Zinc in PDB 2jpa: Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna
(pdb code 2jpa). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna, PDB code: 2jpa:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2jpa
Go back to
Zinc Binding Sites List in 2jpa
Zinc binding site 1 out
of 4 in the Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn131
b:0.0
occ:1.00
|
NE2
|
A:HIS27
|
2.1
|
0.0
|
1.0
|
NE2
|
A:HIS31
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS9
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS14
|
2.3
|
0.0
|
1.0
|
HD2
|
A:HIS31
|
2.5
|
0.0
|
1.0
|
HB3
|
A:CYS14
|
2.5
|
0.0
|
1.0
|
CD2
|
A:HIS31
|
2.6
|
0.0
|
1.0
|
HB2
|
A:CYS9
|
2.7
|
0.0
|
1.0
|
CB
|
A:CYS14
|
2.7
|
0.0
|
1.0
|
CB
|
A:CYS9
|
2.8
|
0.0
|
1.0
|
HB2
|
A:CYS14
|
2.8
|
0.0
|
1.0
|
HB3
|
A:CYS9
|
2.9
|
0.0
|
1.0
|
CE1
|
A:HIS27
|
3.0
|
0.0
|
1.0
|
HE1
|
A:HIS27
|
3.1
|
0.0
|
1.0
|
CD2
|
A:HIS27
|
3.1
|
0.0
|
1.0
|
HB3
|
A:TYR11
|
3.3
|
0.0
|
1.0
|
CE1
|
A:HIS31
|
3.3
|
0.0
|
1.0
|
HD2
|
A:HIS27
|
3.4
|
0.0
|
1.0
|
HE2
|
A:TYR18
|
3.8
|
0.0
|
1.0
|
HH
|
A:TYR18
|
3.8
|
0.0
|
1.0
|
HE1
|
A:HIS31
|
3.9
|
0.0
|
1.0
|
CG
|
A:HIS31
|
3.9
|
0.0
|
1.0
|
H
|
A:ASN15
|
3.9
|
0.0
|
1.0
|
H
|
A:LYS16
|
4.0
|
0.0
|
1.0
|
H
|
A:TYR11
|
4.1
|
0.0
|
1.0
|
HE3
|
A:LYS16
|
4.1
|
0.0
|
1.0
|
ND1
|
A:HIS27
|
4.2
|
0.0
|
1.0
|
HB2
|
A:TYR11
|
4.2
|
0.0
|
1.0
|
ND1
|
A:HIS31
|
4.2
|
0.0
|
1.0
|
CG
|
A:HIS27
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS14
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS9
|
4.2
|
0.0
|
1.0
|
HE2
|
A:LYS16
|
4.3
|
0.0
|
1.0
|
CB
|
A:TYR11
|
4.3
|
0.0
|
1.0
|
HB2
|
A:LYS16
|
4.5
|
0.0
|
1.0
|
N
|
A:ASN15
|
4.6
|
0.0
|
1.0
|
HA
|
A:CYS9
|
4.6
|
0.0
|
1.0
|
HA
|
A:SER28
|
4.6
|
0.0
|
1.0
|
HD2
|
A:TYR11
|
4.7
|
0.0
|
1.0
|
CE2
|
A:TYR18
|
4.7
|
0.0
|
1.0
|
CE
|
A:LYS16
|
4.7
|
0.0
|
1.0
|
HA
|
A:CYS14
|
4.8
|
0.0
|
1.0
|
OH
|
A:TYR18
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS14
|
4.8
|
0.0
|
1.0
|
C
|
A:CYS9
|
4.9
|
0.0
|
1.0
|
HE3
|
A:LYS30
|
4.9
|
0.0
|
1.0
|
N
|
A:TYR11
|
5.0
|
0.0
|
1.0
|
H
|
A:CYS14
|
5.0
|
0.0
|
1.0
|
HD23
|
A:LEU24
|
