Zinc in PDB 8bd4: Tniq-Capped Tns-Atp-Dsdna Complex
Other elements in 8bd4:
The structure of Tniq-Capped Tns-Atp-Dsdna Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Tniq-Capped Tns-Atp-Dsdna Complex
(pdb code 8bd4). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Tniq-Capped Tns-Atp-Dsdna Complex, PDB code: 8bd4:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 8bd4
Go back to
Zinc Binding Sites List in 8bd4
Zinc binding site 1 out
of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn303
b:30.0
occ:1.00
|
CZ
|
A:ARG128
|
1.1
|
215.5
|
1.0
|
|
NH1
|
A:ARG128
|
1.2
|
215.8
|
1.0
|
|
NH2
|
A:ARG128
|
1.3
|
215.7
|
1.0
|
|
SG
|
S:CYS154
|
2.3
|
30.0
|
1.0
|
|
SG
|
S:CYS151
|
2.3
|
30.0
|
1.0
|
|
SG
|
S:CYS136
|
2.3
|
30.0
|
1.0
|
|
SG
|
S:CYS133
|
2.3
|
30.0
|
1.0
|
|
NE
|
A:ARG128
|
2.4
|
215.0
|
1.0
|
|
OE2
|
A:GLU131
|
2.9
|
227.1
|
1.0
|
|
CB
|
S:CYS133
|
3.1
|
30.0
|
1.0
|
|
CB
|
S:CYS151
|
3.2
|
30.0
|
1.0
|
|
CB
|
S:CYS154
|
3.3
|
30.0
|
1.0
|
|
CB
|
S:CYS136
|
3.3
|
30.0
|
1.0
|
|
OE1
|
A:GLU131
|
3.3
|
227.7
|
1.0
|
|
CD
|
A:GLU131
|
3.4
|
227.7
|
1.0
|
|
CD
|
A:ARG128
|
3.4
|
215.0
|
1.0
|
|
N
|
S:CYS154
|
3.7
|
30.0
|
1.0
|
|
N
|
S:CYS136
|
3.7
|
30.0
|
1.0
|
|
CA
|
S:CYS154
|
4.0
|
30.0
|
1.0
|
|
CA
|
S:CYS136
|
4.0
|
30.0
|
1.0
|
|
CG1
|
A:VAL132
|
4.3
|
234.9
|
1.0
|
|
CB
|
S:ASN135
|
4.5
|
30.0
|
1.0
|
|
CD2
|
A:TYR115
|
4.5
|
215.6
|
1.0
|
|
CA
|
S:CYS133
|
4.6
|
30.0
|
1.0
|
|
C
|
S:CYS136
|
4.6
|
30.0
|
1.0
|
|
CA
|
S:CYS151
|
4.6
|
30.0
|
1.0
|
|
CB
|
S:ALA138
|
4.6
|
30.0
|
1.0
|
|
CE2
|
A:TYR115
|
4.6
|
215.9
|
1.0
|
|
CB
|
S:ARG153
|
4.7
|
30.0
|
1.0
|
|
CG
|
A:GLU131
|
4.7
|
227.9
|
1.0
|
|
C
|
S:ASN135
|
4.7
|
30.0
|
1.0
|
|
CG
|
A:ARG128
|
4.7
|
214.7
|
1.0
|
|
C
|
S:CYS154
|
4.7
|
30.0
|
1.0
|
|
N
|
S:ARG155
|
4.8
|
30.0
|
1.0
|
|
N
|
S:GLN137
|
4.8
|
30.0
|
1.0
|
|
C
|
S:ARG153
|
4.8
|
30.0
|
1.0
|
|
N
|
S:ALA138
|
4.9
|
30.0
|
1.0
|
|
ND2
|
S:ASN135
|
4.9
|
30.0
|
1.0
|
|
CB
|
S:MET156
|
4.9
|
30.0
|
1.0
|
|
CA
|
S:ASN135
|
5.0
|
30.0
|
1.0
|
|
CE
|
S:MET161
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 2 out
of 6 in 8bd4
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Zinc Binding Sites List in 8bd4
Zinc binding site 2 out
of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn303
b:30.0
occ:1.00
|
NH1
|
E:ARG128
|
1.6
|
215.8
|
1.0
|
|
CZ
|
E:ARG128
|
2.3
|
215.5
|
1.0
|
|
SG
|
R:CYS154
|
2.3
|
30.0
|
1.0
|
|
SG
|
