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Sodium in PDB 3a6t: Crystal Structure of Mutt-8-Oxo-Dgmp Complex

Protein crystallography data

The structure of Crystal Structure of Mutt-8-Oxo-Dgmp Complex, PDB code: 3a6t was solved by T.Nakamura, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.66 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.972, 56.007, 59.369, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mutt-8-Oxo-Dgmp Complex (pdb code 3a6t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Mutt-8-Oxo-Dgmp Complex, PDB code: 3a6t:

Sodium binding site 1 out of 1 in 3a6t

Go back to Sodium Binding Sites List in 3a6t
Sodium binding site 1 out of 1 in the Crystal Structure of Mutt-8-Oxo-Dgmp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mutt-8-Oxo-Dgmp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na131

b:40.0
occ:1.00
O A:HOH145 2.4 14.2 1.0
O A:HOH267 2.8 47.5 1.0
O A:HOH233 2.9 28.4 1.0
OE1 A:GLU53 3.0 17.1 1.0
O A:HOH252 3.0 19.2 1.0
O A:HOH168 3.2 21.7 1.0
CD A:GLU53 3.8 16.0 1.0
OE2 A:GLU53 3.8 17.6 1.0
N A:LYS39 4.0 14.5 1.0
CA A:GLY38 4.2 13.4 1.0
OP2 A:8OG134 4.3 21.7 1.0
O A:HOH144 4.4 16.1 1.0
C A:GLY38 4.5 15.0 1.0
O A:HOH248 4.6 49.0 1.0
NH1 A:ARG52 4.7 16.4 1.0
O A:LYS39 4.8 14.8 1.0
CB A:LYS39 4.9 18.7 1.0
OE1 A:GLU56 4.9 20.6 1.0
CA A:LYS39 4.9 16.2 1.0

Reference:

T.Nakamura, S.Meshitsuka, S.Kitagawa, N.Abe, J.Yamada, T.Ishino, H.Nakano, T.Tsuzuki, T.Doi, Y.Kobayashi, S.Fujii, M.Sekiguchi, Y.Yamagata. Structural and Dynamic Features of the Mutt Protein in the Recognition of Nucleotides with the Mutagenic 8-Oxoguanine Base J.Biol.Chem. V. 285 444 2010.
ISSN: ISSN 0021-9258
PubMed: 19864691
DOI: 10.1074/JBC.M109.066373
Page generated: Tue Dec 15 06:01:44 2020

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