Magnesium in PDB 9eco: E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
Enzymatic activity of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
All present enzymatic activity of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4:
2.7.7.101;
3.6.4.12;
Other elements in 9eco:
The structure of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4 also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
(pdb code 9eco). 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 Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4, PDB code: 9eco:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 9eco
Go back to
Magnesium Binding Sites List in 9eco
Magnesium binding site 1 out
of 5 in the E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1002
b:97.3
occ:1.00
|
F1
|
A:ALF501
|
2.0
|
127.5
|
1.0
|
|
O1B
|
B:ADP1001
|
2.0
|
100.2
|
1.0
|
|
OG1
|
B:THR238
|
2.1
|
102.7
|
1.0
|
|
HG1
|
B:THR238
|
2.5
|
98.5
|
1.0
|
|
CB
|
B:THR238
|
3.2
|
96.5
|
1.0
|
|
HB
|
B:THR238
|
3.2
|
97.0
|
1.0
|
|
PB
|
B:ADP1001
|
3.3
|
98.4
|
1.0
|
|
H
|
B:THR238
|
3.5
|
93.7
|
1.0
|
|
O2B
|
B:ADP1001
|
3.6
|
91.3
|
1.0
|
|
AL
|
A:ALF501
|
3.6
|
123.0
|
1.0
|
|
HG2
|
B:GLU262
|
3.7
|
113.8
|
1.0
|
|
F4
|
A:ALF501
|
3.8
|
118.0
|
1.0
|
|
OD1
|
B:ASP343
|
3.8
|
106.4
|
1.0
|
|
O2A
|
B:ADP1001
|
3.9
|
92.2
|
1.0
|
|
HG22
|
B:THR238
|
3.9
|
95.8
|
1.0
|
|
HH11
|
A:ARG442
|
4.0
|
115.0
|
1.0
|
|
N
|
B:THR238
|
4.1
|
92.2
|
1.0
|
|
HD2
|
A:ARG442
|
4.1
|
112.8
|
1.0
|
|
CG2
|
B:THR238
|
4.2
|
95.9
|
1.0
|
|
HE3
|
B:LYS237
|
4.2
|
90.6
|
1.0
|
|
O3A
|
B:ADP1001
|
4.2
|
103.8
|
1.0
|
|
CA
|
B:THR238
|
4.2
|
86.1
|
1.0
|
|
HB3
|
B:LYS237
|
4.3
|
93.5
|
1.0
|
|
F3
|
A:ALF501
|
4.3
|
119.7
|
1.0
|
|
O3B
|
B:ADP1001
|
4.4
|
102.5
|
1.0
|
|
PA
|
B:ADP1001
|
4.5
|
101.2
|
1.0
|
|
HA
|
B:THR238
|
4.6
|
88.5
|
1.0
|
|
HH12
|
B:ARG271
|
4.6
|
103.8
|
1.0
|
|
CG
|
B:ASP343
|
4.6
|
104.3
|
1.0
|
|
OD2
|
B:ASP343
|
4.6
|
106.5
|
1.0
|
|
NH1
|
A:ARG442
|
4.6
|
114.5
|
1.0
|
|
HG23
|
B:THR238
|
4.6
|
94.9
|
1.0
|
|
CG
|
B:GLU262
|
4.7
|
114.5
|
1.0
|
|
HD3
|
A:ARG442
|
4.8
|
114.0
|
1.0
|
|
O1A
|
B:ADP1001
|
4.8
|
95.4
|
1.0
|
|
HB3
|
B:GLU262
|
4.9
|
107.3
|
1.0
|
|
CD
|
A:ARG442
|
4.9
|
114.4
|
1.0
|
|
HH12
|
A:ARG442
|
4.9
|
114.9
|
1.0
|
|
HG3
|
B:MET263
|
4.9
|
111.2
|
1.0
|
|
SD
|
B:MET263
|
4.9
|
124.1
|
1.0
|
|
HG21
|
B:THR238
|
4.9
|
94.2
|
1.0
|
|
HD1
|
B:TYR344
|
4.9
|
99.7
|
1.0
|
|
HD11
|
B:LEU382
|
4.9
|
95.5
