Magnesium in PDB 6sko: Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
Enzymatic activity of Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
All present enzymatic activity of Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna:
3.6.4.12;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
(pdb code 6sko). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna, PDB code: 6sko:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6sko
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Magnesium Binding Sites List in 6sko
Magnesium binding site 1 out
of 5 in the Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
 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 the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
6:Mg1501
b:21.6
occ:1.00
|
O2B
|
6:ANP1500
|
2.0
|
22.8
|
1.0
|
|
O3G
|
6:ANP1500
|
2.1
|
27.3
|
1.0
|
|
HB2
|
6:SER582
|
2.3
|
30.0
|
1.0
|
|
OG
|
6:SER582
|
2.5
|
30.0
|
1.0
|
|
CB
|
6:SER582
|
2.9
|
30.0
|
1.0
|
|
PB
|
6:ANP1500
|
3.0
|
24.9
|
1.0
|
|
PG
|
6:ANP1500
|
3.0
|
27.3
|
1.0
|
|
H
|
6:SER582
|
3.1
|
30.0
|
1.0
|
|
O1A
|
6:ANP1500
|
3.2
|
26.3
|
1.0
|
|
N3B
|
6:ANP1500
|
3.3
|
25.2
|
1.0
|
|
HG2
|
4:GLU650
|
3.3
|
30.0
|
1.0
|
|
HNB1
|
6:ANP1500
|
3.4
|
25.2
|
1.0
|
|
O2A
|
6:ANP1500
|
3.4
|
25.0
|
1.0
|
|
HH12
|
4:ARG701
|
3.5
|
0.5
|
1.0
|
|
HG
|
6:SER582
|
3.5
|
30.0
|
1.0
|
|
PA
|
6:ANP1500
|
3.5
|
23.4
|
1.0
|
|
HH22
|
4:ARG796
|
3.6
|
0.8
|
1.0
|
|
HH21
|
4:ARG796
|
3.6
|
0.8
|
1.0
|
|
O2G
|
6:ANP1500
|
3.6
|
27.6
|
1.0
|
|
HB3
|
6:SER582
|
3.6
|
30.0
|
1.0
|
|
O3A
|
6:ANP1500
|
3.7
|
22.8
|
1.0
|
|
N
|
6:SER582
|
3.8
|
30.0
|
1.0
|
|
HG2
|
6:LYS581
|
3.8
|
91.3
|
1.0
|
|
CA
|
6:SER582
|
3.9
|
30.0
|
1.0
|
|
NH2
|
4:ARG796
|
4.0
|
0.8
|
1.0
|
|
O1G
|
6:ANP1500
|
4.2
|
28.4
|
1.0
|
|
O1B
|
6:ANP1500
|
4.3
|
21.7
|
1.0
|
|
CG
|
4:GLU650
|
4.3
|
30.0
|
1.0
|
|
NH1
|
4:ARG701
|
4.4
|
0.5
|
1.0
|
|
HG3
|
4:GLU650
|
4.4
|
30.0
|
1.0
|
|
HG3
|
6:LYS581
|
4.4
|
91.3
|
1.0
|
|
HA
|
6:SER582
|
4.6
|
30.0
|
1.0
|
|
HH22
|
4:ARG701
|
4.7
|
0.5
|
1.0
|
|
CG
|
6:LYS581
|
4.7
|
91.3
|
1.0
|
|
H
|
6:LYS581
|
4.7
|
0.2
|
1.0
|
|
HH11
|
4:ARG701
|
4.7
|
0.5
|
1.0
|
|
H
|
6:GLN583
|
4.7
|
85.5
|
