Magnesium in PDB 6qem: E. Coli Dnabc Complex Bound to Ssdna
Enzymatic activity of E. Coli Dnabc Complex Bound to Ssdna
All present enzymatic activity of E. Coli Dnabc Complex Bound to Ssdna:
3.6.4.12;
Other elements in 6qem:
The structure of E. Coli Dnabc Complex Bound to Ssdna also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the E. Coli Dnabc Complex Bound to Ssdna
(pdb code 6qem). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
E. Coli Dnabc Complex Bound to Ssdna, PDB code: 6qem:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6qem
Go back to
Magnesium Binding Sites List in 6qem
Magnesium binding site 1 out
of 5 in the E. Coli Dnabc Complex Bound to Ssdna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1002
b:10.6
occ:1.00
|
OG1
|
A:THR238
|
2.0
|
25.0
|
1.0
|
F2
|
A:08T1001
|
2.3
|
37.9
|
1.0
|
O2B
|
A:08T1001
|
2.3
|
37.9
|
1.0
|
OE1
|
A:GLU262
|
2.8
|
22.0
|
1.0
|
OD1
|
A:ASP343
|
3.3
|
20.5
|
1.0
|
OD2
|
A:ASP343
|
3.3
|
20.5
|
1.0
|
CB
|
A:THR238
|
3.3
|
25.0
|
1.0
|
HE3
|
A:MET263
|
3.4
|
19.6
|
1.0
|
HG21
|
A:THR238
|
3.5
|
25.0
|
1.0
|
BE
|
A:08T1001
|
3.5
|
37.9
|
1.0
|
HB
|
A:THR238
|
3.6
|
25.0
|
1.0
|
PB
|
A:08T1001
|
3.7
|
37.9
|
1.0
|
CD
|
A:GLU262
|
3.7
|
22.0
|
1.0
|
CG
|
A:ASP343
|
3.7
|
20.5
|
1.0
|
O3B
|
A:08T1001
|
3.9
|
37.9
|
1.0
|
CG2
|
A:THR238
|
3.9
|
25.0
|
1.0
|
OE2
|
A:GLU262
|
4.0
|
22.0
|
1.0
|
HE2
|
A:LYS237
|
4.1
|
37.9
|
1.0
|
H
|
A:THR238
|
4.1
|
25.0
|
1.0
|
CE
|
A:MET263
|
4.2
|
19.6
|
1.0
|
HE1
|
A:MET263
|
4.2
|
19.6
|
1.0
|
HD3
|
F:ARG442
|
4.2
|
21.7
|
1.0
|
F3
|
A:08T1001
|
4.3
|
37.9
|
1.0
|
HG23
|
A:THR238
|
4.3
|
25.0
|
1.0
|
HG3
|
A:LYS237
|
4.3
|
37.9
|
1.0
|
F1
|
A:08T1001
|
4.3
|
37.9
|
1.0
|
HE2
|
A:MET263
|
4.3
|
19.6
|
1.0
|
HB3
|
A:GLU262
|
4.4
|
22.0
|
1.0
|
HD23
|
A:LEU382
|
4.4
|
37.9
|
1.0
|
CA
|
A:THR238
|
4.4
|
25.0
|
1.0
|
HB2
|
A:TYR344
|
4.5
|
20.7
|
1.0
|
HZ3
|
A:LYS237
|
4.6
|
37.9
|
1.0
|
N
|
A:THR238
|
4.6
|
25.0
|
1.0
|
HD22
|
A:LEU382
|
4.6
|
37.9
|
1.0
|
HA
|
A:THR238
|
4.6
|
25.0
|
1.0
|
O3A
|
