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Zinc in PDB 2vpd: 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: 2vpd 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) 66.67 / 2.77
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.720, 100.890, 64.240, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Decoding of Methylated Histone H3 Tail By the Pygo-BCL9 Wnt Signaling Complex (pdb code 2vpd). 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: 2vpd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2vpd

Go back to Zinc Binding Sites List in 2vpd
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:Zn1399

b:54.7
occ:1.00
ND1 A:HIS368 2.1 58.4 1.0
SG A:CYS343 2.2 67.5 1.0
SG A:CYS371 2.4 53.8 1.0
SG A:CYS346 2.4 62.4 1.0
CB A:CYS343 3.0 67.9 1.0
CE1 A:HIS368 3.0 58.1 1.0
CB A:CYS346 3.1 64.0 1.0
CG A:HIS368 3.2 58.0 1.0
CB A:CYS371 3.3 53.1 1.0
CB A:HIS368 3.5 57.9 1.0
N A:CYS346 3.7 64.5 1.0
CA A:CYS346 3.9 64.2 1.0
N A:HIS368 4.1 59.3 1.0
NE2 A:HIS368 4.2 57.8 1.0
CD2 A:HIS368 4.3 58.1 1.0
CA A:HIS368 4.4 58.2 1.0
CA A:CYS343 4.5 67.9 1.0
C A:CYS346 4.6 64.6 1.0
N A:THR347 4.7 64.9 1.0
CA A:CYS371 4.7 53.3 1.0
C A:ILE345 4.8 64.6 1.0
CB A:ILE345 4.9 64.5 1.0
C A:CYS343 5.0 67.4 1.0

Zinc binding site 2 out of 4 in 2vpd

Go back to Zinc Binding Sites List in 2vpd
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:Zn1400

b:66.3
occ:1.00
SG A:CYS359 2.3 60.7 1.0
SG A:CYS395 2.4 68.2 1.0
SG A:CYS392 2.4 64.3 1.0
SG A:CYS363 2.4 67.1 1.0
CB A:CYS363 3.1 67.3 1.0
CB A:CYS359 3.1 60.4 1.0
CB A:CYS395 3.2 68.5 1.0
N A:CYS363 3.5 67.0 1.0
CB A:CYS392 3.6 62.2 1.0
CA A:CYS363 3.8 67.2 1.0
N A:CYS392 4.1 60.6 1.0
CA A:CYS392 4.3 62.1 1.0
CA A:CYS395 4.4 68.5 1.0
C A:SER362 4.5 66.9 1.0
N A:GLN364 4.5 67.0 1.0
C A:CYS363 4.5 67.2 1.0
N A:CYS395 4.5 68.0 1.0
N A:SER362 4.6 66.0 1.0
CA A:CYS359 4.6 60.5 1.0
CZ A:PHE367 4.7 61.5 1.0
CE2 A:PHE367 4.8 61.5 1.0
C A:CYS392 4.9 62.8 1.0
CA A:SER362 4.9 66.7 1.0
O A:CYS392 5.0 62.8 1.0
CB A:ALA361 5.0 64.4 1.0

Zinc binding site 3 out of 4 in 2vpd

Go back to Zinc Binding Sites List in 2vpd
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:59.3
occ:1.00
ND1 C:HIS368 2.2 60.6 1.0
SG C:CYS346 2.3 63.0 1.0
SG C:CYS343 2.4 63.9 1.0
SG C:CYS371 2.4 64.9 1.0
CB C:CYS343 3.0 64.5 1.0
CE1 C:HIS368 3.0 60.5 1.0
CG C:HIS368 3.2 60.4 1.0
CB C:CYS346 3.3 63.9 1.0
CB C:CYS371 3.4 63.7 1.0
CB C:HIS368 3.6 60.9 1.0
N C:CYS346 3.8 64.2 1.0
CA C:CYS346 4.1 64.2 1.0
N C:HIS368 4.2 60.9 1.0
NE2 C:HIS368 4.2 60.2 1.0
CD2 C:HIS368 4.3 60.2 1.0
CA C:CYS343 4.5 64.6 1.0
CA C:HIS368 4.5 61.0 1.0
C C:CYS346 4.8 64.6 1.0
CA C:CYS371 4.8 63.6 1.0
CB C:ILE345 4.9 64.2 1.0
C C:ILE345 4.9 64.3 1.0

Zinc binding site 4 out of 4 in 2vpd

Go back to Zinc Binding Sites List in 2vpd
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:67.5
occ:1.00
SG C:CYS359 2.0 61.0 1.0
SG C:CYS395 2.3 69.9 1.0
SG C:CYS392 2.3 66.2 1.0
SG C:CYS363 2.4 64.1 1.0
CB C:CYS359 3.2 60.9 1.0
CB C:CYS395 3.2 69.4 1.0
CB C:CYS392 3.4 65.0 1.0
CB C:CYS363 3.5 63.6 1.0
N C:CYS363 3.8 63.5 1.0
N C:CYS392 4.0 64.2 1.0
CA C:CYS363 4.2 63.6 1.0
CA C:CYS392 4.2 65.2 1.0
N C:CYS395 4.4 69.2 1.0
CA C:CYS395 4.4 69.5 1.0
CA C:CYS359 4.5 61.2 1.0
N C:GLN364 4.5 63.2 1.0
O C:CYS392 4.6 65.8 1.0
N C:SER362 4.6 62.6 1.0
C C:CYS392 4.7 65.7 1.0
C C:CYS363 4.8 63.6 1.0
C C:SER362 4.8 63.2 1.0
C C:CYS359 4.8 61.3 1.0
O C:CYS359 4.8 61.3 1.0
CB C:ALA361 4.9 61.8 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: Sat Sep 26 04:07:39 2020
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