5.0
|
0.0
|
1.0
|
O
|
A:TYR11
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2jpa
Go back to
Zinc Binding Sites List in 2jpa
Zinc binding site 2 out
of 4 in the Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn132
b:0.0
occ:1.00
|
NE2
|
A:HIS57
|
2.1
|
0.0
|
1.0
|
NE2
|
A:HIS61
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS44
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS39
|
2.3
|
0.0
|
1.0
|
HD2
|
A:HIS57
|
2.6
|
0.0
|
1.0
|
CD2
|
A:HIS57
|
2.6
|
0.0
|
1.0
|
CE1
|
A:HIS61
|
2.9
|
0.0
|
1.0
|
HD2
|
A:ARG46
|
2.9
|
0.0
|
1.0
|
HE1
|
A:HIS61
|
3.0
|
0.0
|
1.0
|
HD2
|
A:PHE41
|
3.1
|
0.0
|
1.0
|
CB
|
A:CYS44
|
3.1
|
0.0
|
1.0
|
HB2
|
A:CYS44
|
3.2
|
0.0
|
1.0
|
HB2
|
A:ARG46
|
3.2
|
0.0
|
1.0
|
HB3
|
A:CYS44
|
3.2
|
0.0
|
1.0
|
HH11
|
A:ARG46
|
3.2
|
0.0
|
1.0
|
CD2
|
A:HIS61
|
3.3
|
0.0
|
1.0
|
CE1
|
A:HIS57
|
3.3
|
0.0
|
1.0
|
HE2
|
A:PHE41
|
3.6
|
0.0
|
1.0
|
CB
|
A:CYS39
|
3.6
|
0.0
|
1.0
|
HD2
|
A:HIS61
|
3.6
|
0.0
|
1.0
|
HB3
|
A:CYS39
|
3.7
|
0.0
|
1.0
|
CD2
|
A:PHE41
|
3.8
|
0.0
|
1.0
|
HB2
|
A:CYS39
|
3.8
|
0.0
|
1.0
|
HE1
|
A:HIS57
|
3.8
|
0.0
|
1.0
|
HE2
|
A:PHE48
|
3.9
|
0.0
|
1.0
|
CG
|
A:HIS57
|
3.9
|
0.0
|
1.0
|
CD
|
A:ARG46
|
4.0
|
0.0
|
1.0
|
H
|
A:ARG46
|
4.0
|
0.0
|
1.0
|
CE2
|
A:PHE41
|
4.0
|
0.0
|
1.0
|
ND1
|
A:HIS61
|
4.1
|
0.0
|
1.0
|
NH1
|
A:ARG46
|
4.2
|
0.0
|
1.0
|
CB
|
A:ARG46
|
4.2
|
0.0
|
1.0
|
ND1
|
A:HIS57
|
4.3
|
0.0
|
1.0
|
CG
|
A:HIS61
|
4.3
|
0.0
|
1.0
|
HG3
|
A:ARG46
|
4.4
|
0.0
|
1.0
|
HD3
|
A:ARG46
|
4.4
|
0.0
|
1.0
|
CG
|
A:ARG46
|
4.5
|
0.0
|
1.0
|
H
|
A:GLU45
|
4.5
|
0.0
|
1.0
|
HZ
|
A:PHE48
|
4.5
|
0.0
|
1.0
|
CA
|
A:CYS44
|
4.6
|
0.0
|
1.0
|
HD3
|
A:ARG60
|
4.7
|
0.0
|
1.0
|
HH12
|
A:ARG46
|
4.7
|
0.0
|
1.0
|
HA
|
A:CYS44
|
4.7
|
0.0
|
1.0
|
HB2
|
A:PHE41
|
4.8
|
0.0
|
1.0
|
CE2
|
A:PHE48
|
4.8
|
0.0
|
1.0
|
HB3
|
A:ARG46
|
4.8
|
0.0
|
1.0
|
HA
|
A:CYS39
|
4.9
|
0.0
|
1.0
|
N
|
A:ARG46
|
4.9
|
0.0
|
1.0
|
CA
|
A:CYS39
|
4.9
|
0.0
|
1.0
|
NE
|
A:ARG46
|
4.9
|
0.0
|
1.0
|
CG
|
A:PHE41
|
5.0
|
0.0
|
1.0
|
HA
|
A:GLN58
|
5.0
|
0.0
|
1.0
|
CZ
|
A:ARG46
|
5.0
|
0.0
|
1.0
|
HD1
|
A:HIS61
|
5.0
|
