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: Thu Oct 17 04:24:29 2024
|