Manganese in PDB 7rpw: Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
Enzymatic activity of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
All present enzymatic activity of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna:
6.5.1.1;
Manganese Binding Sites:
The binding sites of Manganese atom in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
(pdb code 7rpw). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna, PDB code: 7rpw:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 7rpw
Go back to
Manganese Binding Sites List in 7rpw
Manganese binding site 1 out
of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mn101
b:110.4
occ:1.00
|
O
|
E:GLY60
|
1.8
|
106.9
|
1.0
|
O3'
|
X:DG20
|
1.9
|
122.2
|
1.0
|
C
|
E:GLY60
|
2.2
|
106.9
|
1.0
|
C4'
|
X:DG20
|
2.3
|
122.2
|
1.0
|
C3'
|
X:DG20
|
2.4
|
122.2
|
1.0
|
CA
|
E:GLY60
|
2.9
|
106.9
|
1.0
|
O
|
E:ILE61
|
2.9
|
94.3
|
1.0
|
C
|
E:ILE61
|
3.0
|
94.3
|
1.0
|
N
|
E:ILE61
|
3.1
|
94.3
|
1.0
|
P
|
X:DC21
|
3.2
|
136.5
|
1.0
|
OP1
|
X:DC21
|
3.2
|
136.5
|
1.0
|
C5'
|
X:DG20
|
3.3
|
122.2
|
1.0
|
O4'
|
X:DG20
|
3.4
|
122.2
|
1.0
|
N
|
E:GLY62
|
3.5
|
110.6
|
1.0
|
CA
|
E:ILE61
|
3.5
|
94.3
|
1.0
|
C2'
|
X:DG20
|
3.8
|
122.2
|
1.0
|
C5'
|
X:DC21
|
3.9
|
136.5
|
1.0
|
O
|
E:LEU59
|
4.0
|
89.1
|
1.0
|
C1'
|
X:DG20
|
4.0
|
122.2
|
1.0
|
CA
|
E:GLY62
|
4.0
|
110.6
|
1.0
|
O5'
|
X:DC21
|
4.0
|
136.5
|
1.0
|
N
|
E:GLY60
|
4.0
|
106.9
|
1.0
|
OP2
|
X:DC21
|
4.3
|
136.5
|
1.0
|
O5'
|
X:DG20
|
4.4
|
122.2
|
1.0
|
C
|
E:LEU59
|
4.4
|
89.1
|
1.0
|
CB
|
E:ILE61
|
5.0
|
94.3
|
1.0
|
|
Manganese binding site 2 out
of 4 in 7rpw
Go back to
Manganese Binding Sites List in 7rpw
Manganese binding site 2 out
of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mn102
b:117.3
occ:1.00
|
OP1
|
X:DC21
|
2.1
|
136.5
|
1.0
|
O5'
|
X:DC21
|
2.2
|
136.5
|
1.0
|
P
|
X:DC21
|
2.3
|
136.5
|
1.0
|
OP2
|
X:DC21
|
2.6
|
136.5
|
1.0
|
C5'
|
X:DC21
|
3.2
|
136.5
|
1.0
|
C3'
|
X:DC21
|
3.8
|
136.5
|
1.0
|
O3'
|
X:DG20
|
3.9
|
122.2
|
1.0
|
C2'
|
X:DC21
|
4.0
|
136.5
|
1.0
|
C4'
|
X:DC21
|
4.0
|
136.5
|
1.0
|
OP2
|
X:DG22
|
4.5
|
152.2
|
1.0
|
O
|
E:GLU167
|
4.7
|
109.5
|
1.0
|
C6
|
X:DC21
|
4.7
|
136.5
|
1.0
|
O
|
E:ILE61
|
4.8
|
94.3
|
1.0
|
O
|
E:LEU59
|
4.9
|
89.1
|
1.0
|
C3'
|
X:DG20
|
4.9
|
122.2
|
1.0
|
O4'
|
X:DC21
|
4.9
|
136.5
|
1.0
|
|
Manganese binding site 3 out
of 4 in 7rpw
Go back to
Manganese Binding Sites List in 7rpw
