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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: Wed Dec 16 03:32:12 2020

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