Sodium in PDB 5nyf: Selenomethionine Labelled Anbu (Gly-1) Mutant From Hyphomicrobium Sp. Strain MC1

The structure of Selenomethionine Labelled Anbu (Gly-1) Mutant From Hyphomicrobium Sp. Strain MC1, PDB code: 5nyf was solved by M.-T.Vielberg, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	176.130, 176.130, 39.740, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.9

The binding sites of Sodium atom in the Selenomethionine Labelled Anbu (Gly-1) Mutant From Hyphomicrobium Sp. Strain MC1 (pdb code 5nyf). 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 Selenomethionine Labelled Anbu (Gly-1) Mutant From Hyphomicrobium Sp. Strain MC1, PDB code: 5nyf:

Sodium binding site 1 out of 1 in the Selenomethionine Labelled Anbu (Gly-1) Mutant From Hyphomicrobium Sp. Strain MC1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Selenomethionine Labelled Anbu (Gly-1) Mutant From Hyphomicrobium Sp. Strain MC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:65.1 occ:0.50 O A:HOH443 1.6 78.2 0.5 O A:HOH404 2.1 65.3 1.0 OD2 A:ASP167 3.5 52.9 1.0 OD1 A:ASP167 3.6 45.4 1.0 CG A:ASP167 3.9 49.1 1.0 O A:HOH440 4.1 61.4 1.0 CG A:ARG165 4.2 57.8 1.0 CB A:ARG165 4.5 49.9 1.0 CD A:ARG165 4.6 64.7 1.0 NE A:ARG165 4.7 71.8 1.0

M.T.Vielberg, V.C.Bauer, M.Groll. On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral Beta-Subunit Protein Anbu. J. Mol. Biol. V. 430 628 2018.
ISSN: ESSN 1089-8638
PubMed: 29355501
DOI: 10.1016/J.JMB.2018.01.004