Magnesium in PDB 8ff4: Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
(pdb code 8ff4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System, PDB code: 8ff4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 1 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Mg601
b:197.9
occ:1.00
|
O3B
|
Q:ATP600
|
2.0
|
204.4
|
1.0
|
OG1
|
Q:THR64
|
2.1
|
197.8
|
1.0
|
O1G
|
Q:ATP600
|
2.4
|
204.4
|
1.0
|
O3A
|
Q:ATP600
|
2.5
|
204.4
|
1.0
|
PG
|
Q:ATP600
|
2.6
|
204.4
|
1.0
|
O5'
|
Q:ATP600
|
2.9
|
204.4
|
1.0
|
PB
|
Q:ATP600
|
2.9
|
204.4
|
1.0
|
PA
|
Q:ATP600
|
3.0
|
204.4
|
1.0
|
CB
|
Q:THR64
|
3.1
|
197.8
|
1.0
|
O2A
|
Q:ATP600
|
3.1
|
204.4
|
1.0
|
O2G
|
Q:ATP600
|
3.2
|
204.4
|
1.0
|
O2B
|
Q:ATP600
|
3.9
|
204.4
|
1.0
|
C5'
|
Q:ATP600
|
3.9
|
204.4
|
1.0
|
O1B
|
Q:ATP600
|
3.9
|
204.4
|
1.0
|
O3G
|
Q:ATP600
|
3.9
|
204.4
|
1.0
|
CG2
|
Q:THR64
|
4.0
|
197.8
|
1.0
|
N
|
Q:THR64
|
4.1
|
197.8
|
1.0
|
CA
|
Q:THR64
|
4.2
|
197.8
|
1.0
|
O1A
|
Q:ATP600
|
4.5
|
204.4
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 2 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Mg601
b:161.4
occ:1.00
|
O3A
|
R:ATP600
|
2.0
|
167.1
|
1.0
|
O3B
|
R:ATP600
|
2.1
|
167.1
|
1.0
|
OG1
|
R:THR64
|
2.3
|
162.2
|
1.0
|
O2A
|
R:ATP600
|
2.4
|
167.1
|
1.0
|
PA
|
R:ATP600
|
2.5
|
167.1
|
1.0
|
PB
|
R:ATP600
|
2.6
|
167.1
|
1.0
|
O3G
|
R:ATP600
|
2.6
|
167.1
|
1.0
|
PG
|
R:ATP600
|
2.7
|
167.1
|
1.0
|
O5'
|
R:ATP600
|
2.8
|
167.1
|
1.0
|
O1G
|
R:ATP600
|
3.2
|
167.1
|
1.0
|
CB
|
R:THR64
|
3.3
|
162.2
|
1.0
|
O1B
|
R:ATP600
|
3.4
|
167.1
|
1.0
|
N
|
R:THR64
|
3.6
|
162.2
|
1.0
|
O2B
|
R:ATP600
|
3.8
|
167.1
|
1.0
|
O1A
|
R:ATP600
|
3.9
|
167.1
|
1.0
|
C5'
|
R:ATP600
|
4.0
|
167.1
|
1.0
|
O2G
|
R:ATP600
|
4.1
|
167.1
|
1.0
|
CA
|
R:THR64
|
4.1
|
162.2
|
1.0
|
N
|
R:LYS63
|
4.4
|
156.1
|
1.0
|
CG2
|
R:THR64
|
4.5
|
162.2
|
1.0
|
C
|
R:LYS63
|
4.7
|
156.1
|
1.0
|
CB
|
R:LYS63
|
4.8
|
156.1
|
1.0
|
CA
|
R:LYS63
|
4.9
|
156.1
|
1.0
|
NH2
|
S:ARG223
|
4.9
|
155.8
|
1.0
|
NH1
|
S:ARG223
|
5.0
|
155.8
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 3 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Mg601
b:147.3
occ:1.00
|
O3B
|
S:ATP600
|
2.0
|
156.6
|
1.0
|
O3A
|
S:ATP600
|
2.1
|
156.6
|
1.0
|
O1G
|
S:ATP600
|
2.1
|
156.6
|
1.0
|
OG1
|
S:THR64
|
2.4
|
144.3
|
1.0
|
PG
|
S:ATP600
|
2.5
|
156.6
|
1.0
|
PB
|
S:ATP600
|
2.6
|
156.6
|
1.0
|
PA
|
S:ATP600
|
3.0
|
156.6
|
1.0
|
O2A
|
S:ATP600
|
3.0
|
156.6
|
1.0
|
O5'
|
S:ATP600
|
3.2
|
156.6
|
1.0
|
O1B
|
S:ATP600
|
3.3
|
156.6
|
1.0
|
CB
|
S:THR64
|
3.5
|
144.3
|
1.0
|
O3G
|
S:ATP600
|