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 9eco
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Magnesium Binding Sites List in 9eco
Magnesium binding site 2 out
of 5 in the E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1003
b:94.3
occ:1.00
|
F1
|
C:ALF1002
|
2.0
|
118.7
|
1.0
|
|
OG1
|
C:THR238
|
2.0
|
98.0
|
1.0
|
|
O1B
|
C:ADP1001
|
2.1
|
99.9
|
1.0
|
|
HG1
|
C:THR238
|
2.6
|
93.8
|
1.0
|
|
HB
|
C:THR238
|
3.2
|
92.4
|
1.0
|
|
CB
|
C:THR238
|
3.2
|
91.4
|
1.0
|
|
PB
|
C:ADP1001
|
3.3
|
95.2
|
1.0
|
|
H
|
C:THR238
|
3.4
|
89.0
|
1.0
|
|
O2B
|
C:ADP1001
|
3.6
|
95.2
|
1.0
|
|
AL
|
C:ALF1002
|
3.6
|
108.3
|
1.0
|
|
F4
|
C:ALF1002
|
3.8
|
108.0
|
1.0
|
|
HG2
|
C:GLU262
|
3.9
|
109.2
|
1.0
|
|
HG22
|
C:THR238
|
4.0
|
92.1
|
1.0
|
|
N
|
C:THR238
|
4.0
|
86.2
|
1.0
|
|
OD1
|
C:ASP343
|
4.1
|
109.2
|
1.0
|
|
HB3
|
C:LYS237
|
4.1
|
88.7
|
1.0
|
|
O1A
|
C:ADP1001
|
4.1
|
96.6
|
1.0
|
|
CA
|
C:THR238
|
4.2
|
84.6
|
1.0
|
|
CG2
|
C:THR238
|
4.2
|
90.8
|
1.0
|
|
F3
|
C:ALF1002
|
4.2
|
106.7
|
1.0
|
|
O3B
|
C:ADP1001
|
4.2
|
93.4
|
1.0
|
|
HD2
|
B:ARG442
|
4.3
|
105.9
|
1.0
|
|
O3A
|
C:ADP1001
|
4.3
|
92.5
|
1.0
|
|
HZ1
|
C:LYS237
|
4.4
|
92.2
|
1.0
|
|
HA
|
C:THR238
|
4.5
|
87.2
|
1.0
|
|
PA
|
C:ADP1001
|
4.6
|
91.1
|
1.0
|
|
HD2
|
C:LYS237
|
4.7
|
92.2
|
1.0
|
|
HH12
|
C:ARG271
|
4.7
|
99.9
|
1.0
|
|
HG23
|
C:THR238
|
4.7
|
89.4
|
1.0
|
|
HD11
|
C:LEU382
|
4.7
|
90.3
|
1.0
|
|
HH11
|
B:ARG442
|
4.8
|
105.8
|
1.0
|
|
O2A
|
C:ADP1001
|
4.8
|
95.1
|
1.0
|
|
CG
|
C:ASP343
|
4.8
|
104.0
|
1.0
|
|
CG
|
C:GLU262
|
4.8
|
111.0
|
1.0
|
|
HG21
|
C:THR238
|
4.9
|
88.6
|
1.0
|
|
OD2
|
C:ASP343
|
4.9
|
102.2
|
1.0
|
|
HD1
|
C:TYR344
|
5.0
|
97.8
|
1.0
|
|
HB3
|
C:GLU262
|
5.0
|
103.2
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 9eco
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Magnesium Binding Sites List in 9eco
Magnesium binding site 3 out
of 5 in the E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1002
b:86.2
occ:1.00
|
F1
|
C:ALF1004
|
2.0
|
125.3
|
1.0
|
|
OG1
|
D:THR238
|
2.0
|
98.5
|
1.0
|
|
O1B
|
D:ADP1001
|
2.1
|
102.9
|
1.0
|
|
HG1
|
D:THR238
|
2.6
|
94.4
|
1.0
|
|
HB
|
D:THR238
|
3.0
|
91.3
|
1.0
|
|
CB
|
D:THR238
|
3.1
|
91.3
|
1.0
|
|
PB
|
D:ADP1001
|
3.3
|
93.2
|
1.0
|
|
F4
|
C:ALF1004
|
3.4
|
105.6
|
1.0
|
|
H
|
D:THR238
|
3.5
|
90.3
|
1.0
|
|
AL
|
C:ALF1004
|
3.5
|
111.0
|
1.0
|
|
O2B
|
D:ADP1001
|
3.6
|
93.9
|
1.0
|
|
HG2
|
D:GLU262
|
3.7
|
108.3
|