A:08T1001
|
4.6
|
37.9
|
1.0
|
O1B
|
A:08T1001
|
4.7
|
37.9
|
1.0
|
HD2
|
F:ARG442
|
4.7
|
21.7
|
1.0
|
HG22
|
A:THR238
|
4.8
|
25.0
|
1.0
|
CG
|
A:GLU262
|
4.8
|
22.0
|
1.0
|
HZ1
|
A:LYS237
|
4.8
|
37.9
|
1.0
|
CD2
|
A:LEU382
|
4.9
|
37.9
|
1.0
|
O1A
|
A:08T1001
|
4.9
|
37.9
|
1.0
|
CE
|
A:LYS237
|
4.9
|
37.9
|
1.0
|
HB2
|
A:GLU262
|
4.9
|
22.0
|
1.0
|
CD
|
F:ARG442
|
4.9
|
21.7
|
1.0
|
CB
|
A:GLU262
|
4.9
|
22.0
|
1.0
|
NZ
|
A:LYS237
|
5.0
|
37.9
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6qem
Go back to
Magnesium Binding Sites List in 6qem
Magnesium binding site 2 out
of 5 in the E. Coli Dnabc Complex Bound to Ssdna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:5.8
occ:1.00
|
OG1
|
B:THR238
|
2.0
|
26.8
|
1.0
|
F2
|
B:08T1001
|
2.2
|
37.9
|
1.0
|
O2B
|
B:08T1001
|
2.3
|
37.9
|
1.0
|
OE1
|
B:GLU262
|
2.5
|
23.3
|
1.0
|
HG21
|
B:THR238
|
3.1
|
26.8
|
1.0
|
CB
|
B:THR238
|
3.2
|
26.8
|
1.0
|
HB
|
B:THR238
|
3.5
|
26.8
|
1.0
|
BE
|
B:08T1001
|
3.5
|
37.9
|
1.0
|
CD
|
B:GLU262
|
3.5
|
23.3
|
1.0
|
PB
|
B:08T1001
|
3.6
|
37.9
|
1.0
|
OD1
|
B:ASP343
|
3.7
|
26.9
|
1.0
|
CG2
|
B:THR238
|
3.7
|
26.8
|
1.0
|
OD2
|
B:ASP343
|
3.8
|
26.9
|
1.0
|
O3B
|
B:08T1001
|
3.9
|
37.9
|
1.0
|
HD3
|
A:ARG442
|
3.9
|
37.9
|
1.0
|
OE2
|
B:GLU262
|
4.0
|
23.3
|
1.0
|
HG23
|
B:THR238
|
4.1
|
26.8
|
1.0
|
CG
|
B:ASP343
|
4.1
|
26.9
|
1.0
|
F1
|
B:08T1001
|
4.2
|
37.9
|
1.0
|
HE2
|
B:LYS237
|
4.2
|
37.9
|
1.0
|
F3
|
B:08T1001
|
4.3
|
37.9
|
1.0
|
HE2
|
B:MET263
|
4.3
|
20.9
|
1.0
|
H
|
B:THR238
|
4.3
|
26.8
|
1.0
|
O3A
|
B:08T1001
|
4.4
|
37.9
|
1.0
|
HB3
|
B:GLU262
|
4.4
|
23.3
|
1.0
|
CA
|
B:THR238
|
4.4
|
26.8
|
1.0
|
HG22
|
B:THR238
|
4.4
|
26.8
|
1.0
|
HH21
|
A:ARG442
|
4.5
|
37.9
|
1.0
|
HG3
|
B:LYS237
|
4.6
|
37.9
|
1.0
|
HA
|
B:THR238
|
4.6
|
26.8
|
1.0
|
HB2
|
B:TYR344
|
4.7
|
21.7
|
1.0
|
O1A
|
B:08T1001
|
4.7
|
37.9
|
1.0
|
O1B
|
B:08T1001
|
4.7
|
37.9
|
1.0
|
N
|
B:THR238
|
4.7
|
26.8
|
1.0
|
CG
|
B:GLU262
|
4.7
|
23.3
|
1.0
|
HZ3
|
B:LYS237
|
4.8
|
37.9
|
1.0
|
NH2
|
A:ARG442
|
4.8
|
37.9