R:CYS151
|
2.3
|
30.0
|
1.0
|
|
SG
|
R:CYS136
|
2.3
|
30.0
|
1.0
|
|
SG
|
R:CYS133
|
2.3
|
30.0
|
1.0
|
|
NH2
|
E:ARG128
|
2.6
|
215.7
|
1.0
|
|
CB
|
R:CYS133
|
3.1
|
30.0
|
1.0
|
|
CB
|
R:CYS151
|
3.2
|
30.0
|
1.0
|
|
CB
|
R:CYS154
|
3.3
|
30.0
|
1.0
|
|
NE
|
E:ARG128
|
3.3
|
215.0
|
1.0
|
|
CB
|
R:CYS136
|
3.3
|
30.0
|
1.0
|
|
N
|
R:CYS154
|
3.7
|
30.0
|
1.0
|
|
N
|
R:CYS136
|
3.7
|
30.0
|
1.0
|
|
OE2
|
E:GLU131
|
3.9
|
227.1
|
1.0
|
|
OE1
|
E:GLU131
|
3.9
|
227.7
|
1.0
|
|
CD
|
E:ARG128
|
4.0
|
215.0
|
1.0
|
|
CA
|
R:CYS154
|
4.0
|
30.0
|
1.0
|
|
CA
|
R:CYS136
|
4.0
|
30.0
|
1.0
|
|
CD
|
E:GLU131
|
4.4
|
227.7
|
1.0
|
|
CB
|
R:ASN135
|
4.5
|
30.0
|
1.0
|
|
CA
|
R:CYS133
|
4.6
|
30.0
|
1.0
|
|
CA
|
R:CYS151
|
4.6
|
30.0
|
1.0
|
|
C
|
R:CYS136
|
4.6
|
30.0
|
1.0
|
|
CB
|
R:ALA138
|
4.6
|
30.0
|
1.0
|
|
CB
|
R:ARG153
|
4.7
|
30.0
|
1.0
|
|
C
|
R:ASN135
|
4.7
|
30.0
|
1.0
|
|
C
|
R:CYS154
|
4.7
|
30.0
|
1.0
|
|
N
|
R:ARG155
|
4.8
|
30.0
|
1.0
|
|
N
|
R:GLN137
|
4.8
|
30.0
|
1.0
|
|
C
|
R:ARG153
|
4.8
|
30.0
|
1.0
|
|
N
|
R:ALA138
|
4.9
|
30.0
|
1.0
|
|
ND2
|
R:ASN135
|
4.9
|
30.0
|
1.0
|
|
CB
|
R:MET156
|
4.9
|
30.0
|
1.0
|
|
CE
|
R:MET161
|
5.0
|
30.0
|
1.0
|
|
CA
|
R:ASN135
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 3 out
of 6 in 8bd4
Go back to
Zinc Binding Sites List in 8bd4
Zinc binding site 3 out
of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Zn201
b:30.0
occ:1.00
|
ND1
|
R:HIS125
|
2.1
|
30.0
|
1.0
|
|
SG
|
R:CYS103
|
2.3
|
30.0
|
1.0
|
|
SG
|
R:CYS122
|
2.3
|
30.0
|
1.0
|
|
SG
|
R:CYS100
|
2.3
|
30.0
|
1.0
|
|
CE1
|
R:HIS125
|
3.0
|
30.0
|
1.0
|
|
CG
|
R:HIS125
|
3.2
|
30.0
|
1.0
|
|
CB
|
R:CYS100
|
3.3
|
30.0
|
1.0
|
|
CB
|
R:CYS122
|
3.3
|
30.0
|
1.0
|
|
CB
|
R:CYS103
|
3.4
|
30.0
|
1.0
|
|
N
|
R:CYS103
|
3.5
|
30.0
|
1.0
|
|
CB
|
R:HIS125
|
3.6
|
30.0
|
1.0
|
|
CA
|
R:CYS103
|
3.9
|
30.0
|
1.0
|
|
NE2
|
R:HIS125
|
4.1
|
30.0
|
1.0
|
|
CD2
|
R:HIS125
|
4.3
|
30.0
|
1.0
|
|
N
|
R:HIS125
|
4.4
|
30.0
|
1.0
|
|
C
|
R:ALA102
|
4.4
|
30.0
|
1.0
|
|
CB
|
R:ALA102
|
4.4
|
30.0
|
1.0
|
|
CA
|
R:HIS125
|
4.7
|
30.0
|
1.0
|
|
CA
|
R:CYS100
|
4.7
|
30.0
|
1.0
|
|
CA
|
R:CYS122
|
4.7
|
30.0
|
1.0
|
|
CB
|
R:ARG124
|
4.8
|
30.0
|
1.0
|
|
CA
|
R:ALA102
|
4.9
|
30.0
|
1.0
|
|
O
|
R:CYS100
|
5.0
|
30.0
|
1.0
|
|
C
|
R:CYS100
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 4 out
of 6 in 8bd4
Go back to
Zinc Binding Sites List in 8bd4
Zinc binding site 4 out
