Sodium in PDB 2vpb: Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex

The structure of Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex, PDB code: 2vpb was solved by M.Fiedler, M.J.Sanchez-Barrena, M.Nekrasov, J.Mieszczanek, V.Rybin, J.Muller, P.Evans, M.Bienz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.08 / 1.59
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	32.100, 79.470, 91.830, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.5

The structure of Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex (pdb code 2vpb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex, PDB code: 2vpb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1398 b:17.3 occ:1.00 O A:ALA388 2.3 16.1 1.0 O A:GLU385 2.3 18.0 1.0 O A:HOH2055 2.4 39.3 1.0 O A:LEU382 2.4 16.9 1.0 O A:HOH2061 2.4 25.7 1.0 O A:HOH2062 2.5 36.5 1.0 C A:GLU385 3.4 18.5 1.0 C A:ALA388 3.4 15.1 1.0 C A:LEU382 3.5 16.6 1.0 CA A:THR383 4.0 19.1 1.0 O A:THR383 4.0 22.3 1.0 C A:THR383 4.0 20.0 1.0 O A:HOH2026 4.1 31.3 1.0 N A:GLU385 4.1 18.9 1.0 N A:ALA388 4.2 16.6 1.0 CA A:ALA388 4.2 15.9 1.0 N A:THR383 4.2 17.1 1.0 CA A:GLU385 4.3 18.5 1.0 N A:ALA386 4.4 19.0 1.0 CA A:ALA386 4.4 19.3 1.0 CB A:ALA388 4.4 16.1 1.0 N A:VAL389 4.5 14.6 1.0 C A:ALA386 4.5 19.1 1.0 O A:ALA386 4.6 20.4 1.0 CA A:VAL389 4.6 14.4 1.0 CA A:LEU382 4.6 15.6 1.0 N A:ALA384 4.7 19.6 1.0 O A:HOH2003 4.7 33.3 1.0 CB A:GLU385 4.7 18.7 1.0 CG1 A:VAL389 4.7 15.6 1.0 CD1 A:LEU382 4.8 22.9 1.0 CG A:LEU382 4.8 18.3 1.0 C A:ALA384 4.9 20.0 1.0

Sodium binding site 2 out of 2 in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1399 b:25.0 occ:1.00 O A:HOH2003 2.7 33.3 1.0 O A:LEU358 2.7 17.2 1.0 OE2 A:GLU360 2.8 21.2 1.0 N A:TRP390 3.0 13.4 1.0 CD A:GLU360 3.6 23.1 1.0 CG A:GLU360 3.6 20.7 1.0 CB A:TRP390 3.7 13.7 1.0 O A:TRP390 3.7 14.9 1.0 CB A:VAL389 3.7 14.5 1.0 O A:HOH2023 3.7 27.5 1.0 CA A:TRP390 3.8 13.4 1.0 CA A:VAL389 3.9 14.4 1.0 C A:VAL389 3.9 13.4 1.0 C A:LEU358 3.9 17.6 1.0 CB A:GLU360 4.0 19.6 1.0 C A:TRP390 4.2 14.4 1.0 O A:HOH2027 4.3 37.8 1.0 O A:HOH2026 4.3 31.3 1.0 CG1 A:ILE357 4.3 20.5 1.0 N A:GLU360 4.4 19.1 1.0 O A:HOH2061 4.4 25.7 1.0 N A:LEU358 4.4 17.8 1.0 CG1 A:VAL389 4.5 15.6 1.0 CA A:LEU358 4.6 17.8 1.0 CB A:LEU358 4.6 18.3 1.0 OE1 A:GLU360 4.7 25.9 1.0 CG2 A:VAL389 4.8 15.1 1.0 CD1 A:ILE357 4.8 23.3 1.0 CA A:GLU360 4.9 19.8 1.0 CG A:TRP390 4.9 14.3 1.0 CE3 A:TRP390 5.0 13.7 1.0 N A:CYS359 5.0 17.3 1.0

M.Fiedler, M.J.Sanchez-Barrena, M.Nekrasov, J.Mieszczanek, V.Rybin, J.Muller, P.Evans, M.Bienz. Decoding of Methylated Histone H3 Tail By the Pygo- BCL9 Wnt Signaling Complex. Mol.Cell V. 30 507 2008.
ISSN: ISSN 1097-2765
PubMed: 18498752
DOI: 10.1016/J.MOLCEL.2008.03.011