|
1.0
|
HB2
|
B:GLU262
|
4.8
|
23.3
|
1.0
|
CD
|
A:ARG442
|
4.9
|
37.9
|
1.0
|
HZ1
|
B:LYS237
|
4.9
|
37.9
|
1.0
|
CB
|
B:GLU262
|
4.9
|
23.3
|
1.0
|
HG2
|
B:GLU262
|
4.9
|
23.3
|
1.0
|
HD22
|
B:LEU382
|
5.0
|
37.9
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6qem
Go back to
Magnesium Binding Sites List in 6qem
Magnesium binding site 3 out
of 5 in the E. Coli Dnabc Complex Bound to Ssdna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1002
b:37.9
occ:1.00
|
OG1
|
C:THR238
|
2.0
|
26.2
|
1.0
|
O2B
|
C:08T1001
|
2.0
|
37.9
|
1.0
|
F2
|
C:08T1001
|
2.2
|
37.9
|
1.0
|
OE1
|
C:GLU262
|
3.1
|
26.2
|
1.0
|
CB
|
C:THR238
|
3.2
|
26.2
|
1.0
|
PB
|
C:08T1001
|
3.4
|
37.9
|
1.0
|
HB
|
C:THR238
|
3.4
|
26.2
|
1.0
|
BE
|
C:08T1001
|
3.4
|
37.9
|
1.0
|
HE3
|
C:MET263
|
3.5
|
21.9
|
1.0
|
HG21
|
C:THR238
|
3.5
|
26.2
|
1.0
|
HD3
|
B:ARG442
|
3.5
|
37.9
|
1.0
|
O3B
|
C:08T1001
|
3.7
|
37.9
|
1.0
|
CD
|
C:GLU262
|
3.8
|
26.2
|
1.0
|
OD2
|
C:ASP343
|
3.9
|
23.4
|
1.0
|
H
|
C:THR238
|
3.9
|
26.2
|
1.0
|
CG2
|
C:THR238
|
3.9
|
26.2
|
1.0
|
OD1
|
C:ASP343
|
3.9
|
23.4
|
1.0
|
OE2
|
C:GLU262
|
4.0
|
26.2
|
1.0
|
HE1
|
C:MET263
|
4.1
|
21.9
|
1.0
|
CE
|
C:MET263
|
4.1
|
21.9
|
1.0
|
O3A
|
C:08T1001
|
4.1
|
37.9
|
1.0
|
F1
|
C:08T1001
|
4.1
|
37.9
|
1.0
|
HH21
|
B:ARG442
|
4.2
|
37.9
|
1.0
|
HE2
|
C:MET263
|
4.3
|
21.9
|
1.0
|
HG23
|
C:THR238
|
4.3
|
26.2
|
1.0
|
CG
|
C:ASP343
|
4.3
|
23.4
|
1.0
|
O1A
|
C:08T1001
|
4.3
|
37.9
|
1.0
|
F3
|
C:08T1001
|
4.3
|
37.9
|
1.0
|
CA
|
C:THR238
|
4.3
|
26.2
|
1.0
|
CD
|
B:ARG442
|
4.4
|
37.9
|
1.0
|
HG3
|
C:LYS237
|
4.5
|
37.9
|
1.0
|
HE2
|
C:LYS237
|
4.5
|
37.9
|
1.0
|
O1B
|
C:08T1001
|
4.5
|
37.9
|
1.0
|
N
|
C:THR238
|
4.5
|
26.2
|
1.0
|
HZ3
|
C:LYS237
|
4.5
|
37.9
|
1.0
|
HD2
|
B:ARG442
|
4.5
|
37.9
|
1.0
|
HA
|
C:THR238
|
4.6
|
26.2
|
1.0
|
HB3
|
C:GLU262
|
4.6
|
26.2
|
1.0
|
HG22
|
C:THR238
|
4.7
|
26.2
|
1.0
|
PA
|
C:08T1001
|
4.7
|
37.9
|
1.0
|
HD23
|
C:LEU382
|
4.7
|
28.6
|
1.0
|
NH2
|
B:ARG442
|
4.8
|
37.9
|
1.0
|
HG2
|
B:ARG442
|
4.9
|
37.9
|
1.0
|
CG