1.0
|
|
HZ1
|
6:LYS581
|
4.9
|
1.0
|
1.0
|
|
HA
|
6:SER580
|
5.0
|
0.4
|
1.0
|
|
C
|
6:SER582
|
5.0
|
30.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6sko
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Magnesium Binding Sites List in 6sko
Magnesium binding site 2 out
of 5 in the Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
 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 the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
7:Mg1501
b:21.6
occ:1.00
|
O2G
|
7:ANP1500
|
2.0
|
27.6
|
1.0
|
|
O1B
|
7:ANP1500
|
2.0
|
21.7
|
1.0
|
|
OG
|
7:SER467
|
2.1
|
30.0
|
1.0
|
|
HB2
|
7:SER467
|
2.6
|
30.0
|
1.0
|
|
CB
|
7:SER467
|
2.9
|
30.0
|
1.0
|
|
HG
|
7:SER467
|
2.9
|
30.0
|
1.0
|
|
HH22
|
3:ARG542
|
3.1
|
91.4
|
1.0
|
|
PG
|
7:ANP1500
|
3.1
|
27.3
|
1.0
|
|
PB
|
7:ANP1500
|
3.2
|
24.9
|
1.0
|
|
H
|
7:SER467
|
3.2
|
30.0
|
1.0
|
|
N3B
|
7:ANP1500
|
3.6
|
25.2
|
1.0
|
|
HB3
|
7:SER467
|
3.6
|
30.0
|
1.0
|
|
O1G
|
7:ANP1500
|
3.8
|
28.4
|
1.0
|
|
NH2
|
3:ARG542
|
3.8
|
91.4
|
1.0
|
|
N
|
7:SER467
|
3.9
|
30.0
|
1.0
|
|
HH21
|
3:ARG542
|
3.9
|
91.4
|
1.0
|
|
CA
|
7:SER467
|
3.9
|
30.0
|
1.0
|
|
HB2
|
7:LYS466
|
4.0
|
61.1
|
1.0
|
|
O2A
|
7:ANP1500
|
4.0
|
25.0
|
1.0
|
|
HH22
|
3:ARG700
|
4.2
|
85.3
|
1.0
|
|
O1A
|
7:ANP1500
|
4.2
|
26.3
|
1.0
|
|
O3A
|
7:ANP1500
|
4.2
|
22.8
|
1.0
|
|
PA
|
7:ANP1500
|
4.2
|
23.4
|
1.0
|
|
O3G
|
7:ANP1500
|
4.3
|
27.3
|
1.0
|
|
O2B
|
7:ANP1500
|
4.3
|
22.8
|
1.0
|
|
HNB1
|
7:ANP1500
|
4.3
|
25.2
|
1.0
|
|
OD1
|
7:ASP524
|
4.4
|
0.1
|
1.0
|
|
HA
|
7:SER467
|
4.4
|
30.0
|
1.0
|
|
HE2
|
7:LYS466
|
4.4
|
70.0
|
1.0
|
|
OD2
|
7:ASP524
|
4.5
|
0.3
|
1.0
|
|
HZ1
|
7:LYS466
|
4.5
|
55.7
|
1.0
|
|
HH12
|
3:ARG542
|
4.7
|
90.2
|
1.0
|
|
HZ2
|
7:LYS466
|
4.8
|
55.7
|
1.0
|
|
H
|
7:GLN468
|
4.8
|
48.1
|
1.0
|
|
H
|
7:LYS466
|
4.9
|
71.8
|
1.0
|
|
HH21
|
3:ARG700
|
4.9
|
85.3
|
1.0
|
|
CG
|
7:ASP524
|
4.9
|
83.6
|
1.0
|
|
NH2
|
3:ARG700
|
4.9
|
85.3
|
1.0
|
|
CB
|
7:LYS466
|
5.0
|
61.1
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6sko
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Magnesium Binding Sites List in 6sko
Magnesium binding site 3 out
