Sodium in PDB 6ms4: Crystal Structure of the Denr-Mct-1 Complex

The structure of Crystal Structure of the Denr-Mct-1 Complex, PDB code: 6ms4 was solved by I.B.Lomakin, T.A.Steitz, S.E.Dmitriev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.58 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.810, 67.810, 124.750, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27.1

The structure of Crystal Structure of the Denr-Mct-1 Complex also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Denr-Mct-1 Complex (pdb code 6ms4). 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 the Denr-Mct-1 Complex, PDB code: 6ms4:

Sodium binding site 1 out of 1 in the Crystal Structure of the Denr-Mct-1 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 the Denr-Mct-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:0.0 occ:1.00 ND1 A:HIS58 2.5 0.1 1.0 CB A:HIS58 2.8 0.1 1.0 CG A:HIS58 2.9 0.8 1.0 CB A:ARG74 3.3 1.0 1.0 CE1 A:HIS58 3.6 0.9 1.0 CA A:ARG74 3.8 0.8 1.0 CD2 A:HIS58 4.0 0.2 1.0 CA A:HIS58 4.3 0.0 1.0 NE2 A:HIS58 4.3 0.1 1.0 N A:ARG74 4.4 0.3 1.0 O A:HIS58 4.5 0.2 1.0 C A:HIS58 4.9 0.4 1.0

I.B.Lomakin, S.E.Dmitriev, T.A.Steitz. Crystal Structure of the Denr-Mct-1 Complex Revealed Zinc-Binding Site Essential For Heterodimer Formation. Proc. Natl. Acad. Sci. V. 116 528 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30584092
DOI: 10.1073/PNAS.1809688116