Zinc in PDB 2jmj: uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide
Zinc Binding Sites:
The binding sites of Zinc atom in the uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide
(pdb code 2jmj). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the
uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide, PDB code: 2jmj:
Jump to Zinc binding site number:
1;
2;
Zinc binding site 1 out
of 2 in 2jmj
Go back to
Zinc Binding Sites List in 2jmj
Zinc binding site 1 out
of 2 in the uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:12.5
occ:1.00
|
SG
|
A:CYS73
|
1.3
|
12.5
|
1.0
|
SG
|
A:CYS42
|
1.4
|
12.5
|
1.0
|
SG
|
A:CYS69
|
1.5
|
100.0
|
1.0
|
SG
|
A:CYS47
|
1.6
|
12.5
|
1.0
|
HB2
|
A:CYS69
|
2.3
|
0.0
|
1.0
|
CB
|
A:CYS69
|
2.4
|
100.0
|
1.0
|
CB
|
A:CYS73
|
2.6
|
12.5
|
1.0
|
HB2
|
A:CYS73
|
2.7
|
0.0
|
1.0
|
CB
|
A:CYS47
|
2.7
|
12.5
|
1.0
|
CB
|
A:CYS42
|
2.8
|
12.5
|
1.0
|
HA
|
A:CYS47
|
2.8
|
0.0
|
1.0
|
HB3
|
A:CYS47
|
2.8
|
0.0
|
1.0
|
HB2
|
A:CYS42
|
2.9
|
0.0
|
1.0
|
HB3
|
A:CYS69
|
3.0
|
0.0
|
1.0
|
CA
|
A:CYS47
|
3.2
|
12.5
|
1.0
|
HA
|
A:CYS73
|
3.3
|
0.0
|
1.0
|
HB3
|
A:CYS73
|
3.3
|
0.0
|
1.0
|
HB3
|
A:CYS42
|
3.4
|
0.0
|
1.0
|
HZ
|
A:PHE52
|
3.4
|
0.0
|
1.0
|
HD2
|
A:PRO48
|
3.5
|
0.0
|
1.0
|
CA
|
A:CYS73
|
3.6
|
12.5
|
1.0
|
CZ
|
A:PHE52
|
3.6
|
12.5
|
1.0
|
HB2
|
A:CYS47
|
3.6
|
0.0
|
1.0
|
CA
|
A:CYS69
|
3.7
|
100.0
|
1.0
|
HA
|
A:CYS42
|
3.8
|
0.0
|
1.0
|
H
|
A:SER70
|
3.9
|
0.0
|
1.0
|
CA
|
A:CYS42
|
3.9
|
12.5
|
1.0
|
C
|
A:CYS47
|
4.0
|
12.5
|
1.0
|
H
|
A:PHE49
|
4.0
|
0.0
|
1.0
|
H
|
A:CYS69
|
4.0
|
0.0
|
1.0
|
CE1
|
A:PHE52
|
4.0
|
12.5
|
1.0
|
HB3
|
A:ASN44
|
4.0
|
0.0
|
1.0
|
N
|
A:CYS69
|
4.1
|
100.0
|
1.0
|
HE1
|
A:PHE52
|
4.1
|
0.0
|
1.0
|
C
|
A:CYS69
|
4.1
|
100.0
|
1.0
|
CE2
|
A:PHE52
|
4.1
|
12.5
|
1.0
|
O
|
A:PHE49
|
4.1
|
12.5
|
1.0
|
HB2
|
A:SER70
|
4.1
|
0.0
|
1.0
|
N
|
A:SER70
|
4.2
|
100.0
|
1.0
|
H
|
A:CYS73
|
4.3
|
0.0
|
1.0
|
HE2
|
A:PHE52
|
4.3
|
0.0
|
1.0
|
CD
|
A:PRO48
|
4.4
|
25.0
|
1.0
|
N
|
A:PRO48
|
4.4
|
12.5
|
1.0
|
N
|
A:CYS73
|
4.4
|
12.5
|
1.0
|
N
|
A:CYS47
|
4.5
|
12.5
|
1.0
|
HA
|
A:CYS69
|
4.5
|
0.0
|
1.0
|
O
|
A:CYS47
|
4.6
|
12.5
|
1.0
|
HD21
|
A:ASN44
|
4.6
|
0.0
|
1.0
|
HD13
|
A:ILE76
|
4.7
|
0.0
|
1.0
|
C
|
A:CYS73
|
4.7
|
12.5
|
1.0
|
H
|
A:CYS47
|
4.8
|
0.0
|
1.0
|
CD1
|
A:PHE52
|
4.8
|
12.5
|
1.0
|
H
|
A:CYS42
|
4.8
|
0.0
|
1.0
|
N
|
A:CYS42
|
4.9
|
12.5
|
1.0
|
N
|
A:PHE49
|
4.9
|
12.5
|
1.0
|
HD3
|
A:PRO48
|
4.9
|
0.0
|
1.0
|
HD11
|
A:ILE76
|
4.9
|
0.0
|
1.0
|
CB
|
A:SER70
|
4.9
|
100.0
|
1.0
|
O
|
A:CYS69
|
4.9
|
100.0
|
1.0
|
CD2
|
A:PHE52
|
4.9
|
12.5
|
1.0
|
C
|
A:CYS42
|
4.9
|
12.5
|
1.0
|
HD1
|
A:TYR68
|
5.0
|
0.0
|
1.0
|
CB
|
A:ASN44
|
5.0
|
12.5
|
1.0
|
|
Zinc binding site 2 out
of 2 in 2jmj
Go back to
Zinc Binding Sites List in 2jmj