of 5 in the Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
 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 the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mg1501
b:21.6
occ:1.00
|
HB2
|
2:SER550
|
1.8
|
0.4
|
1.0
|
|
HG3
|
2:LYS549
|
1.9
|
0.9
|
1.0
|
|
O1B
|
2:ANP1500
|
1.9
|
21.7
|
1.0
|
|
O2G
|
2:ANP1500
|
2.0
|
27.6
|
1.0
|
|
H
|
2:SER550
|
2.2
|
0.6
|
1.0
|
|
N
|
2:SER550
|
2.3
|
0.6
|
1.0
|
|
HZ1
|
2:LYS549
|
2.4
|
0.8
|
1.0
|
|
CB
|
2:SER550
|
2.4
|
0.4
|
1.0
|
|
CA
|
2:SER550
|
2.5
|
0.6
|
1.0
|
|
HA
|
2:SER550
|
2.6
|
0.6
|
1.0
|
|
HZ2
|
2:LYS549
|
2.7
|
0.8
|
1.0
|
|
CG
|
2:LYS549
|
2.9
|
0.9
|
1.0
|
|
PB
|
2:ANP1500
|
2.9
|
24.9
|
1.0
|
|
HNB1
|
2:ANP1500
|
2.9
|
25.2
|
1.0
|
|
PG
|
2:ANP1500
|
3.0
|
27.3
|
1.0
|
|
NZ
|
2:LYS549
|
3.1
|
0.8
|
1.0
|
|
HG2
|
2:LYS549
|
3.1
|
0.9
|
1.0
|
|
N3B
|
2:ANP1500
|
3.1
|
25.2
|
1.0
|
|
C
|
2:LYS549
|
3.2
|
0.7
|
1.0
|
|
OG
|
2:SER550
|
3.3
|
0.1
|
1.0
|
|
HB3
|
2:SER550
|
3.3
|
0.4
|
1.0
|
|
H
|
2:LYS549
|
3.5
|
0.5
|
1.0
|
|
HG
|
2:SER550
|
3.6
|
0.1
|
1.0
|
|
HZ3
|
2:LYS549
|
3.7
|
0.8
|
1.0
|
|
O1A
|
2:ANP1500
|
3.7
|
26.3
|
1.0
|
|
CD
|
2:LYS549
|
3.7
|
0.5
|
1.0
|
|
HD2
|
2:LYS549
|
3.8
|
0.5
|
1.0
|
|
CB
|
2:LYS549
|
3.8
|
0.5
|
1.0
|
|
CA
|
2:LYS549
|
3.8
|
0.7
|
1.0
|
|
O2B
|
2:ANP1500
|
3.9
|
22.8
|
1.0
|
|
O3G
|
2:ANP1500
|
3.9
|
27.3
|
1.0
|
|
PA
|
2:ANP1500
|
3.9
|
23.4
|
1.0
|
|
HB3
|
2:ALA649
|
3.9
|
0.7
|
1.0
|
|
CE
|
2:LYS549
|
4.0
|
0.2
|
1.0
|
|
O3A
|
2:ANP1500
|
4.0
|
22.8
|
1.0
|
|
O
|
2:LYS549
|
4.0
|
0.1
|
1.0
|
|
C
|
2:SER550
|
4.0
|
0.4
|
1.0
|
|
HB2
|
2:LYS549
|
4.0
|
0.5
|
1.0
|
|
N
|
2:LYS549
|
4.0
|
0.5
|
1.0
|
|
O2A
|
2:ANP1500
|
4.1
|
25.0
|
1.0
|
|
O1G
|
2:ANP1500
|
4.1
|
28.4
|
1.0
|
|
H
|
2:GLN551
|
4.2
|
0.3
|
1.0
|
|
N
|
2:GLN551
|
4.6
|
0.3
|
1.0
|
|
HE2
|
2:LYS549
|
4.6
|
0.2
|
1.0
|
|
H
|
2:ALA548
|
4.6
|
0.5
|
1.0
|
|
HE3
|
2:LYS549
|
4.7
|
0.2
|
1.0
|
|
HB3
|
2:LYS549
|
4.7
|
0.5
|
1.0
|
|
HE22
|
6:GLN658
|
4.7
|
0.5
|
1.0
|
|
HD3
|
2:LYS549
|
4.7
|
0.5
|
1.0
|
|
CB
|
2:ALA649
|
4.8
|
0.7
|
1.0
|
|
HG22
|
2:THR547
|
4.8
|
30.0
|
1.0
|
|
HA
|
2:LYS549
|
4.9
|
0.7
|
1.0
|
|
HB1
|
2:ALA649
|
4.9
|
0.7
|
1.0
|
|
HH12
|
6:ARG708
|
4.9
|
0.5
|
1.0
|
|
