Zinc in PDB 8edg: Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
(pdb code 8edg). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon, PDB code: 8edg:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 8edg
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Zinc Binding Sites List in 8edg
Zinc binding site 1 out
of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn701
b:236.4
occ:1.00
|
CB
|
A:CYS54
|
1.5
|
149.7
|
1.0
|
NE2
|
A:HIS71
|
2.1
|
132.9
|
1.0
|
SG
|
A:CYS73
|
2.3
|
166.3
|
1.0
|
SG
|
A:CYS51
|
2.3
|
140.5
|
1.0
|
SG
|
A:CYS54
|
2.3
|
149.7
|
1.0
|
CA
|
A:CYS54
|
2.8
|
149.7
|
1.0
|
CD2
|
A:HIS71
|
2.8
|
132.9
|
1.0
|
CB
|
A:CYS73
|
2.9
|
166.3
|
1.0
|
N
|
A:CYS54
|
3.2
|
149.7
|
1.0
|
CE1
|
A:HIS71
|
3.2
|
132.9
|
1.0
|
CB
|
A:CYS51
|
3.6
|
140.5
|
1.0
|
C
|
A:CYS54
|
4.0
|
149.7
|
1.0
|
CG
|
A:HIS71
|
4.1
|
132.9
|
1.0
|
CA
|
A:CYS73
|
4.1
|
166.3
|
1.0
|
ND1
|
A:HIS71
|
4.2
|
132.9
|
1.0
|
C
|
A:LYS53
|
4.2
|
137.3
|
1.0
|
N
|
A:CYS73
|
4.2
|
166.3
|
1.0
|
CE
|
A:LYS72
|
4.3
|
144.4
|
1.0
|
O
|
A:CYS54
|
4.5
|
149.7
|
1.0
|
NZ
|
A:LYS72
|
4.6
|
144.4
|
1.0
|
N
|
A:GLU55
|
4.8
|
134.5
|
1.0
|
O
|
A:LYS53
|
4.8
|
137.3
|
1.0
|
CD
|
A:LYS72
|
4.8
|
144.4
|
1.0
|
CA
|
A:CYS51
|
5.0
|
140.5
|
1.0
|
|
Zinc binding site 2 out
of 6 in 8edg
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Zinc Binding Sites List in 8edg
Zinc binding site 2 out
of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn701
b:289.9
occ:1.00
|
CB
|
C:CYS73
|
2.0
|
186.2
|
1.0
|
NE2
|
C:HIS71
|
2.1
|
174.4
|
1.0
|
SG
|
C:CYS51
|
2.3
|
176.1
|
1.0
|
SG
|
C:CYS54
|
2.3
|
183.9
|
1.0
|
SG
|
C:CYS73
|
2.3
|
186.2
|
1.0
|
CD2
|
C:HIS71
|
3.0
|
174.4
|
1.0
|
CE1
|
C:HIS71
|
3.1
|
174.4
|
1.0
|
CA
|
C:CYS73
|
3.5
|
186.2
|
1.0
|
CB
|
C:CYS51
|
3.6
|
176.1
|
1.0
|
CB
|
C:CYS54
|
3.9
|
183.9
|
1.0
|
N
|
C:CYS54
|
4.0
|
183.9
|
1.0
|
N
|
C:CYS73
|
4.1
|
186.2
|
1.0
|
CG
|
C:HIS71
|
4.2
|
174.4
|
1.0
|
ND1
|
C:HIS71
|
4.2
|
174.4
|
1.0
|
C
|
C:CYS73
|
4.3
|
186.2
|
1.0
|
CA
|
C:CYS54
|
4.6
|
183.9
|
1.0
|
CB
|
C:LYS53
|
4.7
|
168.7
|
1.0
|
O
|
C:CYS73
|
4.8
|
186.2
|
1.0
|
N
|
C:LYS53
|
4.9
|
168.7
|
1.0
|
N
|
C:CYS74
|
4.9
|
160.8
|
1.0
|
CA
|
C:CYS51
|
5.0
|
176.1
|