Manganese binding site 3 out
of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn701
b:115.0
occ:1.00
|
OP1
|
X:DG22
|
1.8
|
152.2
|
1.0
|
OD2
|
E:ASP52
|
3.0
|
79.4
|
1.0
|
P
|
X:DG22
|
3.0
|
152.2
|
1.0
|
OE1
|
E:GLU58
|
3.2
|
119.2
|
1.0
|
O5'
|
X:DG22
|
3.5
|
152.2
|
1.0
|
C5'
|
X:DG22
|
3.7
|
152.2
|
1.0
|
OP2
|
X:DG22
|
3.7
|
152.2
|
1.0
|
CD
|
E:GLU58
|
4.0
|
119.2
|
1.0
|
CG
|
E:ASP52
|
4.1
|
79.4
|
1.0
|
CB
|
E:GLU58
|
4.2
|
119.2
|
1.0
|
O3'
|
X:DC21
|
4.3
|
136.5
|
1.0
|
NH2
|
E:ARG281
|
4.4
|
115.6
|
1.0
|
CG
|
E:GLU58
|
4.5
|
119.2
|
1.0
|
OE2
|
E:GLU58
|
4.8
|
119.2
|
1.0
|
CB
|
E:ASP52
|
4.8
|
79.4
|
1.0
|
CG
|
E:GLU283
|
4.8
|
106.3
|
1.0
|
|
Manganese binding site 4 out
of 4 in 7rpw
Go back to
Manganese Binding Sites List in 7rpw
Manganese binding site 4 out
of 4 in the Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Archaeal Dna Ligase and Heterotrimeric Pcna in Complex with Adenylated Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn702
b:216.3
occ:1.00
|
NZ
|
E:LYS260
|
2.2
|
197.3
|
1.0
|
O5'
|
Y:AMP101
|
2.2
|
192.9
|
1.0
|
O
|
E:TYR261
|
2.7
|
192.7
|
1.0
|
O4'
|
Y:AMP101
|
2.8
|
192.9
|
1.0
|
C5'
|
Y:AMP101
|
2.8
|
192.9
|
1.0
|
P
|
Y:AMP101
|
2.9
|
192.9
|
1.0
|
OE2
|
E:GLU409
|
3.0
|
193.3
|
1.0
|
O1P
|
Y:AMP101
|
3.0
|
192.9
|
1.0
|
C8
|
Y:AMP101
|
3.0
|
192.9
|
1.0
|
O2P
|
Y:AMP101
|
3.1
|
192.9
|
1.0
|
C4'
|
Y:AMP101
|
3.3
|
192.9
|
1.0
|
OE2
|
E:GLU310
|
3.4
|
185.3
|
1.0
|
CE
|
E:LYS260
|
3.6
|
197.3
|
1.0
|
C
|
E:TYR261
|
3.7
|
192.7
|
1.0
|
C1'
|
Y:AMP101
|
3.8
|
192.9
|
1.0
|
N9
|
Y:AMP101
|
3.8
|
192.9
|
1.0
|
CA
|
E:ASP262
|
3.8
|
191.5
|
1.0
|
CD
|
E:GLU409
|
3.9
|
193.3
|
1.0
|
C3'
|
Y:AMP101
|
4.1
|
192.9
|
1.0
|
CD
|
E:LYS260
|
4.1
|
197.3
|
1.0
|
N7
|
Y:AMP101
|
4.1
|
192.9
|
1.0
|
N
|
E:ASP262
|
4.1
|
191.5
|
1.0
|
OE1
|
E:GLU409
|
4.2
|
193.3
|
1.0
|
C2'
|
Y:AMP101
|
4.2
|
192.9
|
1.0
|
OP1
|
Y:DG1
|
4.4
|
190.5
|
1.0
|
N
|
E:GLY263
|
4.4
|
182.5
|
1.0
|
C
|
E:ASP262
|
4.5
|
191.5
|
1.0
|
CD
|
E:GLU310
|
4.6
|
185.3
|
1.0
|
OD1
|
E:ASP262
|
4.7
|
191.5
|
1.0
|
OP2
|
Y:DG1
|
4.7
|
190.5
|
1.0
|
O
|
E:GLY263
|
4.7
|
182.5
|
1.0
|
CB
|
E:ASP262
|
4.7
|
191.5
|
1.0
|
CG
|
E:ASP262
|
4.8
|
191.5
|
1.0
|
CA
|
E:TYR261
|
5.0
|
192.7
|
1.0
|
|
Reference:
A.Sverzhinsky,
A.E.Tomkinson,
J.M.Pascal.
Cryo-Em Structures and Biochemical Insights Into Heterotrimeric Pcna Regulation of Dna Ligase To Be Published.
Page generated: Sun Oct 6 10:28:46 2024
|