1.0
|
|
HH11
|
C:ARG442
|
3.8
|
105.1
|
1.0
|
|
HG22
|
D:THR238
|
3.9
|
91.7
|
1.0
|
|
O1A
|
D:ADP1001
|
3.9
|
92.9
|
1.0
|
|
N
|
D:THR238
|
4.0
|
88.5
|
1.0
|
|
CG2
|
D:THR238
|
4.1
|
90.7
|
1.0
|
|
HH12
|
C:ARG442
|
4.1
|
104.0
|
1.0
|
|
HB3
|
D:LYS237
|
4.1
|
91.1
|
1.0
|
|
CA
|
D:THR238
|
4.2
|
84.0
|
1.0
|
|
O3B
|
D:ADP1001
|
4.3
|
91.0
|
1.0
|
|
OD1
|
D:ASP343
|
4.3
|
109.7
|
1.0
|
|
NH1
|
C:ARG442
|
4.3
|
107.2
|
1.0
|
|
O3A
|
D:ADP1001
|
4.4
|
92.7
|
1.0
|
|
HE3
|
D:LYS237
|
4.4
|
93.9
|
1.0
|
|
F3
|
C:ALF1004
|
4.4
|
108.7
|
1.0
|
|
PA
|
D:ADP1001
|
4.5
|
92.5
|
1.0
|
|
OD2
|
D:ASP343
|
4.5
|
107.1
|
1.0
|
|
HA
|
D:THR238
|
4.5
|
87.5
|
1.0
|
|
O2A
|
D:ADP1001
|
4.6
|
93.2
|
1.0
|
|
HG23
|
D:THR238
|
4.6
|
90.5
|
1.0
|
|
CG
|
D:GLU262
|
4.7
|
111.0
|
1.0
|
|
HH12
|
D:ARG271
|
4.7
|
92.0
|
1.0
|
|
HG21
|
D:THR238
|
4.8
|
88.3
|
1.0
|
|
CG
|
D:ASP343
|
4.8
|
104.7
|
1.0
|
|
SD
|
D:MET263
|
4.8
|
116.5
|
1.0
|
|
HD11
|
D:LEU382
|
4.9
|
94.0
|
1.0
|
|
HB3
|
D:GLU262
|
4.9
|
101.8
|
1.0
|
|
HG3
|
D:MET263
|
5.0
|
105.0
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 9eco
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Magnesium Binding Sites List in 9eco
Magnesium binding site 4 out
of 5 in the E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1003
b:93.2
occ:1.00
|
F1
|
E:ALF1002
|
2.0
|
114.3
|
1.0
|
|
O1B
|
E:ADP1001
|
2.0
|
101.0
|
1.0
|
|
OG1
|
E:THR238
|
2.0
|
100.8
|
1.0
|
|
HG1
|
E:THR238
|
2.5
|
96.5
|
1.0
|
|
CB
|
E:THR238
|
3.2
|
90.6
|
1.0
|
|
HB
|
E:THR238
|
3.3
|
92.4
|
1.0
|
|
PB
|
E:ADP1001
|
3.3
|
102.7
|
1.0
|
|
H
|
E:THR238
|
3.4
|
89.0
|
1.0
|
|
OE1
|
E:GLU262
|
3.6
|
116.1
|
1.0
|
|
AL
|
E:ALF1002
|
3.6
|
111.8
|
1.0
|
|
F4
|
E:ALF1002
|
3.6
|
106.0
|
1.0
|
|
O2B
|
E:ADP1001
|
3.6
|
102.0
|
1.0
|
|
N
|
E:THR238
|
4.0
|
87.1
|
1.0
|
|
HG22
|
E:THR238
|
4.0
|
94.9
|
1.0
|
|
O1A
|
E:ADP1001
|
4.0
|
94.2
|
1.0
|
|
HB2
|
E:LYS237
|
4.1
|
88.4
|
1.0
|
|
OD2
|
E:ASP343
|
4.1
|
103.9
|
1.0
|
|
O3B
|
E:ADP1001
|
4.1
|
92.8
|
1.0
|
|
OD1
|
E:ASP343
|
4.2
|
108.5
|
1.0
|
|
CA
|
E:THR238
|
4.2
|
85.1
|
1.0
|
|
CG2
|
E:THR238
|
4.2
|
93.0
|
1.0
|
|
HE2
|
E:LYS237
|
4.3
|
90.4
|
1.0
|
|
F3
|
E:ALF1002
|
4.4
|
113.1
|
1.0
|
|
O3A
|
E:ADP1001
|
4.4
|
97.9
|
1.0
|
|
HD2
|
D:ARG442
|
4.5
|
96.3
|
1.0
|
|
HD13
|
E:LEU382
|
4.5
|
92.5
|
1.0
|
|
HH11
|
D:ARG442
|
4.5
|
100.8
|
1.0
|
|
CG
|
E:ASP343
|
4.5
|
102.7
|
1.0
|
|
HA
|
E:THR238
|
4.6
|
87.7
|
1.0
|
|
PA
|
E:ADP1001
