Sodium in PDB 5tdr: SET3 Phd Finger in Complex with Histone H3K4ME2

The structure of SET3 Phd Finger in Complex with Histone H3K4ME2, PDB code: 5tdr was solved by F.H.Andrews, M.Ali, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.85 / 1.42
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.931, 43.720, 84.698, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 20

The structure of SET3 Phd Finger in Complex with Histone H3K4ME2 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the SET3 Phd Finger in Complex with Histone H3K4ME2 (pdb code 5tdr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the SET3 Phd Finger in Complex with Histone H3K4ME2, PDB code: 5tdr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the SET3 Phd Finger in Complex with Histone H3K4ME2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SET3 Phd Finger in Complex with Histone H3K4ME2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:13.5 occ:1.00 OD1 A:ASP8 2.7 7.8 1.0 O A:HOH324 2.8 12.1 1.0 O A:CYS5 2.8 6.2 1.0 ND2 A:ASN10 3.0 6.3 1.0 N A:CYS5 3.6 5.5 1.0 OD1 A:ASN10 3.6 6.8 1.0 CA A:ASP8 3.7 6.4 1.0 CG A:ASN10 3.8 6.3 1.0 CG A:ASP8 3.8 9.2 1.0 O A:HOH246 3.8 12.3 1.0 CG2 A:THR4 3.9 7.7 1.0 C A:CYS5 3.9 6.8 1.0 N A:ASP8 4.1 4.9 1.0 C A:THR4 4.3 6.9 1.0 CB A:ASP8 4.3 6.5 1.0 CA A:THR4 4.3 6.0 1.0 O A:HOH302 4.4 26.4 1.0 CA A:CYS5 4.4 5.0 1.0 O A:HOH295 4.7 37.1 1.0 O A:HOH328 4.7 16.1 1.0 C A:ASP8 4.7 6.0 1.0 CB A:THR4 4.7 7.0 1.0 OD2 A:ASP8 4.9 12.6 1.0

Sodium binding site 2 out of 2 in the SET3 Phd Finger in Complex with Histone H3K4ME2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of SET3 Phd Finger in Complex with Histone H3K4ME2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:14.5 occ:1.00 OD2 A:ASP13 2.6 6.8 1.0 O A:HOH316 2.7 14.9 1.0 O A:PHE15 2.8 6.6 1.0 N A:ILE29 3.0 4.9 1.0 N A:ALA28 3.3 5.2 1.0 CG A:ASP13 3.4 8.5 1.0 OD1 A:ASP13 3.4 8.3 1.0 CG2 A:ILE29 3.4 6.9 1.0 CB A:ILE29 3.5 6.6 1.0 CB A:PHE15 3.6 7.5 1.0 C A:PHE15 3.8 6.3 1.0 CA A:ILE29 3.9 5.9 1.0 C A:HIS27 3.9 5.1 1.0 CB A:HIS27 3.9 4.5 1.0 C A:ALA28 4.0 5.9 1.0 CA A:ALA28 4.0 5.2 1.0 CB A:ALA28 4.1 6.8 1.0 CA A:HIS27 4.1 4.5 1.0 CA A:PHE15 4.1 6.5 1.0 CD2 A:PHE15 4.1 7.4 1.0 CG A:PHE15 4.1 6.3 1.0 O A:HOH255 4.3 15.1 1.0 N A:PHE15 4.3 7.1 1.0 O A:HOH254 4.6 16.9 1.0 O A:HIS27 4.7 6.8 1.0 CB A:ASP13 4.8 7.2 1.0 NE2 A:GLN62 4.9 5.7 1.0 CG1 A:ILE29 4.9 9.3 1.0 CG A:HIS27 4.9 4.1 1.0 N A:THR16 5.0 6.3 1.0 C A:ILE29 5.0 5.5 1.0

J.Gatchalian, M.Ali, F.H.Andrews, Y.Zhang, A.S.Barrett, T.G.Kutateladze. Structural Insight Into Recognition of Methylated Histone H3K4 By SET3. J. Mol. Biol. V. 429 2066 2017.
ISSN: ESSN 1089-8638
PubMed: 27697561
DOI: 10.1016/J.JMB.2016.09.020