Sodium in PDB 3a6v: Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form

The structure of Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form, PDB code: 3a6v 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)	19.94 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.750, 55.950, 74.120, 90.00, 96.40, 90.00
R / Rfree (%)	19.2 / 22.7

The structure of Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form (pdb code 3a6v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form, PDB code: 3a6v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form


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 the Mutt Protein in Mn(II) Bound Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1005 b:6.9 occ:1.00 O A:HOH153 2.3 13.1 1.0 OE1 A:GLU57 2.4 13.0 1.0 O A:GLY37 2.4 7.1 1.0 OD1 B:ASP77 2.4 12.2 1.0 O B:HOH186 2.6 23.8 1.0 OE2 A:GLU57 2.7 7.5 1.0 CD A:GLU57 2.9 11.1 1.0 CG B:ASP77 3.2 11.7 1.0 C A:GLY37 3.5 7.0 1.0 N A:GLY37 3.6 10.2 1.0 OD2 B:ASP77 3.6 8.8 1.0 MN A:MN1003 3.9 8.7 1.0 N B:ASP77 4.0 9.7 1.0 CA A:GLY37 4.1 8.1 1.0 O A:HOH155 4.1 23.9 1.0 O A:HOH133 4.2 7.0 1.0 CB B:PRO76 4.2 11.4 1.0 O A:HOH140 4.2 13.3 1.0 CB B:ASP77 4.3 10.4 1.0 C B:PRO76 4.3 10.0 1.0 CG A:GLU57 4.3 6.7 1.0 CA B:PRO76 4.4 9.8 1.0 C A:PRO36 4.4 10.4 1.0 CA B:ASP77 4.5 10.2 1.0 OE2 A:GLU34 4.6 23.4 1.0 CA A:PRO36 4.6 10.8 1.0 N A:GLY38 4.6 8.2 1.0 O A:HOH186 4.7 37.3 1.0 O A:PHE35 4.7 10.6 1.0 OE2 A:GLU53 4.8 9.6 1.0 CA A:GLY38 4.9 5.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Mutt Protein in Mn(II) Bound Holo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:7.2 occ:1.00 OE1 B:GLU57 2.3 13.7 1.0 O B:HOH140 2.3 15.3 1.0 OD1 A:ASP77 2.3 10.0 1.0 O B:GLY37 2.4 10.2 1.0 O A:HOH163 2.5 27.8 1.0 OE2 B:GLU57 2.8 11.8 1.0 CD B:GLU57 2.8 13.2 1.0 CG A:ASP77 3.1 12.0 1.0 C B:GLY37 3.5 9.4 1.0 N B:GLY37 3.6 12.1 1.0 OD2 A:ASP77 3.6 8.1 1.0 MN B:MN1001 3.9 11.1 1.0 N A:ASP77 3.9 9.5 1.0 O B:HOH131 4.1 23.0 1.0 O B:HOH137 4.1 15.3 1.0 CA B:GLY37 4.1 10.7 1.0 O B:HOH141 4.2 16.8 1.0 CB A:ASP77 4.2 10.7 1.0 CB A:PRO76 4.3 11.1 1.0 CG B:GLU57 4.3 11.5 1.0 C A:PRO76 4.3 11.2 1.0 CA A:ASP77 4.4 10.4 1.0 CA A:PRO76 4.5 11.3 1.0 C B:PRO36 4.5 11.8 1.0 N B:GLY38 4.6 9.3 1.0 O B:HOH180 4.6 42.7 1.0 O B:HOH183 4.6 41.1 1.0 OE2 B:GLU34 4.6 25.6 1.0 CA B:PRO36 4.7 12.0 1.0 OE2 B:GLU53 4.8 11.6 1.0 O B:PHE35 4.8 13.7 1.0 CA B:GLY38 4.9 8.1 1.0

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