3.5
|
156.6
|
1.0
|
O2G
|
S:ATP600
|
3.7
|
156.6
|
1.0
|
N
|
S:THR64
|
3.8
|
144.3
|
1.0
|
O2B
|
S:ATP600
|
3.8
|
156.6
|
1.0
|
CA
|
S:THR64
|
4.3
|
144.3
|
1.0
|
O1A
|
S:ATP600
|
4.3
|
156.6
|
1.0
|
C5'
|
S:ATP600
|
4.4
|
156.6
|
1.0
|
CG2
|
S:THR64
|
4.6
|
144.3
|
1.0
|
N
|
S:LYS63
|
4.7
|
144.0
|
1.0
|
CB
|
S:LYS63
|
4.7
|
144.0
|
1.0
|
NH1
|
T:ARG223
|
4.8
|
142.8
|
1.0
|
NH2
|
T:ARG224
|
4.8
|
147.3
|
1.0
|
C
|
S:LYS63
|
4.8
|
144.0
|
1.0
|
CE
|
S:LYS63
|
5.0
|
144.0
|
1.0
|
NH1
|
T:ARG224
|
5.0
|
147.3
|
1.0
|
CA
|
S:LYS63
|
5.0
|
144.0
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 4 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mg601
b:148.1
occ:1.00
|
O3B
|
T:ATP600
|
2.0
|
160.3
|
1.0
|
O3A
|
T:ATP600
|
2.1
|
160.3
|
1.0
|
O1G
|
T:ATP600
|
2.3
|
160.3
|
1.0
|
OG1
|
T:THR64
|
2.3
|
144.8
|
1.0
|
PB
|
T:ATP600
|
2.6
|
160.3
|
1.0
|
PG
|
T:ATP600
|
2.6
|
160.3
|
1.0
|
O2A
|
T:ATP600
|
2.7
|
160.3
|
1.0
|
PA
|
T:ATP600
|
2.8
|
160.3
|
1.0
|
O5'
|
T:ATP600
|
3.1
|
160.3
|
1.0
|
CB
|
T:THR64
|
3.2
|
144.8
|
1.0
|
O1B
|
T:ATP600
|
3.4
|
160.3
|
1.0
|
N
|
T:THR64
|
3.6
|
144.8
|
1.0
|
O2G
|
T:ATP600
|
3.7
|
160.3
|
1.0
|
O3G
|
T:ATP600
|
3.7
|
160.3
|
1.0
|
O2B
|
T:ATP600
|
3.8
|
160.3
|
1.0
|
CA
|
T:THR64
|
4.0
|
144.8
|
1.0
|
O1A
|
T:ATP600
|
4.2
|
160.3
|
1.0
|
C5'
|
T:ATP600
|
4.3
|
160.3
|
1.0
|
CG2
|
T:THR64
|
4.4
|
144.8
|
1.0
|
N
|
T:LYS63
|
4.6
|
144.1
|
1.0
|
C
|
T:LYS63
|
4.7
|
144.1
|
1.0
|
CB
|
T:LYS63
|
4.8
|
144.1
|
1.0
|
NH2
|
U:ARG223
|
4.8
|
152.9
|
1.0
|
CA
|
T:LYS63
|
4.9
|
144.1
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 5 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Mg601
b:138.8
occ:1.00
|
O3B
|
U:ATP600
|
2.0
|
151.8
|
1.0
|
O3A
|
U:ATP600
|
2.0
|
151.8
|
1.0
|
OG1
|
U:THR64
|
2.3
|
146.0
|
1.0
|
PB
|
U:ATP600
|
2.5
|
151.8
|
1.0
|
O1G
|
U:ATP600
|
2.6
|
151.8
|
1.0
|
PG
|
U:ATP600
|
2.8
|
151.8
|
1.0
|
PA
|
U:ATP600
|
3.1
|
151.8
|
1.0
|
O2A
|
U:ATP600
|
3.2
|
151.8
|
1.0
|
CB
|
U:THR64
|
3.3
|
146.0
|
1.0
|
O5'
|
U:ATP600
|
3.3
|
151.8
|
1.0
|
O1B
|
U:ATP600
|
3.4
|
151.8
|
1.0
|
O3G
|
U:ATP600
|
3.7
|
151.8
|
1.0
|
O2B
|
U:ATP600
|
3.7
|
151.8
|
1.0
|
N
|
U:THR64
|
3.8
|
146.0
|
1.0
|
O2G
|
U:ATP600
|
4.0
|
151.8
|
1.0
|
CA
|
U:THR64
|
4.2
|
146.0
|
1.0
|
O1A
|
U:ATP600
|
4.4
|
151.8
|
1.0
|
CG2
|
U:THR64
|
4.4
|
146.0
|
1.0
|
C5'
|
U:ATP600
|
4.5
|
151.8
|
1.0
|
NH2
|
V:ARG223
|
4.6
|
143.7
|
1.0
|
N
|
U:LYS63
|
4.8
|
142.2
|
1.0
|
C
|
U:LYS63
|
4.9
|
142.2
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 6 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg601
