Zinc in PDB 2vpg: 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: 2vpg was solved by M.Fiedler, M.J.Sanchez-Barrena, M.Nekrasov, J.Mieszczanek, V.Rybin, J.Muller, M.Bienz, P.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.74 / 1.60
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.750, 105.750, 51.420, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 21.8

The binding sites of Zinc atom in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex (pdb code 2vpg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex, PDB code: 2vpg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn1400 b:9.5 occ:1.00 ND1 A:HIS368 2.1 10.8 1.0 SG A:CYS371 2.3 10.2 1.0 SG A:CYS346 2.3 10.6 1.0 SG A:CYS343 2.3 9.3 1.0 CE1 A:HIS368 3.0 9.8 1.0 CB A:CYS343 3.0 8.9 1.0 CG A:HIS368 3.1 9.8 1.0 CB A:CYS346 3.3 10.2 1.0 CB A:CYS371 3.4 10.0 1.0 CB A:HIS368 3.4 9.2 1.0 N A:CYS346 3.7 10.4 1.0 N A:HIS368 4.0 9.3 1.0 CA A:CYS346 4.1 10.8 1.0 O A:HOH2092 4.1 13.2 1.0 NE2 A:HIS368 4.2 10.0 1.0 CD2 A:HIS368 4.2 10.4 1.0 CA A:HIS368 4.4 8.7 1.0 O1 A:GOL1399 4.4 47.3 1.0 CA A:CYS343 4.5 9.4 1.0 CA A:CYS371 4.7 9.8 1.0 C A:CYS346 4.8 11.2 1.0 C A:ILE345 4.8 10.7 1.0 CB A:ILE345 4.8 11.2 1.0 CB C:CYS346 4.9 9.7 1.0 N A:THR347 4.9 11.4 1.0

Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn1401 b:15.9 occ:1.00 SG A:CYS359 2.2 15.0 1.0 SG A:CYS363 2.3 15.1 1.0 SG A:CYS395 2.4 17.2 1.0 SG A:CYS392 2.4 14.7 1.0 CB A:CYS359 3.2 13.2 1.0 CB A:CYS395 3.2 20.2 1.0 CB A:CYS363 3.3 16.2 1.0 CB A:CYS392 3.5 15.3 1.0 N A:CYS363 3.6 17.8 1.0 N A:CYS392 3.8 14.8 1.0 CA A:CYS363 4.0 16.2 1.0 CA A:CYS392 4.2 15.1 1.0 O A:HOH2042 4.2 23.9 1.0 CZ A:PHE367 4.3 9.1 1.0 CE2 A:PHE367 4.4 8.7 1.0 N A:CYS395 4.4 20.3 1.0 CA A:CYS395 4.4 20.4 1.0 CA A:CYS359 4.6 13.5 1.0 C A:SER362 4.8 19.5 1.0 O A:CYS392 4.8 15.9 1.0 C A:CYS363 4.8 15.8 1.0 CB A:SER362 4.8 20.3 1.0 C A:CYS392 4.8 15.8 1.0 N A:GLN364 4.9 14.3 1.0 N A:SER362 4.9 20.6 1.0 O A:CYS359 4.9 14.9 1.0 C A:GLY391 5.0 15.1 1.0

Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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 C:Zn1399 b:10.9 occ:1.00 ND1 C:HIS368 2.1 11.2 1.0 SG C:CYS371 2.3 11.1 1.0 SG C:CYS346 2.3 9.9 1.0 SG C:CYS343 2.4 10.2 1.0 CB C:CYS343 3.0 11.0 1.0 CE1 C:HIS368 3.1 9.5 1.0 CG C:HIS368 3.1 9.6 1.0 CB C:CYS346 3.2 9.7 1.0 CB C:CYS371 3.4 9.8 1.0 CB C:HIS368 3.4 10.0 1.0 N C:CYS346 3.7 10.5 1.0 CA C:CYS346 4.0 10.0 1.0 N C:HIS368 4.1 9.7 1.0 O A:HOH2011 4.1 17.5 1.0 NE2 C:HIS368 4.2 11.2 1.0 CD2 C:HIS368 4.3 10.7 1.0 CA C:HIS368 4.4 9.5 1.0 O A:HOH2014 4.4 32.7 1.0 CA C:CYS343 4.5 10.8 1.0 CA C:CYS371 4.7 9.7 1.0 CB A:CYS346 4.8 10.2 1.0 C C:CYS346 4.8 10.5 1.0 CB C:ILE345 4.8 10.2 1.0 N C:THR347 4.9 9.8 1.0 C C:ILE345 4.9 10.4 1.0 N C:CYS371 5.0 9.4 1.0

Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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 C:Zn1400 b:17.7 occ:1.00 SG C:CYS359 2.3 15.6 1.0 SG C:CYS363 2.3 16.2 1.0 SG C:CYS395 2.4 19.9 1.0 SG C:CYS392 2.5 16.8 1.0 CB C:CYS359 3.2 13.4 1.0 CB C:CYS363 3.2 17.1 1.0 CB C:CYS395 3.3 22.9 1.0 CB C:CYS392 3.5 17.1 1.0 N C:CYS363 3.6 18.7 1.0 N C:CYS392 3.9 16.1 1.0 CA C:CYS363 4.0 17.4 1.0 CA C:CYS392 4.2 16.4 1.0 O C:HOH2040 4.3 29.4 1.0 N C:CYS395 4.4 22.5 1.0 CZ C:PHE367 4.4 10.5 1.0 CE2 C:PHE367 4.4 10.3 1.0 CA C:CYS395 4.4 23.0 1.0 CA C:CYS359 4.6 13.8 1.0 C C:SER362 4.8 20.4 1.0 C C:CYS363 4.8 16.9 1.0 CB C:SER362 4.9 21.8 1.0 O C:CYS392 4.9 17.4 1.0 C C:CYS392 4.9 17.8 1.0 N C:SER362 4.9 21.4 1.0 O C:CYS359 4.9 14.5 1.0 N C:GLN364 4.9 16.8 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