HH12
|
6:ARG798
|
4.9
|
0.9
|
1.0
|
|
O
|
2:SER550
|
4.9
|
0.3
|
1.0
|
|
HB2
|
2:ALA649
|
4.9
|
0.7
|
1.0
|
|
C
|
2:ALA548
|
5.0
|
0.9
|
1.0
|
|
H
|
2:THR547
|
5.0
|
0.3
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6sko
Go back to
Magnesium Binding Sites List in 6sko
Magnesium binding site 4 out
of 5 in the Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
 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 the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Mg1501
b:21.6
occ:1.00
|
O2B
|
3:ANP1500
|
1.9
|
22.8
|
1.0
|
|
HB2
|
3:SER416
|
2.1
|
0.2
|
1.0
|
|
O2G
|
3:ANP1500
|
2.1
|
27.6
|
1.0
|
|
HB3
|
3:SER416
|
2.2
|
0.2
|
1.0
|
|
CB
|
3:SER416
|
2.5
|
0.2
|
1.0
|
|
PB
|
3:ANP1500
|
2.5
|
24.9
|
1.0
|
|
O3A
|
3:ANP1500
|
2.7
|
22.8
|
1.0
|
|
PG
|
3:ANP1500
|
3.0
|
27.3
|
1.0
|
|
OG
|
3:SER416
|
3.1
|
0.7
|
1.0
|
|
N3B
|
3:ANP1500
|
3.1
|
25.2
|
1.0
|
|
HNB1
|
3:ANP1500
|
3.3
|
25.2
|
1.0
|
|
HG
|
3:SER416
|
3.3
|
0.7
|
1.0
|
|
PA
|
3:ANP1500
|
3.4
|
23.4
|
1.0
|
|
H
|
3:SER416
|
3.6
|
93.5
|
1.0
|
|
O1A
|
3:ANP1500
|
3.6
|
26.3
|
1.0
|
|
O2A
|
3:ANP1500
|
3.6
|
25.0
|
1.0
|
|
HH22
|
5:ARG549
|
3.7
|
0.1
|
1.0
|
|
HZ1
|
3:LYS415
|
3.7
|
30.0
|
1.0
|
|
HH11
|
5:ARG651
|
3.8
|
0.1
|
1.0
|
|
CA
|
3:SER416
|
3.9
|
0.7
|
1.0
|
|
O1G
|
3:ANP1500
|
3.9
|
28.4
|
1.0
|
|
HH12
|
5:ARG549
|
3.9
|
0.1
|
1.0
|
|
O1B
|
3:ANP1500
|
4.0
|
21.7
|
1.0
|
|
HH12
|
5:ARG651
|
4.0
|
0.1
|
1.0
|
|
N
|
3:SER416
|
4.1
|
93.5
|
1.0
|
|
O3G
|
3:ANP1500
|
4.1
|
27.3
|
1.0
|
|
HZ2
|
3:LYS415
|
4.2
|
30.0
|
1.0
|
|
NH1
|
5:ARG651
|
4.3
|
0.1
|
1.0
|
|
HG3
|
3:LYS415
|
4.4
|
30.0
|
1.0
|
|
HA
|
3:SER416
|
4.4
|
0.7
|
1.0
|
|
OD2
|
3:ASP473
|
4.5
|
0.3
|
1.0
|
|
NH2
|
5:ARG549
|
4.5
|
0.1
|
1.0
|
|
NZ
|
3:LYS415
|
4.5
|
30.0
|
1.0
|
|
H
|
3:GLN417
|
4.5
|
86.2
|
1.0
|
|
HG2
|
3:LYS415
|
4.7
|
30.0
|
1.0
|
|
HG2
|
5:GLU498
|
4.7
|
0.5
|
1.0
|
|
OD1
|
3:ASP473
|
4.7
|
0.7
|
1.0
|
|
H
|
3:SER412
|
4.7
|
1.0
|
1.0
|
|
NH1
|
5:ARG549
|
4.8
|
0.1
|
1.0
|
|
O5'
|
3:ANP1500
|
4.8
|
24.2
|
1.0
|
|
C
|
3:SER416
|
4.9
|
98.9
|
1.0
|
|
HE2
|
3:LYS415
|
4.9
|
30.0
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6sko
Go back to
Magnesium Binding Sites List in 6sko