of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Zn201
b:30.0
occ:1.00
|
ND1
|
S:HIS125
|
2.1
|
30.0
|
1.0
|
|
SG
|
S:CYS103
|
2.3
|
30.0
|
1.0
|
|
SG
|
S:CYS122
|
2.3
|
30.0
|
1.0
|
|
SG
|
S:CYS100
|
2.3
|
30.0
|
1.0
|
|
CE1
|
S:HIS125
|
3.0
|
30.0
|
1.0
|
|
CG
|
S:HIS125
|
3.2
|
30.0
|
1.0
|
|
CB
|
S:CYS100
|
3.3
|
30.0
|
1.0
|
|
CB
|
S:CYS122
|
3.3
|
30.0
|
1.0
|
|
CB
|
S:CYS103
|
3.4
|
30.0
|
1.0
|
|
N
|
S:CYS103
|
3.5
|
30.0
|
1.0
|
|
CB
|
S:HIS125
|
3.6
|
30.0
|
1.0
|
|
CA
|
S:CYS103
|
3.9
|
30.0
|
1.0
|
|
NE2
|
S:HIS125
|
4.1
|
30.0
|
1.0
|
|
CD2
|
S:HIS125
|
4.3
|
30.0
|
1.0
|
|
N
|
S:HIS125
|
4.4
|
30.0
|
1.0
|
|
C
|
S:ALA102
|
4.4
|
30.0
|
1.0
|
|
CB
|
S:ALA102
|
4.4
|
30.0
|
1.0
|
|
CA
|
S:CYS100
|
4.7
|
30.0
|
1.0
|
|
CA
|
S:HIS125
|
4.7
|
30.0
|
1.0
|
|
CA
|
S:CYS122
|
4.7
|
30.0
|
1.0
|
|
CB
|
S:ARG124
|
4.8
|
30.0
|
1.0
|
|
CA
|
S:ALA102
|
4.9
|
30.0
|
1.0
|
|
O
|
S:CYS100
|
5.0
|
30.0
|
1.0
|
|
C
|
S:CYS100
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 5 out
of 6 in 8bd4
Go back to
Zinc Binding Sites List in 8bd4
Zinc binding site 5 out
of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Zn201
b:30.0
occ:1.00
|
NH1
|
C:ARG128
|
0.6
|
215.8
|
1.0
|
|
CZ
|
C:ARG128
|
1.8
|
215.5
|
1.0
|
|
SG
|
T:CYS154
|
2.3
|
30.0
|
1.0
|
|
SG
|
T:CYS151
|
2.3
|
30.0
|
1.0
|
|
SG
|
T:CYS136
|
2.3
|
30.0
|
1.0
|
|
SG
|
T:CYS133
|
2.3
|
30.0
|
1.0
|
|
NH2
|
C:ARG128
|
2.5
|
215.7
|
1.0
|
|
OE1
|
C:GLU131
|
2.7
|
227.7
|
1.0
|
|
NE
|
C:ARG128
|
2.8
|
215.0
|
1.0
|
|
OE2
|
C:GLU131
|
3.0
|
227.1
|
1.0
|
|
CB
|
T:CYS133
|
3.1
|
30.0
|
1.0
|
|
CB
|
T:CYS151
|
3.2
|
30.0
|
1.0
|
|
CD
|
C:GLU131
|
3.2
|
227.7
|
1.0
|
|
CB
|
T:CYS154
|
3.3
|
30.0
|
1.0
|
|
CD
|
C:ARG128
|
3.3
|
215.0
|
1.0
|
|
CB
|
T:CYS136
|
3.3
|
30.0
|
1.0
|
|
N
|
T:CYS154
|
3.7
|
30.0
|
1.0
|
|
N
|
T:CYS136
|
3.7
|
30.0
|
1.0
|
|
CA
|
T:CYS154
|
4.0
|
30.0
|
1.0
|
|
CA
|
T:CYS136
|
4.0
|
30.0
|
1.0
|
|
CB
|
T:ASN135
|
4.5
|
30.0
|
1.0
|
|
CA
|
T:CYS133
|
4.6
|
30.0
|
1.0
|
|
CG
|
C:GLU131
|
4.6
|
227.9
|
1.0
|
|
CA
|
T:CYS151
|
4.6
|
30.0
|
1.0
|
|
C
|
T:CYS136
|
4.6
|
30.0
|
1.0
|
|
CB
|
T:ALA138
|
4.6
|
30.0
|
1.0
|
|
CB
|
T:ARG153
|
4.7
|
30.0
|
1.0
|
|
C
|
T:ASN135
|
4.7
|
30.0
|
1.0
|
|
C
|
T:CYS154
|
4.7
|
30.0
|
1.0
|
|
N
|
T:ARG155
|
4.8
|
30.0
|
1.0
|
|
CG
|
C:ARG128
|
4.8
|
214.7
|
1.0
|
|
N
|
T:GLN137
|
4.8
|
30.0
|
1.0
|
|
C
|
T:ARG153
|
4.8
|
30.0
|
1.0
|
|
N
|
T:ALA138
|
4.9
|
30.0
|
1.0
