Sodium in PDB 5ohq: Crystal Structure of the KOW6-KOW7 Domain of Human Dsif

The structure of Crystal Structure of the KOW6-KOW7 Domain of Human Dsif, PDB code: 5ohq was solved by C.Bernecky, J.M.Plitzko, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.37 / 1.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	35.091, 75.657, 96.749, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 14

The structure of Crystal Structure of the KOW6-KOW7 Domain of Human Dsif also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the KOW6-KOW7 Domain of Human Dsif (pdb code 5ohq). 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 KOW6-KOW7 Domain of Human Dsif, PDB code: 5ohq:

Sodium binding site 1 out of 1 in the Crystal Structure of the KOW6-KOW7 Domain of Human Dsif


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 KOW6-KOW7 Domain of Human Dsif within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:33.5 occ:0.85 HG3 A:GLU1028 2.2 11.7 0.3 H A:GLU1028 2.5 17.2 0.3 H A:GLU1028 2.5 17.2 0.7 OG A:SER1026 2.6 22.2 0.6 O A:HOH1208 2.8 36.2 1.0 OG A:SER1027 2.8 14.7 0.5 HG A:SER1026 2.8 26.6 0.6 OE2 A:GLU1028 2.9 14.2 0.7 HB3 A:SER1026 2.9 26.1 0.4 HG2 A:GLU1028 2.9 16.2 0.7 HB2 A:SER1027 3.0 26.5 0.6 H A:SER1027 3.0 22.6 0.5 H A:SER1027 3.0 22.6 0.6 CG A:GLU1028 3.1 9.8 0.3 HG A:SER1027 3.1 17.7 0.5 HB3 A:GLU1028 3.2 16.9 0.7 OE1 A:GLU1028 3.2 10.9 0.3 N A:GLU1028 3.3 14.3 1.0 O A:GLY1010 3.3 30.2 1.0 O A:HOH1342 3.4 40.2 1.0 N A:SER1027 3.4 18.8 1.0 CD A:GLU1028 3.4 10.7 0.3 CG A:GLU1028 3.5 13.5 0.7 HB2 A:GLU1028 3.6 14.9 0.3 CD A:GLU1028 3.6 13.0 0.7 HG2 A:GLU1028 3.7 11.7 0.3 CB A:GLU1028 3.7 14.1 0.7 CB A:GLU1028 3.8 12.4 0.3 CB A:SER1027 3.8 22.1 0.6 CB A:SER1026 3.8 19.3 0.6 CB A:SER1026 3.8 21.8 0.4 CB A:SER1027 3.8 19.0 0.5 HA3 A:GLY1010 3.9 30.6 1.0 CA A:SER1027 3.9 19.2 0.6 CA A:SER1027 4.0 18.6 0.5 HA A:SER1026 4.0 21.5 0.6 HA A:SER1026 4.0 22.9 0.4 C A:SER1026 4.0 18.4 1.0 O A:HOH1386 4.1 35.7 0.5 C A:SER1027 4.1 16.8 1.0 CA A:GLU1028 4.1 14.1 0.3 HB3 A:SER1027 4.1 22.8 0.5 HB2 A:SER1026 4.1 23.1 0.6 O A:HOH1222 4.1 19.3 0.7 CA A:GLU1028 4.1 15.4 0.7 CA A:SER1026 4.2 17.9 0.6 CA A:SER1026 4.2 19.1 0.4 C A:GLY1010 4.3 24.6 1.0 OG A:SER1027 4.3 22.1 0.6 HB2 A:SER1026 4.4 26.1 0.4 HG3 A:GLU1028 4.4 16.2 0.7 HA A:GLU1028 4.4 16.9 0.3 HG A:SER1026 4.4 30.0 0.4 OE2 A:GLU1028 4.5 10.5 0.3 CA A:GLY1010 4.5 25.5 1.0 HB3 A:SER1026 4.5 23.1 0.6 HA2 A:GLY1010 4.5 30.6 1.0 HB3 A:SER1027 4.6 26.5 0.6 OG A:SER1026 4.6 25.0 0.4 HB2 A:GLU1028 4.6 16.9 0.7 HA A:GLU1028 4.6 18.4 0.7 HB2 A:SER1027 4.6 22.8 0.5 HB3 A:GLU1028 4.7 14.9 0.3 O A:HOH1222 4.8 16.0 0.3 OE1 A:GLU1028 4.8 12.6 0.7 O A:SER1026 4.9 17.4 1.0 HA A:SER1027 4.9 23.0 0.6 HA A:SER1027 4.9 22.3 0.5

C.Bernecky, J.M.Plitzko, P.Cramer. Structure of A Transcribing Rna Polymerase II-Dsif Complex Reveals A Multidentate Dna-Rna Clamp. Nat. Struct. Mol. Biol. V. 24 809 2017.
ISSN: ESSN 1545-9985
PubMed: 28892040
DOI: 10.1038/NSMB.3465