Zinc in PDB 2vpe: 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: 2vpe 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)	106.00 / 1.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.720, 105.720, 51.430, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23

The binding sites of Zinc atom in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex (pdb code 2vpe). 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: 2vpe:
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:17.7 occ:1.00 ND1 A:HIS368 2.1 17.7 1.0 SG A:CYS343 2.3 16.1 1.0 SG A:CYS371 2.3 17.6 1.0 SG A:CYS346 2.4 18.3 1.0 CB A:CYS343 3.0 16.1 1.0 CG A:HIS368 3.1 15.8 1.0 CE1 A:HIS368 3.1 14.6 1.0 CB A:CYS346 3.3 17.1 1.0 CB A:CYS371 3.3 15.9 1.0 CB A:HIS368 3.4 16.1 1.0 N A:CYS346 3.7 16.9 1.0 CA A:CYS346 4.1 17.6 1.0 N A:HIS368 4.1 14.8 1.0 O A:HOH2078 4.1 23.1 1.0 NE2 A:HIS368 4.2 16.2 1.0 CD2 A:HIS368 4.2 16.9 1.0 CA A:HIS368 4.3 14.3 1.0 CA A:CYS343 4.5 16.5 1.0 O1 A:GOL1399 4.5 50.9 1.0 CA A:CYS371 4.7 15.8 1.0 CB A:ILE345 4.8 17.8 1.0 C A:ILE345 4.8 17.6 1.0 C A:CYS346 4.8 17.9 1.0 CB C:CYS346 4.9 19.5 1.0 N A:THR347 4.9 18.6 1.0 C1 A:GOL1399 4.9 50.9 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:22.4 occ:1.00 SG A:CYS359 2.3 21.0 1.0 SG A:CYS395 2.3 25.4 1.0 SG A:CYS363 2.4 21.6 1.0 SG A:CYS392 2.4 22.3 1.0 CB A:CYS395 3.2 27.5 1.0 CB A:CYS359 3.2 18.2 1.0 CB A:CYS363 3.3 22.0 1.0 CB A:CYS392 3.5 23.1 1.0 N A:CYS363 3.6 23.5 1.0 N A:CYS392 3.8 21.8 1.0 CA A:CYS363 4.0 22.2 1.0 CA A:CYS392 4.2 21.8 1.0 O A:HOH2034 4.2 27.4 1.0 N A:CYS395 4.3 27.6 1.0 CA A:CYS395 4.3 28.0 1.0 CZ A:PHE367 4.4 16.0 1.0 CE2 A:PHE367 4.4 15.0 1.0 CA A:CYS359 4.7 18.5 1.0 CB A:SER362 4.7 28.4 1.0 C A:SER362 4.8 26.1 1.0 O A:CYS392 4.8 21.5 1.0 C A:CYS392 4.8 23.1 1.0 C A:CYS363 4.8 21.1 1.0 N A:GLN364 4.9 20.2 1.0 C A:GLY391 4.9 21.3 1.0 O A:CYS359 5.0 20.6 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:Zn1398 b:21.0 occ:1.00 ND1 C:HIS368 2.1 22.7 1.0 SG C:CYS371 2.3 21.2 1.0 SG C:CYS346 2.4 20.6 1.0 SG C:CYS343 2.4 19.3 1.0 CB C:CYS343 3.0 20.3 1.0 CG C:HIS368 3.1 21.6 1.0 CE1 C:HIS368 3.1 20.9 1.0 CB C:CYS346 3.3 19.5 1.0 CB C:CYS371 3.3 20.4 1.0 CB C:HIS368 3.4 20.9 1.0 N C:CYS346 3.7 19.6 1.0 CA C:CYS346 4.0 19.7 1.0 N C:HIS368 4.1 20.4 1.0 NE2 C:HIS368 4.2 23.4 1.0 CD2 C:HIS368 4.2 20.9 1.0 O A:HOH2011 4.2 25.9 1.0 CA C:HIS368 4.3 20.6 1.0 O A:HOH2014 4.4 39.6 1.0 CA C:CYS343 4.5 20.3 1.0 CA C:CYS371 4.7 20.4 1.0 CB A:CYS346 4.8 17.1 1.0 C C:ILE345 4.8 19.6 1.0 C C:CYS346 4.8 20.8 1.0 CB C:ILE345 4.8 18.7 1.0 N C:THR347 4.9 20.1 1.0 N C:CYS371 4.9 20.3 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:Zn1399 b:26.7 occ:1.00 SG C:CYS363 2.3 25.4 1.0 SG C:CYS359 2.4 22.5 1.0 SG C:CYS395 2.4 27.9 1.0 SG C:CYS392 2.4 23.1 1.0 CB C:CYS359 3.2 21.2 1.0 CB C:CYS363 3.2 26.9 1.0 CB C:CYS395 3.2 29.5 1.0 CB C:CYS392 3.5 23.1 1.0 N C:CYS363 3.6 28.7 1.0 N C:CYS392 3.9 22.8 1.0 CA C:CYS363 4.0 27.4 1.0 O C:HOH2032 4.2 36.4 1.0 CA C:CYS392 4.3 23.2 1.0 N C:CYS395 4.3 29.9 1.0 CE2 C:PHE367 4.4 19.2 1.0 CA C:CYS395 4.4 30.3 1.0 CZ C:PHE367 4.4 21.4 1.0 CA C:CYS359 4.7 22.0 1.0 O C:CYS392 4.7 23.3 1.0 C C:SER362 4.8 30.2 1.0 CB C:SER362 4.8 31.8 1.0 C C:CYS392 4.8 24.0 1.0 C C:CYS363 4.9 26.9 1.0 O C:HOH2061 4.9 50.9 1.0 N C:SER362 4.9 31.1 1.0 O C:CYS359 4.9 22.7 1.0 C C:GLY391 5.0 22.8 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