Atomistry » Sodium » PDB 2uzz-2vrp » 2vpb
Atomistry »
  Sodium »
    PDB 2uzz-2vrp »
      2vpb »

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

Protein crystallography data

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

Other elements in 2vpb:

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

Sodium Binding Sites:

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 2vpb

Go back to Sodium Binding Sites List in 2vpb
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 2vpb

Go back to Sodium Binding Sites List in 2vpb
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

Reference:

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
Page generated: Tue Dec 15 05:56:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy