Magnesium in PDB 8dqx: Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction
(pdb code 8dqx). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction, PDB code: 8dqx:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8dqx
Go back to
Magnesium Binding Sites List in 8dqx
Magnesium binding site 1 out
of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg902
b:2.6
occ:1.00
|
O
|
A:HOH1035
|
1.9
|
1.0
|
1.0
|
|
O2G
|
A:AGS901
|
2.0
|
4.5
|
1.0
|
|
O
|
A:HOH1057
|
2.2
|
2.4
|
1.0
|
|
O
|
A:HOH1076
|
2.3
|
1.8
|
1.0
|
|
OG1
|
A:THR360
|
2.3
|
3.8
|
1.0
|
|
O1B
|
A:AGS901
|
2.3
|
4.5
|
1.0
|
|
HOG2
|
A:AGS901
|
2.5
|
4.5
|
1.0
|
|
HB
|
A:THR360
|
3.1
|
3.8
|
1.0
|
|
PG
|
A:AGS901
|
3.3
|
4.5
|
1.0
|
|
CB
|
A:THR360
|
3.3
|
3.8
|
1.0
|
|
HH22
|
B:ARG157
|
3.5
|
2.0
|
1.0
|
|
PB
|
A:AGS901
|
3.5
|
4.5
|
1.0
|
|
H
|
A:THR360
|
3.6
|
3.8
|
1.0
|
|
O1A
|
A:AGS901
|
3.7
|
4.5
|
1.0
|
|
O3B
|
A:AGS901
|
3.7
|
4.5
|
1.0
|
|
HH21
|
B:ARG128
|
3.8
|
2.0
|
1.0
|
|
O3G
|
A:AGS901
|
3.8
|
4.5
|
1.0
|
|
HG21
|
A:THR360
|
3.9
|
3.8
|
1.0
|
|
OD2
|
A:ASP424
|
3.9
|
3.9
|
1.0
|
|
HH12
|
A:ARG515
|
4.0
|
3.4
|
1.0
|
|
H21
|
A:AGS901
|
4.1
|
4.5
|
1.0
|
|
NH2
|
B:ARG157
|
4.2
|
2.0
|
1.0
|
|
OD1
|
A:ASP424
|
4.2
|
3.9
|
1.0
|
|
CG2
|
A:THR360
|
4.2
|
3.8
|
1.0
|
|
HH21
|
B:ARG157
|
4.3
|
2.0
|
1.0
|
|
OE1
|
B:GLU132
|
4.3
|
2.4
|
1.0
|
|
N
|
A:THR360
|
4.3
|
3.8
|
1.0
|
|
HD3
|
B:ARG129
|
4.3
|
2.3
|
1.0
|
|
CA
|
A:THR360
|
4.4
|
3.8
|
1.0
|
|
CG
|
A:ASP424
|
4.4
|
3.9
|
1.0
|
|
O3A
|
A:AGS901
|
4.5
|
4.5
|
1.0
|
|
NH2
|
B:ARG128
|
4.5
|
2.0
|
1.0
|
|
PA
|
A:AGS901
|
4.6
|
4.5
|
1.0
|
|
HH22
|
B:ARG128
|
4.6
|
2.0
|
1.0
|
|
HB2
|
A:LYS359
|
4.6
|
3.8
|
1.0
|
|
O2B
|
A:AGS901
|
4.6
|
4.5
|
1.0
|
|
HA
|
A:THR360
|
4.7
|
3.8
|
1.0
|
|
HH22
|
A:ARG515
|
4.8
|
3.4
|
1.0
|
|
HG3
|
A:GLU425
|
4.8
|
4.1
|
1.0
|
|
HG23
|
A:THR360
|
4.8
|
3.8
|
1.0
|
|
OE2
|
A:GLU425
|
4.8
|
4.1
|
1.0
|
|
OE2
|
B:GLU132
|
4.8
|
2.4
|
1.0
|
|
NH1
|
A:ARG515
|
4.8
|
3.4
|
1.0
|
|
HG22
|
A:THR360
|
4.9
|
3.8
|
1.0
|
|
HG22
|
A:ILE454
|
4.9
|
4.4
|
1.0
|
|
S1G
|
A:AGS901
|
4.9
|
4.5
|
1.0
|
|
HZ3
|
A:LYS359
|
4.9
|
3.8
|
1.0
|
|
CD
|
B:GLU132
|
5.0
|
2.4
|
1.0
|
|
HE2
|
A:LYS359
|
5.0
|
3.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8dqx
Go back to
Magnesium Binding Sites List in 8dqx
Magnesium binding site 2 out
of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:1.4
occ:1.00
|
O
|
B:HOH548
|
2.1
|
1.3
|
1.0
|
|
O2G
|
B:AGS402
|
2.1
|
3.1
|
1.0
|
|
O2B
|
B:AGS402
|
2.1
|
3.1
|
1.0
|
|
OG1
|
B:THR56
|
2.2
|
2.7
|
1.0
|
|
O
|
B:HOH592
|
2.3
|
1.8
|
1.0
|
|
O
|
B:HOH597
|
2.4
|
2.2
|
1.0
|
|
HOG2
|
B:AGS402
|
2.7
|
3.1
|
1.0
|
|
HB
|
B:THR56
|
3.0
|
2.7
|
1.0
|
|
CB
|
B:THR56
|
3.2
|
2.7
|
1.0
|
|
PG
|
B:AGS402
|
3.3
|
3.1
|
1.0
|
|
HH22
|
C:ARG160
|
3.3
|
1.6
|
1.0
|
|
PB
|
B:AGS402
|
3.3
|
3.1
|
1.0
|
|
H
|
B:THR56
|
3.4
|
2.7
|
1.0
|
|
H21
|
B:AGS402
|
3.5
|
3.1
|
1.0
|
|
O3B
|
B:AGS402
|
3.5
|
3.1
|
1.0
|
|
HH21
|
C:ARG131
|
3.7
|
0.8
|
1.0
|
|
HH22
|
B:ARG203
|
3.8
|
4.3
|
1.0
|
|
O3G
|
B:AGS402
|
3.8
|
3.1
|
1.0
|
|
O2A
|
B:AGS402
|
3.9
|
3.1
|
1.0
|
|
NH2
|
C:ARG160
|
3.9
|
1.6
|
1.0
|
|
HG21
|
B:THR56
|
4.0
|
2.7
|
1.0
|
|
HH21
|
C:ARG160
|
4.0
|
1.6
|
1.0
|
|
N
|
B:THR56
|
4.1
|
2.7
|
1.0
|
|
OD1
|
B:ASP114
|
4.2
|
2.7
|
1.0
|
|
OD2
|
B:ASP114
|
4.2
|
2.7
|
1.0
|
|
CG2
|
B:THR56
|
4.2
|
2.7
|
1.0
|
|
CA
|
B:THR56
|
4.2
|
2.7
|
1.0
|
|
O3A
|
B:AGS402
|
4.3
|
3.1
|
1.0
|
|
HB2
|
B:LYS55
|
4.3
|
2.8
|
1.0
|
|
HD3
|
C:ARG132
|
4.4
|
1.2
|
1.0
|
|
O1B
|
B:AGS402
|
4.4
|
3.1
|
1.0
|
|
NH2
|
B:ARG203
|
4.4
|
4.3
|
1.0
|
|
HH21
|
B:ARG203
|
4.5
|
4.3
|
1.0
|
|
NH2
|
C:ARG131
|
4.5
|
0.8
|
1.0
|
|
O
|
B:HOH546
|
4.5
|
2.8
|
1.0
|
|
CG
|
B:ASP114
|
4.6
|
2.7
|
1.0
|
|
HA
|
B:THR56
|
4.6
|
2.7
|
1.0
|
|
OE1
|
C:GLU135
|
4.6
|
1.9
|
1.0
|
|
PA
|
B:AGS402
|
4.6
|
3.1
|
1.0
|
|
HH22
|
C:ARG131
|
4.7
|
0.8
|
1.0
|
|
HE2
|
B:LYS55
|
4.7
|
2.8
|
1.0
|
|
HG23
|
B:THR56
|
4.7
|
2.7
|
1.0
|
|
HG3
|
B:GLU115
|
4.8
|
3.0
|
1.0
|
|
HG22
|
B:THR56
|
4.9
|
2.7
|
1.0
|
|
S1G
|
B:AGS402
|
4.9
|
3.1
|
1.0
|
|
HZ1
|
B:LYS55
|
5.0
|
2.8
|
1.0
|
|
O1A
|
B:AGS402
|
5.0
|
3.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8dqx
Go back to
Magnesium Binding Sites List in 8dqx
Magnesium binding site 3 out
of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg401
b:3.2
occ:1.00
|
O2B
|
C:AGS402
|
1.9
|
3.2
|
1.0
|
|
O2G
|
C:AGS402
|
2.0
|
3.2
|
1.0
|
|
O
|
C:HOH595
|
2.3
|
3.2
|
1.0
|
|
O
|
C:HOH515
|
2.3
|
3.2
|
1.0
|
|
OG1
|
C:THR60
|
2.3
|
1.1
|
1.0
|
|
O
|
C:HOH581
|
2.4
|
3.2
|
1.0
|
|
HOG2
|
C:AGS402
|
2.7
|
3.2
|
1.0
|
|
HG1
|
C:THR60
|
3.0
|
1.1
|
1.0
|
|
HB
|
C:THR60
|
3.0
|
1.1
|
1.0
|
|
PG
|
C:AGS402
|
3.1
|
3.2
|
1.0
|
|
PB
|
C:AGS402
|
3.1
|
3.2
|
1.0
|
|
CB
|
C:THR60
|
3.2
|
1.1
|
1.0
|
|
H
|
C:THR60
|
3.3
|
1.1
|
1.0
|
|
O3B
|
C:AGS402
|
3.4
|
3.2
|
1.0
|
|
HH22
|
D:ARG183
|
3.5
|
1.2
|
1.0
|
|
O3G
|
C:AGS402
|
3.7
|
3.2
|
1.0
|
|
HH22
|
C:ARG206
|
3.8
|
1.3
|
1.0
|
|
HH21
|
D:ARG154
|
3.8
|
0.9
|
1.0
|
|
O2A
|
C:AGS402
|
3.9
|
3.2
|
1.0
|
|
H21
|
C:AGS402
|
3.9
|
3.2
|
1.0
|
|
N
|
C:THR60
|
4.0
|
1.1
|
1.0
|
|
HB2
|
C:LYS59
|
4.1
|
0.7
|
1.0
|
|
O3A
|
C:AGS402
|
4.1
|
3.2
|
1.0
|
|
NH2
|
D:ARG183
|
4.2
|
1.2
|
1.0
|
|
OD1
|
C:ASP117
|
4.2
|
0.7
|
1.0
|
|
CA
|
C:THR60
|
4.2
|
1.1
|
1.0
|
|
O1B
|
C:AGS402
|
4.2
|
3.2
|
1.0
|
|
HG21
|
C:THR60
|
4.2
|
1.1
|
1.0
|
|
OD2
|
C:ASP117
|
4.2
|
0.7
|
1.0
|
|
HH21
|
D:ARG183
|
4.3
|
1.2
|
1.0
|
|
CG2
|
C:THR60
|
4.4
|
1.1
|
1.0
|
|
HD3
|
D:ARG155
|
4.4
|
0.9
|
1.0
|
|
HH21
|
C:ARG206
|
4.5
|
1.3
|
1.0
|
|
NH2
|
C:ARG206
|
4.5
|
1.3
|
1.0
|
|
HE2
|
C:LYS59
|
4.5
|
0.7
|
1.0
|
|
NH2
|
D:ARG154
|
4.5
|
0.9
|
1.0
|
|
PA
|
C:AGS402
|
4.5
|
3.2
|
1.0
|
|
HD23
|
C:LEU146
|
4.5
|
0.3
|
1.0
|
|
HH22
|
D:ARG154
|
4.6
|
0.9
|
1.0
|
|
O
|
C:HOH568
|
4.6
|
1.1
|
1.0
|
|
HA
|
C:THR60
|
4.6
|
1.1
|
1.0
|
|
CG
|
C:ASP117
|
4.6
|
0.7
|
1.0
|
|
HZ3
|
C:LYS59
|
4.8
|
0.7
|
1.0
|
|
OE1
|
D:GLU158
|
4.8
|
1.2
|
1.0
|
|
HD22
|
C:LEU146
|
4.8
|
0.3
|
1.0
|
|
S1G
|
C:AGS402
|
4.8
|
3.2
|
1.0
|
|
HG3
|
C:GLU118
|
4.8
|
0.7
|
1.0
|
|
HH12
|
D:ARG183
|
4.9
|
1.2
|
1.0
|
|
O1A
|
C:AGS402
|
4.9
|
3.2
|
1.0
|
|
HG23
|
C:THR60
|
5.0
|
1.1
|
1.0
|
|
HG22
|
C:THR60
|
5.0
|
1.1
|
1.0
|
|
HZ1
|
C:LYS59
|
5.0
|
0.7
|
1.0
|
|
OE2
|
C:GLU118
|
5.0
|
0.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8dqx
Go back to
Magnesium Binding Sites List in 8dqx
Magnesium binding site 4 out
of 4 in the Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Open State of Rfc:Pcna Bound to A 3' Ss/Dsdna Junction within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg401
b:0.8
occ:1.00
|
O2G
|
D:AGS402
|
2.0
|
1.2
|
1.0
|
|
O2B
|
D:AGS402
|
2.0
|
1.2
|
1.0
|
|
O
|
D:HOH508
|
2.3
|
0.0
|
1.0
|
|
O
|
D:HOH630
|
2.3
|
0.7
|
1.0
|
|
O
|
D:HOH530
|
2.5
|
1.2
|
1.0
|
|
OG1
|
D:THR72
|
2.6
|
1.5
|
1.0
|
|
HOG2
|
D:AGS402
|
2.6
|
1.2
|
1.0
|
|
PG
|
D:AGS402
|
3.0
|
1.2
|
1.0
|
|
PB
|
D:AGS402
|
3.2
|
1.2
|
1.0
|
|
HG1
|
D:THR72
|
3.2
|
1.5
|
1.0
|
|
HH22
|
E:ARG184
|
3.2
|
0.7
|
1.0
|
|
HB
|
D:THR72
|
3.2
|
1.5
|
1.0
|
|
O3B
|
D:AGS402
|
3.3
|
1.2
|
1.0
|
|
H21
|
D:AGS402
|
3.4
|
1.2
|
1.0
|
|
CB
|
D:THR72
|
3.5
|
1.5
|
1.0
|
|
HH21
|
E:ARG155
|
3.6
|
0.7
|
1.0
|
|
H
|
D:THR72
|
3.6
|
1.5
|
1.0
|
|
O3G
|
D:AGS402
|
3.6
|
1.2
|
1.0
|
|
HH22
|
D:ARG229
|
3.7
|
5.3
|
1.0
|
|
NH2
|
E:ARG184
|
3.9
|
0.7
|
1.0
|
|
O2A
|
D:AGS402
|
4.0
|
1.2
|
1.0
|
|
HH21
|
E:ARG184
|
4.1
|
0.7
|
1.0
|
|
OD2
|
D:ASP140
|
4.2
|
1.0
|
1.0
|
|
O1B
|
D:AGS402
|
4.2
|
1.2
|
1.0
|
|
O3A
|
D:AGS402
|
4.2
|
1.2
|
1.0
|
|
HG21
|
D:THR72
|
4.3
|
1.5
|
1.0
|
|
N
|
D:THR72
|
4.3
|
1.5
|
1.0
|
|
OD1
|
D:ASP140
|
4.3
|
1.0
|
1.0
|
|
NH2
|
E:ARG155
|
4.3
|
0.7
|
1.0
|
|
HB2
|
D:LYS71
|
4.4
|
1.2
|
1.0
|
|
HH21
|
D:ARG229
|
4.4
|
5.3
|
1.0
|
|
NH2
|
D:ARG229
|
4.4
|
5.3
|
1.0
|
|
HD3
|
E:ARG156
|
4.4
|
1.8
|
1.0
|
|
HE2
|
D:LYS71
|
4.4
|
1.2
|
1.0
|
|
CA
|
D:THR72
|
4.5
|
1.5
|
1.0
|
|
CG2
|
D:THR72
|
4.5
|
1.5
|
1.0
|
|
OE1
|
E:GLU159
|
4.5
|
1.8
|
1.0
|
|
O
|
D:HOH576
|
4.6
|
1.0
|
1.0
|
|
HH22
|
E:ARG155
|
4.6
|
0.7
|
1.0
|
|
HG21
|
D:ILE169
|
4.6
|
0.8
|
1.0
|
|
PA
|
D:AGS402
|
4.6
|
1.2
|
1.0
|
|
CG
|
D:ASP140
|
4.7
|
1.0
|
1.0
|
|
S1G
|
D:AGS402
|
4.7
|
1.2
|
1.0
|
|
OE2
|
D:GLU141
|
4.8
|
1.7
|
1.0
|
|
HZ1
|
D:LYS71
|
4.8
|
1.2
|
1.0
|
|
HH12
|
E:ARG184
|
4.8
|
0.7
|
1.0
|
|
HA
|
D:THR72
|
4.9
|
1.5
|
1.0
|
|
HZ3
|
D:LYS71
|
4.9
|
1.2
|
1.0
|
|
HE
|
E:ARG155
|
5.0
|
0.7
|
1.0
|
|
HG22
|
D:ILE169
|
5.0
|
0.8
|
1.0
|
|
O1A
|
D:AGS402
|
5.0
|
1.2
|
1.0
|
|
Reference:
M.Schrecker,
J.C.Castaneda,
S.Devbhandari,
C.Kumar,
D.Remus,
R.K.Hite.
Multistep Loading of A Dna Sliding Clamp Onto Dna By Replication Factor C. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35939393
DOI: 10.7554/ELIFE.78253
Page generated: Fri Apr 7 09:10:19 2023
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