b:152.4
occ:1.00
|
O3A
|
V:ATP600
|
2.0
|
168.4
|
1.0
|
O1G
|
V:ATP600
|
2.0
|
168.4
|
1.0
|
O3B
|
V:ATP600
|
2.1
|
168.4
|
1.0
|
O2A
|
V:ATP600
|
2.2
|
168.4
|
1.0
|
PA
|
V:ATP600
|
2.4
|
168.4
|
1.0
|
PG
|
V:ATP600
|
2.5
|
168.4
|
1.0
|
OG1
|
V:THR64
|
2.5
|
150.8
|
1.0
|
PB
|
V:ATP600
|
2.6
|
168.4
|
1.0
|
O5'
|
V:ATP600
|
2.9
|
168.4
|
1.0
|
O2G
|
V:ATP600
|
3.4
|
168.4
|
1.0
|
CB
|
V:THR64
|
3.4
|
150.8
|
1.0
|
O1B
|
V:ATP600
|
3.4
|
168.4
|
1.0
|
N
|
V:THR64
|
3.4
|
150.8
|
1.0
|
O3G
|
V:ATP600
|
3.7
|
168.4
|
1.0
|
O2B
|
V:ATP600
|
3.8
|
168.4
|
1.0
|
O1A
|
V:ATP600
|
3.8
|
168.4
|
1.0
|
C5'
|
V:ATP600
|
3.9
|
168.4
|
1.0
|
CA
|
V:THR64
|
4.0
|
150.8
|
1.0
|
N
|
V:LYS63
|
4.1
|
153.4
|
1.0
|
NH2
|
W:ARG224
|
4.3
|
181.5
|
1.0
|
C
|
V:LYS63
|
4.5
|
153.4
|
1.0
|
CB
|
V:LYS63
|
4.6
|
153.4
|
1.0
|
CA
|
V:LYS63
|
4.6
|
153.4
|
1.0
|
CG2
|
V:THR64
|
4.7
|
150.8
|
1.0
|
C
|
V:GLY62
|
4.7
|
152.0
|
1.0
|
CA
|
V:GLY62
|
4.9
|
152.0
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 8ff4
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Magnesium Binding Sites List in 8ff4
Magnesium binding site 7 out
of 7 in the Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Cryo-Em Structure of Cascade-Dna-Tniq-Tnsc Complex (Composite) in Type I-B Cast System within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Mg601
b:207.5
occ:1.00
|
O3A
|
W:ATP600
|
2.0
|
203.4
|
1.0
|
O3B
|
W:ATP600
|
2.1
|
203.4
|
1.0
|
O1G
|
W:ATP600
|
2.2
|
203.4
|
1.0
|
OG1
|
W:THR64
|
2.2
|
192.0
|
1.0
|
PB
|
W:ATP600
|
2.4
|
203.4
|
1.0
|
PG
|
W:ATP600
|
2.5
|
203.4
|
1.0
|
O2A
|
W:ATP600
|
2.7
|
203.4
|
1.0
|
PA
|
W:ATP600
|
2.8
|
203.4
|
1.0
|
O1B
|
W:ATP600
|
3.0
|
203.4
|
1.0
|
O3G
|
W:ATP600
|
3.1
|
203.4
|
1.0
|
CB
|
W:THR64
|
3.3
|
192.0
|
1.0
|
O5'
|
W:ATP600
|
3.3
|
203.4
|
1.0
|
N
|
W:THR64
|
3.5
|
192.0
|
1.0
|
O2B
|
W:ATP600
|
3.8
|
203.4
|
1.0
|
O2G
|
W:ATP600
|
3.9
|
203.4
|
1.0
|
CA
|
W:THR64
|
4.0
|
192.0
|
1.0
|
O1A
|
W:ATP600
|
4.2
|
203.4
|
1.0
|
C5'
|
W:ATP600
|
4.3
|
203.4
|
1.0
|
N
|
W:LYS63
|
4.4
|
190.2
|
1.0
|
CG2
|
W:THR64
|
4.5
|
192.0
|
1.0
|
C
|
W:LYS63
|
4.5
|
190.2
|
1.0
|
CB
|
W:LYS63
|
4.6
|
190.2
|
1.0
|
CA
|
W:LYS63
|
4.7
|
190.2
|
1.0
|
C
|
W:GLY62
|
4.9
|
194.9
|
1.0
|
|
Reference:
S.Wang,
C.Gabel,
R.Siddique,
T.Klose,
L.Chang.
Cryo-Em Structure of Cascade-Dna Complex with 23 Bp Recognized in Type I-B Cast System Cell(Cambridge,Mass.) 2023.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2023.07.010
Page generated: Fri Oct 4 02:30:23 2024
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