|
C:GLU262
|
4.9
|
26.2
|
1.0
|
HZ1
|
C:LYS237
|
4.9
|
37.9
|
1.0
|
HG2
|
C:GLU262
|
5.0
|
26.2
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6qem
Go back to
Magnesium Binding Sites List in 6qem
Magnesium binding site 4 out
of 5 in the E. Coli Dnabc Complex Bound to Ssdna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1002
b:9.0
occ:1.00
|
O2B
|
D:08T1001
|
1.9
|
37.9
|
1.0
|
OG1
|
D:THR238
|
2.0
|
24.2
|
1.0
|
F2
|
D:08T1001
|
2.3
|
37.9
|
1.0
|
OE1
|
D:GLU262
|
3.1
|
21.3
|
1.0
|
PB
|
D:08T1001
|
3.2
|
37.9
|
1.0
|
CB
|
D:THR238
|
3.2
|
24.2
|
1.0
|
OD1
|
D:ASP343
|
3.3
|
24.2
|
1.0
|
HB
|
D:THR238
|
3.3
|
24.2
|
1.0
|
H
|
D:THR238
|
3.4
|
24.2
|
1.0
|
BE
|
D:08T1001
|
3.5
|
37.9
|
1.0
|
OD2
|
D:ASP343
|
3.6
|
24.2
|
1.0
|
O3B
|
D:08T1001
|
3.6
|
37.9
|
1.0
|
HE2
|
D:LYS237
|
3.8
|
37.9
|
1.0
|
HB2
|
D:LYS237
|
3.8
|
37.9
|
1.0
|
CG
|
D:ASP343
|
3.8
|
24.2
|
1.0
|
HG21
|
D:THR238
|
3.9
|
24.2
|
1.0
|
N
|
D:THR238
|
4.0
|
24.2
|
1.0
|
O1B
|
D:08T1001
|
4.1
|
37.9
|
1.0
|
HD23
|
D:LEU382
|
4.2
|
37.9
|
1.0
|
CA
|
D:THR238
|
4.2
|
24.2
|
1.0
|
CG2
|
D:THR238
|
4.2
|
24.2
|
1.0
|
CD
|
D:GLU262
|
4.2
|
21.3
|
1.0
|
O3A
|
D:08T1001
|
4.2
|
37.9
|
1.0
|
F3
|
D:08T1001
|
4.3
|
37.9
|
1.0
|
F1
|
D:08T1001
|
4.4
|
37.9
|
1.0
|
HA
|
D:THR238
|
4.4
|
24.2
|
1.0
|
HD3
|
C:ARG442
|
4.5
|
37.9
|
1.0
|
HD22
|
D:LEU382
|
4.5
|
37.9
|
1.0
|
O1A
|
D:08T1001
|
4.5
|
37.9
|
1.0
|
HE2
|
D:MET263
|
4.5
|
24.3
|
1.0
|
HD21
|
D:LEU382
|
4.6
|
37.9
|
1.0
|
OE2
|
D:GLU262
|
4.6
|
21.3
|
1.0
|
CD2
|
D:LEU382
|
4.6
|
37.9
|
1.0
|
HG23
|
D:THR238
|
4.6
|
24.2
|
1.0
|
CB
|
D:LYS237
|
4.7
|
37.9
|
1.0
|
HB2
|
D:TYR344
|
4.7
|
20.9
|
1.0
|
CE
|
D:LYS237
|
4.8
|
37.9
|
1.0
|
PA
|
D:08T1001
|
4.8
|
37.9
|
1.0
|
HG22
|
D:THR238
|
4.9
|
24.2
|
1.0
|
HB3
|
D:LYS237
|
4.9
|
37.9
|
1.0
|
O2A
|
D:08T1001
|
5.0
|
37.9
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6qem
Go back to
Magnesium Binding Sites List in 6qem
Magnesium binding site 5 out
of 5 in the E. Coli Dnabc Complex Bound to Ssdna