|
4.6
|
88.5
|
1.0
|
|
HG23
|
E:THR238
|
4.6
|
92.0
|
1.0
|
|
CD
|
E:GLU262
|
4.6
|
116.6
|
1.0
|
|
HH12
|
E:ARG271
|
4.7
|
101.2
|
1.0
|
|
O2A
|
E:ADP1001
|
4.8
|
89.7
|
1.0
|
|
SD
|
E:MET263
|
4.8
|
114.5
|
1.0
|
|
HG3
|
E:MET263
|
4.9
|
109.3
|
1.0
|
|
HG21
|
E:THR238
|
5.0
|
91.4
|
1.0
|
|
HD12
|
E:LEU382
|
5.0
|
90.4
|
1.0
|
|
HD1
|
E:TYR344
|
5.0
|
99.8
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 9eco
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Magnesium Binding Sites List in 9eco
Magnesium binding site 5 out
of 5 in the E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4
 Mono view
 Stereo pair view
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A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of E. Coli Dnab Bound to Three Dnag C-Terminal Domains, Ssdna, Adp and ALF4 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1003
b:104.5
occ:1.00
|
F1
|
F:ALF1002
|
2.0
|
124.3
|
1.0
|
|
OG1
|
F:THR238
|
2.0
|
114.4
|
1.0
|
|
O1B
|
F:ADP1001
|
2.1
|
123.0
|
1.0
|
|
HG1
|
F:THR238
|
2.6
|
111.3
|
1.0
|
|
HB
|
F:THR238
|
3.0
|
107.1
|
1.0
|
|
CB
|
F:THR238
|
3.1
|
107.3
|
1.0
|
|
PB
|
F:ADP1001
|
3.3
|
119.2
|
1.0
|
|
H
|
F:THR238
|
3.5
|
106.3
|
1.0
|
|
O2B
|
F:ADP1001
|
3.5
|
112.2
|
1.0
|
|
AL
|
F:ALF1002
|
3.6
|
122.9
|
1.0
|
|
F4
|
F:ALF1002
|
3.8
|
124.8
|
1.0
|
|
HG22
|
F:THR238
|
3.8
|
107.1
|
1.0
|
|
OD1
|
F:ASP343
|
3.9
|
120.4
|
1.0
|
|
OE1
|
F:GLU262
|
3.9
|
130.5
|
1.0
|
|
O1A
|
F:ADP1001
|
4.0
|
114.5
|
1.0
|
|
N
|
F:THR238
|
4.0
|
103.5
|
1.0
|
|
CG2
|
F:THR238
|
4.1
|
106.5
|
1.0
|
|
CA
|
F:THR238
|
4.1
|
102.6
|
1.0
|
|
O3A
|
F:ADP1001
|
4.2
|
111.0
|
1.0
|
|
HB3
|
F:LYS237
|
4.2
|
110.2
|
1.0
|
|
F3
|
F:ALF1002
|
4.3
|
116.2
|
1.0
|
|
PA
|
F:ADP1001
|
4.4
|
104.3
|
1.0
|
|
O2A
|
F:ADP1001
|
4.4
|
107.5
|
1.0
|
|
O3B
|
F:ADP1001
|
4.4
|
115.8
|
1.0
|
|
HA
|
F:THR238
|
4.5
|
105.1
|
1.0
|
|
HE3
|
F:LYS237
|
4.5
|
108.7
|
1.0
|
|
HG23
|
F:THR238
|
4.6
|
105.0
|
1.0
|
|
CG
|
F:ASP343
|
4.7
|
123.8
|
1.0
|
|
HH12
|
F:ARG271
|
4.7
|
111.4
|
1.0
|
|
HG21
|
F:THR238
|
4.7
|
105.4
|
1.0
|
|
OD2
|
F:ASP343
|
4.7
|
130.5
|
1.0
|
|
SD
|
F:MET263
|
4.9
|
127.5
|
1.0
|
|
HD11
|
F:LEU382
|
5.0
|
114.0
|
1.0
|
|
Reference:
A.J.Oakley,
Z.Q.Xu.
Sequence of Conformation Changes of Dnab Helicase During Dna Unwinding and Priming in Escherichia Coli To Be Published.
Page generated: Sun Dec 15 11:23:17 2024
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