0.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2jpa
Go back to
Zinc Binding Sites List in 2jpa
Zinc binding site 3 out
of 4 in the Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn133
b:0.0
occ:1.00
|
NE2
|
A:HIS85
|
2.1
|
0.0
|
1.0
|
NE2
|
A:HIS89
|
2.1
|
0.0
|
1.0
|
SG
|
A:CYS72
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS69
|
2.3
|
0.0
|
1.0
|
HD2
|
A:HIS89
|
2.4
|
0.0
|
1.0
|
H
|
A:CYS72
|
2.5
|
0.0
|
1.0
|
CD2
|
A:HIS89
|
2.5
|
0.0
|
1.0
|
CE1
|
A:HIS85
|
2.8
|
0.0
|
1.0
|
HE1
|
A:HIS85
|
2.8
|
0.0
|
1.0
|
HG1
|
A:THR71
|
2.9
|
0.0
|
1.0
|
HB2
|
A:CYS69
|
3.0
|
0.0
|
1.0
|
CB
|
A:CYS69
|
3.1
|
0.0
|
1.0
|
HB3
|
A:CYS69
|
3.2
|
0.0
|
1.0
|
CD2
|
A:HIS85
|
3.3
|
0.0
|
1.0
|
HB
|
A:THR71
|
3.3
|
0.0
|
1.0
|
HB3
|
A:CYS72
|
3.3
|
0.0
|
1.0
|
CB
|
A:CYS72
|
3.3
|
0.0
|
1.0
|
CE1
|
A:HIS89
|
3.4
|
0.0
|
1.0
|
N
|
A:CYS72
|
3.4
|
0.0
|
1.0
|
HD2
|
A:HIS85
|
3.7
|
0.0
|
1.0
|
HB2
|
A:ARG74
|
3.7
|
0.0
|
1.0
|
OG1
|
A:THR71
|
3.7
|
0.0
|
1.0
|
CG
|
A:HIS89
|
3.8
|
0.0
|
1.0
|
H
|
A:ARG74
|
3.9
|
0.0
|
1.0
|
HE1
|
A:HIS89
|
3.9
|
0.0
|
1.0
|
CA
|
A:CYS72
|
3.9
|
0.0
|
1.0
|
CB
|
A:THR71
|
4.0
|
0.0
|
1.0
|
H
|
A:THR71
|
4.0
|
0.0
|
1.0
|
ND1
|
A:HIS85
|
4.1
|
0.0
|
1.0
|
HD3
|
A:ARG74
|
4.2
|
0.0
|
1.0
|
H
|
A:GLN73
|
4.2
|
0.0
|
1.0
|
ND1
|
A:HIS89
|
4.2
|
0.0
|
1.0
|
CG
|
A:HIS85
|
4.3
|
0.0
|
1.0
|
HB2
|
A:CYS72
|
4.3
|
0.0
|
1.0
|
HE2
|
A:PHE76
|
4.4
|
0.0
|
1.0
|
C
|
A:THR71
|
4.4
|
0.0
|
1.0
|
CA
|
A:CYS69
|
4.5
|
0.0
|
1.0
|
CA
|
A:THR71
|
4.6
|
0.0
|
1.0
|
N
|
A:THR71
|
4.6
|
0.0
|
1.0
|
C
|
A:CYS72
|
4.6
|
0.0
|
1.0
|
N
|
A:GLN73
|
4.7
|
0.0
|
1.0
|
CB
|
A:ARG74
|
4.7
|
0.0
|
1.0
|
HG3
|
A:ARG74
|
4.8
|
0.0
|
1.0
|
HA
|
A:CYS69
|
4.8
|
0.0
|
1.0
|
HA
|
A:CYS72
|
4.9
|
0.0
|
1.0
|
N
|
A:ARG74
|
4.9
|
0.0
|
1.0
|
HD1
|
A:HIS85
|
4.9
|
0.0
|
1.0
|
HB2
|
A:HIS89
|
4.9
|
0.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2jpa
Go back to
Zinc Binding Sites List in 2jpa
Zinc binding site 4 out
of 4 in the Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn134
b:0.0
occ:1.00
|
NE2
|
A:HIS115
|
2.0
|
0.0
|
1.0
|
NE2
|
A:HIS119
|
2.0
|
0.0
|
1.0
|
SG
|
A:CYS102