1.0
|
|
Zinc binding site 3 out
of 6 in 8edg
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Zinc Binding Sites List in 8edg
Zinc binding site 3 out
of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn701
b:289.4
occ:1.00
|
NE2
|
I:HIS71
|
2.1
|
159.2
|
1.0
|
SG
|
I:CYS54
|
2.3
|
166.9
|
1.0
|
SG
|
I:CYS51
|
2.3
|
157.6
|
1.0
|
SG
|
I:CYS73
|
2.3
|
176.8
|
1.0
|
CD2
|
I:HIS71
|
2.7
|
159.2
|
1.0
|
CB
|
I:CYS73
|
2.8
|
176.8
|
1.0
|
CB
|
I:CYS51
|
3.1
|
157.6
|
1.0
|
CB
|
I:CYS54
|
3.2
|
166.9
|
1.0
|
CE1
|
I:HIS71
|
3.3
|
159.2
|
1.0
|
N
|
I:CYS54
|
3.5
|
166.9
|
1.0
|
CA
|
I:CYS54
|
3.9
|
166.9
|
1.0
|
CG
|
I:HIS71
|
4.0
|
159.2
|
1.0
|
CA
|
I:CYS73
|
4.1
|
176.8
|
1.0
|
ND1
|
I:HIS71
|
4.2
|
159.2
|
1.0
|
N
|
I:CYS73
|
4.3
|
176.8
|
1.0
|
N
|
I:LYS53
|
4.4
|
146.4
|
1.0
|
C
|
I:LYS53
|
4.4
|
146.4
|
1.0
|
CA
|
I:CYS51
|
4.6
|
157.6
|
1.0
|
CB
|
I:LYS53
|
4.6
|
146.4
|
1.0
|
CA
|
I:LYS53
|
4.7
|
146.4
|
1.0
|
N
|
I:GLU55
|
4.7
|
157.2
|
1.0
|
C
|
I:CYS54
|
4.8
|
166.9
|
1.0
|
N
|
I:ARG52
|
4.8
|
156.1
|
1.0
|
|
Zinc binding site 4 out
of 6 in 8edg
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Zinc Binding Sites List in 8edg
Zinc binding site 4 out
of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn701
b:236.0
occ:1.00
|
NE2
|
E:HIS71
|
2.1
|
140.9
|
1.0
|
SG
|
E:CYS54
|
2.3
|
169.5
|
1.0
|
SG
|
E:CYS73
|
2.3
|
153.2
|
1.0
|
SG
|
E:CYS51
|
2.3
|
162.3
|
1.0
|
CD2
|
E:HIS71
|
2.5
|
140.9
|
1.0
|
CB
|
E:CYS54
|
2.8
|
169.5
|
1.0
|
CB
|
E:CYS73
|
2.9
|
153.2
|
1.0
|
CB
|
E:CYS51
|
3.0
|
162.3
|
1.0
|
CE1
|
E:HIS71
|
3.3
|
140.9
|
1.0
|
N
|
E:CYS54
|
3.5
|
169.5
|
1.0
|
CA
|
E:CYS54
|
3.7
|
169.5
|
1.0
|
CG
|
E:HIS71
|
3.8
|
140.9
|
1.0
|
ND1
|
E:HIS71
|
4.2
|
140.9
|
1.0
|
CA
|
E:CYS73
|
4.2
|
153.2
|
1.0
|
N
|
E:CYS73
|
4.3
|
153.2
|
1.0
|
CA
|
E:CYS51
|
4.5
|
162.3
|
1.0
|
C
|
E:CYS54
|
4.6
|
169.5
|
1.0
|
C
|
E:LYS53
|
4.6
|
159.1
|
1.0
|
N
|
E:GLU55
|
4.7
|
159.2
|
1.0
|
N
|
E:LYS53
|
4.8
|
159.1
|
1.0
|
|
Zinc binding site 5 out
of 6 in 8edg
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Zinc Binding Sites List in 8edg
Zinc binding site 5 out
of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn701
b:236.6
occ:1.00
|
NE2
|
G:HIS71
