1.0 N3 K:DU6 4.2 19.2 1.0 N7 K:DG7 4.2 25.8 1.0 C5 K:DU6 4.3 19.4 1.0 C5 K:DG7 4.4 25.7 1.0 NA G:NA14 4.4 14.5 1.0 O6 G:DG6 4.6 27.1 1.0 O4 G:DT3 4.6 35.2 1.0 N1 G:DG4 4.7 19.8 1.0 O K:HOH191 4.7 21.4 1.0 C4 G:DT3 4.8 33.9 1.0 O K:HOH235 4.9 34.1 1.0 N1 K:DG7 4.9 25.1 1.0 C7 G:DT3 4.9 28.5 1.0

K.Lakomek, A.Dickmanns, E.Ciirdaeva, L.Schomacher, R.Ficner. Crystal Structure Analysis of Dna Uridine Endonuclease MTH212 Bound to Dna J.Mol.Biol. V. 399 604 2010.
ISSN: ISSN 0022-2836
PubMed: 20434457
DOI: 10.1016/J.JMB.2010.04.044