|
2.3
|
0.0
|
1.0
|
SG
|
A:CYS97
|
2.3
|
0.0
|
1.0
|
HE1
|
A:HIS115
|
2.5
|
0.0
|
1.0
|
HB3
|
A:CYS102
|
2.6
|
0.0
|
1.0
|
CE1
|
A:HIS115
|
2.6
|
0.0
|
1.0
|
HB2
|
A:CYS97
|
2.7
|
0.0
|
1.0
|
CB
|
A:CYS102
|
2.8
|
0.0
|
1.0
|
CB
|
A:CYS97
|
2.8
|
0.0
|
1.0
|
HB3
|
A:CYS97
|
2.9
|
0.0
|
1.0
|
HB2
|
A:CYS102
|
3.0
|
0.0
|
1.0
|
CE1
|
A:HIS119
|
3.0
|
0.0
|
1.0
|
CD2
|
A:HIS119
|
3.1
|
0.0
|
1.0
|
HB2
|
A:TRP99
|
3.2
|
0.0
|
1.0
|
HE1
|
A:HIS119
|
3.2
|
0.0
|
1.0
|
CD2
|
A:HIS115
|
3.3
|
0.0
|
1.0
|
HD2
|
A:HIS119
|
3.3
|
0.0
|
1.0
|
HD1
|
A:HIS116
|
3.4
|
0.0
|
1.0
|
H
|
A:GLN103
|
3.7
|
0.0
|
1.0
|
H
|
A:LYS104
|
3.7
|
0.0
|
1.0
|
HB2
|
A:LYS104
|
3.8
|
0.0
|
1.0
|
HD2
|
A:HIS115
|
3.8
|
0.0
|
1.0
|
ND1
|
A:HIS115
|
3.9
|
0.0
|
1.0
|
HD1
|
A:TRP99
|
4.1
|
0.0
|
1.0
|
H
|
A:TRP99
|
4.1
|
0.0
|
1.0
|
HZ1
|
A:LYS104
|
4.1
|
0.0
|
1.0
|
HD2
|
A:LYS104
|
4.2
|
0.0
|
1.0
|
ND1
|
A:HIS119
|
4.2
|
0.0
|
1.0
|
CB
|
A:TRP99
|
4.2
|
0.0
|
1.0
|
CG
|
A:HIS119
|
4.2
|
0.0
|
1.0
|
CA
|
A:CYS102
|
4.2
|
0.0
|
1.0
|
CG
|
A:HIS115
|
4.2
|
0.0
|
1.0
|
N
|
A:GLN103
|
4.3
|
0.0
|
1.0
|
CA
|
A:CYS97
|
4.3
|
0.0
|
1.0
|
ND1
|
A:HIS116
|
4.3
|
0.0
|
1.0
|
CD1
|
A:TRP99
|
4.3
|
0.0
|
1.0
|
HE1
|
A:HIS116
|
4.4
|
0.0
|
1.0
|
CG
|
A:TRP99
|
4.4
|
0.0
|
1.0
|
HA
|
A:HIS116
|
4.6
|
0.0
|
1.0
|
C
|
A:CYS102
|
4.6
|
0.0
|
1.0
|
N
|
A:LYS104
|
4.6
|
0.0
|
1.0
|
HA
|
A:CYS97
|
4.7
|
0.0
|
1.0
|
HD1
|
A:HIS115
|
4.7
|
0.0
|
1.0
|
HA
|
A:CYS102
|
4.7
|
0.0
|
1.0
|
HB3
|
A:TRP99
|
4.7
|
0.0
|
1.0
|
CB
|
A:LYS104
|
4.8
|
0.0
|
1.0
|
CE1
|
A:HIS116
|
4.8
|
0.0
|
1.0
|
HE2
|
A:PHE106
|
4.8
|
0.0
|
1.0
|
H
|
A:ARG98
|
4.9
|
0.0
|
1.0
|
HD11
|
A:LEU112
|
4.9
|
0.0
|
1.0
|
HG3
|
A:LYS104
|
4.9
|
0.0
|
1.0
|
N
|
A:TRP99
|
5.0
|
0.0
|
1.0
|
H
|
A:CYS97
|
5.0
|
0.0
|
1.0
|
|
Reference:
R.Stoll,
B.M.Lee,
E.W.Debler,
J.H.Laity,
I.A.Wilson,
H.J.Dyson,
P.E.Wright.
Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to Dna J.Mol.Biol. V. 372 1227 2007.
ISSN: ISSN 0022-2836
PubMed: 17716689
DOI: 10.1016/J.JMB.2007.07.017
Page generated: Thu Oct 17 01:19:30 2024
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