|
2.1
|
103.8
|
1.0
|
SG
|
G:CYS73
|
2.3
|
124.0
|
1.0
|
SG
|
G:CYS54
|
2.3
|
158.5
|
1.0
|
SG
|
G:CYS51
|
2.3
|
147.5
|
1.0
|
CD2
|
G:HIS71
|
2.6
|
103.8
|
1.0
|
CB
|
G:CYS54
|
2.8
|
158.5
|
1.0
|
CB
|
G:CYS51
|
3.0
|
147.5
|
1.0
|
CB
|
G:CYS73
|
3.1
|
124.0
|
1.0
|
N
|
G:CYS54
|
3.2
|
158.5
|
1.0
|
CE1
|
G:HIS71
|
3.3
|
103.8
|
1.0
|
CA
|
G:CYS54
|
3.5
|
158.5
|
1.0
|
CG
|
G:HIS71
|
3.9
|
103.8
|
1.0
|
ND1
|
G:HIS71
|
4.2
|
103.8
|
1.0
|
C
|
G:LYS53
|
4.3
|
145.7
|
1.0
|
CB
|
G:LYS53
|
4.4
|
145.7
|
1.0
|
CA
|
G:CYS73
|
4.4
|
124.0
|
1.0
|
CA
|
G:CYS51
|
4.5
|
147.5
|
1.0
|
C
|
G:CYS54
|
4.5
|
158.5
|
1.0
|
N
|
G:CYS73
|
4.5
|
124.0
|
1.0
|
N
|
G:LYS53
|
4.6
|
145.7
|
1.0
|
CA
|
G:LYS53
|
4.6
|
145.7
|
1.0
|
N
|
G:GLU55
|
4.7
|
142.2
|
1.0
|
C
|
G:CYS51
|
4.9
|
147.5
|
1.0
|
CD1
|
G:LEU34
|
5.0
|
111.6
|
1.0
|
|
Zinc binding site 6 out
of 6 in 8edg
Go back to
Zinc Binding Sites List in 8edg
Zinc binding site 6 out
of 6 in the Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/ed/8edg-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Cryo-Em Structure of the Hermes Transposase Bound to Two Left-Ends of Its Dna Transposon within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn701
b:254.6
occ:1.00
|
NE2
|
K:HIS71
|
2.1
|
151.5
|
1.0
|
SG
|
K:CYS54
|
2.3
|
165.2
|
1.0
|
SG
|
K:CYS73
|
2.3
|
156.7
|
1.0
|
SG
|
K:CYS51
|
2.3
|
176.2
|
1.0
|
CD2
|
K:HIS71
|
2.9
|
151.5
|
1.0
|
CE1
|
K:HIS71
|
3.1
|
151.5
|
1.0
|
CB
|
K:CYS51
|
3.2
|
176.2
|
1.0
|
CG
|
K:LYS56
|
3.8
|
164.7
|
1.0
|
CB
|
K:CYS54
|
3.8
|
165.2
|
1.0
|
CG
|
K:HIS71
|
4.1
|
151.5
|
1.0
|
CB
|
K:CYS73
|
4.1
|
156.7
|
1.0
|
ND1
|
K:HIS71
|
4.1
|
151.5
|
1.0
|
CD
|
K:LYS56
|
4.1
|
164.7
|
1.0
|
CE
|
K:LYS56
|
4.4
|
164.7
|
1.0
|
CA
|
K:CYS51
|
4.6
|
176.2
|
1.0
|
CA
|
K:CYS54
|
4.8
|
165.2
|
1.0
|
N
|
K:CYS54
|
4.8
|
165.2
|
1.0
|
N
|
K:CYS73
|
4.9
|
156.7
|
1.0
|
CG
|
K:LYS72
|
4.9
|
149.3
|
1.0
|
|
Reference:
L.Lannes,
C.M.Furman,
A.B.Hickman,
F.Dyda.
Zinc-Finger Bed Domains Drive the Formation of the Active Hermes Transpososome By Asymmetric Dna Binding. Nat Commun V. 14 4470 2023.
ISSN: ESSN 2041-1723
PubMed: 37491363
DOI: 10.1038/S41467-023-40210-3
Page generated: Thu Dec 28 12:57:42 2023
|