Magnesium binding site 5 out
of 5 in the Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna
 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 the Fork Protection Complex Bound to Cmg at A Replication Fork - Conformation 2 Mcm Ctd:Ssdna within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Mg1501
b:21.6
occ:1.00
|
O1B
|
4:ANP1500
|
1.9
|
21.7
|
1.0
|
|
O3G
|
4:ANP1500
|
1.9
|
27.3
|
1.0
|
|
HB2
|
4:SER575
|
2.3
|
66.2
|
1.0
|
|
O3A
|
4:ANP1500
|
2.4
|
22.8
|
1.0
|
|
PB
|
4:ANP1500
|
2.5
|
24.9
|
1.0
|
|
HB3
|
4:SER575
|
2.5
|
66.2
|
1.0
|
|
CB
|
4:SER575
|
2.8
|
66.2
|
1.0
|
|
PG
|
4:ANP1500
|
2.9
|
27.3
|
1.0
|
|
HH22
|
7:ARG593
|
2.9
|
67.4
|
1.0
|
|
N3B
|
4:ANP1500
|
3.1
|
25.2
|
1.0
|
|
H
|
4:SER575
|
3.2
|
74.9
|
1.0
|
|
HH12
|
7:ARG687
|
3.4
|
93.2
|
1.0
|
|
HH21
|
7:ARG593
|
3.4
|
67.4
|
1.0
|
|
NH2
|
7:ARG593
|
3.6
|
67.4
|
1.0
|
|
PA
|
4:ANP1500
|
3.6
|
23.4
|
1.0
|
|
OG
|
4:SER575
|
3.7
|
68.2
|
1.0
|
|
O1A
|
4:ANP1500
|
3.7
|
26.3
|
1.0
|
|
O1G
|
4:ANP1500
|
3.8
|
28.4
|
1.0
|
|
O2B
|
4:ANP1500
|
3.9
|
22.8
|
1.0
|
|
HG
|
4:SER575
|
3.9
|
68.2
|
1.0
|
|
HNB1
|
4:ANP1500
|
3.9
|
25.2
|
1.0
|
|
N
|
4:SER575
|
4.0
|
74.9
|
1.0
|
|
O2G
|
4:ANP1500
|
4.0
|
27.6
|
1.0
|
|
CA
|
4:SER575
|
4.0
|
60.1
|
1.0
|
|
NH1
|
7:ARG687
|
4.2
|
93.2
|
1.0
|
|
O2A
|
4:ANP1500
|
4.2
|
25.0
|
1.0
|
|
HZ1
|
4:LYS574
|
4.2
|
75.9
|
1.0
|
|
HZ2
|
4:LYS574
|
4.3
|
75.9
|
1.0
|
|
HB2
|
4:LYS574
|
4.4
|
53.4
|
1.0
|
|
HH22
|
7:ARG687
|
4.4
|
43.0
|
1.0
|
|
HH11
|
7:ARG687
|
4.5
|
93.2
|
1.0
|
|
HA
|
4:SER575
|
4.7
|
60.1
|
1.0
|
|
HG2
|
7:GLU542
|
4.7
|
0.7
|
1.0
|
|
H
|
4:LYS574
|
4.7
|
43.2
|
1.0
|
|
H
|
4:GLN576
|
4.7
|
40.7
|
1.0
|
|
HH12
|
7:ARG593
|
4.7
|
61.9
|
1.0
|
|
CZ
|
7:ARG593
|
4.7
|
58.3
|
1.0
|
|
O5'
|
4:ANP1500
|
4.8
|
24.2
|
1.0
|
|
NZ
|
4:LYS574
|
4.8
|
75.9
|
1.0
|
|
OD2
|
4:ASP632
|
4.9
|
69.9
|
1.0
|
|
H
|
4:SER571
|
4.9
|
63.6
|
1.0
|
|
HE2
|
4:LYS574
|
4.9
|
78.8
|
1.0
|
|
Reference:
D.Baretic,
M.Jenkyn-Bedford,
V.Aria,
G.Cannone,
M.Skehel,
J.T.P.Yeeles.
Cryo-Em Structure of the Fork Protection Complex Bound to Cmg at A Replication Fork To Be Published.
Page generated: Tue Oct 1 17:58:35 2024
|