Zinc binding site 2 out
of 2 in the uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of uc(Nmr) Solution Structure of the Phd Domain From the Yeast YNG1 Protein in Complex with H3(1-9)K4ME3 Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:12.5
occ:1.00
|
SG
|
A:CYS56
|
1.3
|
12.5
|
1.0
|
SG
|
A:CYS31
|
1.4
|
12.5
|
1.0
|
SG
|
A:CYS29
|
1.5
|
12.5
|
1.0
|
CB
|
A:CYS56
|
2.4
|
12.5
|
1.0
|
HB2
|
A:CYS56
|
2.4
|
0.0
|
1.0
|
HD22
|
A:ASN33
|
2.5
|
0.0
|
1.0
|
CB
|
A:CYS31
|
2.5
|
12.5
|
1.0
|
HB2
|
A:CYS31
|
2.5
|
0.0
|
1.0
|
HH
|
A:TYR36
|
2.6
|
0.0
|
1.0
|
HB3
|
A:CYS29
|
2.6
|
0.0
|
1.0
|
CB
|
A:CYS29
|
2.7
|
12.5
|
1.0
|
CE1
|
A:HIS53
|
3.1
|
12.5
|
1.0
|
ND1
|
A:HIS53
|
3.1
|
12.5
|
1.0
|
HB3
|
A:CYS31
|
3.1
|
0.0
|
1.0
|
HB3
|
A:CYS56
|
3.1
|
0.0
|
1.0
|
H
|
A:CYS31
|
3.2
|
0.0
|
1.0
|
NE2
|
A:HIS53
|
3.2
|
12.5
|
1.0
|
CG
|
A:HIS53
|
3.2
|
12.5
|
1.0
|
CD2
|
A:HIS53
|
3.2
|
12.5
|
1.0
|
ND2
|
A:ASN33
|
3.3
|
50.0
|
1.0
|
HA
|
A:CYS56
|
3.4
|
0.0
|
1.0
|
HB2
|
A:CYS29
|
3.4
|
0.0
|
1.0
|
CA
|
A:CYS56
|
3.5
|
12.5
|
1.0
|
HD1
|
A:HIS53
|
3.5
|
0.0
|
1.0
|
OH
|
A:TYR36
|
3.5
|
12.5
|
1.0
|
H
|
A:HIS53
|
3.5
|
0.0
|
1.0
|
HE1
|
A:HIS53
|
3.6
|
0.0
|
1.0
|
H
|
A:CYS29
|
3.6
|
0.0
|
1.0
|
HE2
|
A:HIS53
|
3.7
|
0.0
|
1.0
|
CA
|
A:CYS29
|
3.7
|
12.5
|
1.0
|
HB2
|
A:HIS53
|
3.7
|
0.0
|
1.0
|
HD21
|
A:ASN33
|
3.7
|
0.0
|
1.0
|
CA
|
A:CYS31
|
3.7
|
12.5
|
1.0
|
N
|
A:CYS31
|
3.8
|
12.5
|
1.0
|
HD2
|
A:HIS53
|
3.8
|
0.0
|
1.0
|
C
|
A:CYS29
|
3.9
|
12.5
|
1.0
|
N
|
A:CYS29
|
3.9
|
12.5
|
1.0
|
O
|
A:CYS29
|
4.0
|
12.5
|
1.0
|
CB
|
A:HIS53
|
4.0
|
12.5
|
1.0
|
HE2
|
A:TYR36
|
4.0
|
0.0
|
1.0
|
H
|
A:CYS56
|
4.2
|
0.0
|
1.0
|
N
|
A:CYS56
|
4.2
|
12.5
|
1.0
|
CZ
|
A:TYR36
|
4.2
|
12.5
|
1.0
|
CG
|
A:ASN33
|
4.2
|
12.5
|
1.0
|
H
|
A:ASN33
|
4.2
|
0.0
|
1.0
|
OD1
|
A:ASN33
|
4.3
|
50.0
|
1.0
|
CE2
|
A:TYR36
|
4.4
|
12.5
|
1.0
|
N
|
A:HIS53
|
4.4
|
12.5
|
1.0
|
HA
|
A:CYS31
|
4.5
|
0.0
|
1.0
|
H
|
A:ARG32
|
4.5
|
0.0
|
1.0
|
C
|
A:CYS31
|
4.6
|
12.5
|
1.0
|
HA
|
A:CYS29
|
4.6
|
0.0
|
1.0
|
C
|
A:CYS56
|
4.7
|
12.5
|
1.0
|
N
|
A:PHE30
|
4.7
|
12.5
|
1.0
|
CA
|
A:HIS53
|
4.7
|
12.5
|
1.0
|
O
|
A:ASN33
|
4.9
|
12.5
|
1.0
|
N
|
A:ARG32
|
4.9
|
12.5
|
1.0
|
HB3
|
A:HIS53
|
4.9
|
0.0
|
1.0
|
HA
|
A:PHE52
|
4.9
|
0.0
|
1.0
|
O
|
A:HIS53
|
5.0
|
12.5
|
1.0
|
H
|
A:PHE30
|
5.0
|
0.0
|
1.0
|
|
Reference:
S.D.Taverna,
S.Ilin,
R.S.Rogers,
J.C.Tanny,
H.Lavender,
H.Li,
L.Baker,
J.Boyle,
L.P.Blair,
B.T.Chait,
D.J.Patel,
J.D.Aitchison,
A.J.Tackett,
C.D.Allis.
YNG1 Phd Finger Binding to H3 Trimethylated at K4 Promotes NUA3 Hat Activity at K14 of H3 and Transcription at A Subset of Targeted Orfs Mol.Cell V. 24 785 2006.
ISSN: ISSN 1097-2765
PubMed: 17157260
DOI: 10.1016/J.MOLCEL.2006.10.026
Page generated: Thu Oct 17 01:17:51 2024
|