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of E. Coli Dnabc Complex Bound to Ssdna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1002
b:21.6
occ:1.00
|
HG1
|
E:THR238
|
1.7
|
28.9
|
1.0
|
O2B
|
E:08T1001
|
2.0
|
26.6
|
1.0
|
F2
|
E:08T1001
|
2.0
|
26.6
|
1.0
|
OE1
|
E:GLU262
|
2.3
|
42.1
|
1.0
|
OG1
|
E:THR238
|
2.4
|
28.9
|
1.0
|
CD
|
E:GLU262
|
3.2
|
42.1
|
1.0
|
BE
|
E:08T1001
|
3.2
|
26.6
|
1.0
|
PB
|
E:08T1001
|
3.3
|
26.6
|
1.0
|
OE2
|
E:GLU262
|
3.5
|
42.1
|
1.0
|
HG21
|
E:THR238
|
3.5
|
28.9
|
1.0
|
CB
|
E:THR238
|
3.6
|
28.9
|
1.0
|
O3B
|
E:08T1001
|
3.6
|
26.6
|
1.0
|
HB
|
E:THR238
|
3.7
|
28.9
|
1.0
|
OD1
|
E:ASP343
|
3.8
|
46.8
|
1.0
|
HD3
|
D:ARG442
|
3.9
|
22.2
|
1.0
|
F1
|
E:08T1001
|
3.9
|
26.6
|
1.0
|
HD2
|
D:ARG442
|
4.0
|
22.2
|
1.0
|
CG2
|
E:THR238
|
4.0
|
28.9
|
1.0
|
O3A
|
E:08T1001
|
4.1
|
26.6
|
1.0
|
F3
|
E:08T1001
|
4.1
|
26.6
|
1.0
|
O1B
|
E:08T1001
|
4.4
|
26.6
|
1.0
|
CD
|
D:ARG442
|
4.4
|
22.2
|
1.0
|
HG23
|
E:THR238
|
4.4
|
28.9
|
1.0
|
OD2
|
E:ASP343
|
4.5
|
46.8
|
1.0
|
O1A
|
E:08T1001
|
4.5
|
26.6
|
1.0
|
H
|
E:THR238
|
4.5
|
28.9
|
1.0
|
HE2
|
E:LYS237
|
4.5
|
31.3
|
1.0
|
HZ3
|
E:LYS237
|
4.5
|
31.3
|
1.0
|
CG
|
E:ASP343
|
4.6
|
46.8
|
1.0
|
HB3
|
E:GLU262
|
4.6
|
42.1
|
1.0
|
CG
|
E:GLU262
|
4.6
|
42.1
|
1.0
|
HB2
|
E:TYR344
|
4.6
|
43.7
|
1.0
|
HE2
|
E:MET263
|
4.7
|
39.5
|
1.0
|
HZ1
|
E:LYS237
|
4.7
|
31.3
|
1.0
|
HB2
|
E:GLU262
|
4.8
|
42.1
|
1.0
|
HG22
|
E:THR238
|
4.8
|
28.9
|
1.0
|
PA
|
E:08T1001
|
4.8
|
26.6
|
1.0
|
CA
|
E:THR238
|
4.8
|
28.9
|
1.0
|
HH21
|
D:ARG442
|
4.8
|
22.2
|
1.0
|
HD22
|
E:LEU382
|
4.8
|
35.7
|
1.0
|
HG3
|
E:LYS237
|
4.9
|
31.3
|
1.0
|
CB
|
E:GLU262
|
4.9
|
42.1
|
1.0
|
HG2
|
E:GLU262
|
5.0
|
42.1
|
1.0
|
NZ
|
E:LYS237
|
5.0
|
31.3
|
1.0
|
|
Reference:
E.Arias-Palomo,
N.Puri,
V.L.O'shea Murray,
Q.Yan,
J.M.Berger.
Physical Basis For the Loading of A Bacterial Replicative Helicase Onto Dna. Mol.Cell V. 74 173 2019.
ISSN: ISSN 1097-2765
PubMed: 30797687
DOI: 10.1016/J.MOLCEL.2019.01.023
Page generated: Tue Oct 1 15:28:08 2024
|