|
|
ND2
|
T:ASN135
|
4.9
|
30.0
|
1.0
|
|
CB
|
T:MET156
|
4.9
|
30.0
|
1.0
|
|
CA
|
T:ASN135
|
5.0
|
30.0
|
1.0
|
|
CE
|
T:MET161
|
5.0
|
30.0
|
1.0
|
|
Zinc binding site 6 out
of 6 in 8bd4
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Zinc Binding Sites List in 8bd4
Zinc binding site 6 out
of 6 in the Tniq-Capped Tns-Atp-Dsdna Complex
 Mono view
 Stereo pair view
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A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Tniq-Capped Tns-Atp-Dsdna Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Zn202
b:30.0
occ:1.00
|
ND1
|
T:HIS125
|
2.1
|
30.0
|
1.0
|
|
SG
|
T:CYS103
|
2.3
|
30.0
|
1.0
|
|
SG
|
T:CYS122
|
2.3
|
30.0
|
1.0
|
|
SG
|
T:CYS100
|
2.3
|
30.0
|
1.0
|
|
CE1
|
T:HIS125
|
3.0
|
30.0
|
1.0
|
|
CG
|
T:HIS125
|
3.2
|
30.0
|
1.0
|
|
CB
|
T:CYS100
|
3.3
|
30.0
|
1.0
|
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CB
|
T:CYS122
|
3.3
|
30.0
|
1.0
|
|
CB
|
T:CYS103
|
3.4
|
30.0
|
1.0
|
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N
|
T:CYS103
|
3.5
|
30.0
|
1.0
|
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CB
|
T:HIS125
|
3.6
|
30.0
|
1.0
|
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CA
|
T:CYS103
|
3.9
|
30.0
|
1.0
|
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NE2
|
T:HIS125
|
4.1
|
30.0
|
1.0
|
|
CD2
|
T:HIS125
|
4.3
|
30.0
|
1.0
|
|
N
|
T:HIS125
|
4.4
|
30.0
|
1.0
|
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C
|
T:ALA102
|
4.4
|
30.0
|
1.0
|
|
CB
|
T:ALA102
|
4.4
|
30.0
|
1.0
|
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CA
|
T:HIS125
|
4.7
|
30.0
|
1.0
|
|
CA
|
T:CYS100
|
4.7
|
30.0
|
1.0
|
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CA
|
T:CYS122
|
4.7
|
30.0
|
1.0
|
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CB
|
T:ARG124
|
4.8
|
30.0
|
1.0
|
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CA
|
T:ALA102
|
4.9
|
30.0
|
1.0
|
|
O
|
T:CYS100
|
5.0
|
30.0
|
1.0
|
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C
|
T:CYS100
|
5.0
|
30.0
|
1.0
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Reference:
M.Schmitz,
I.Querques,
S.Oberli,
C.Chanez,
M.Jinek.
Structural Basis For the Assembly of the Type V Crispr-Associated Transposon Complex. Cell V. 185 4999 2022.
ISSN: ISSN 1097-4172
PubMed: 36435179
DOI: 10.1016/J.CELL.2022.11.009
Page generated: Wed Oct 30 18:13:55 2024
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