Magnesium in PDB 8umf: Structure of PSCAS9 in Complex with Grna and Dna in Product State
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
(pdb code 8umf). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Structure of PSCAS9 in Complex with Grna and Dna in Product State, PDB code: 8umf:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 8umf
Go back to
Magnesium Binding Sites List in 8umf
Magnesium binding site 1 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1501
b:41.1
occ:1.00
|
OP2
|
C:DC43
|
2.1
|
42.3
|
1.0
|
OD1
|
A:ASP10
|
2.4
|
34.8
|
1.0
|
OE1
|
A:GLU690
|
2.6
|
43.5
|
1.0
|
CD
|
A:GLU690
|
3.1
|
43.5
|
1.0
|
OE2
|
A:GLU690
|
3.3
|
43.5
|
1.0
|
CG
|
A:ASP10
|
3.4
|
34.8
|
1.0
|
P
|
C:DC43
|
3.6
|
42.3
|
1.0
|
OD2
|
A:ASP10
|
3.8
|
34.8
|
1.0
|
ND2
|
A:ASN692
|
4.0
|
41.3
|
1.0
|
CG
|
A:GLU690
|
4.1
|
43.5
|
1.0
|
OD1
|
A:ASN692
|
4.1
|
41.3
|
1.0
|
O
|
A:MET11
|
4.2
|
35.4
|
1.0
|
O5'
|
C:DC43
|
4.2
|
42.3
|
1.0
|
C5'
|
C:DC43
|
4.4
|
42.3
|
1.0
|
CB
|
A:GLU690
|
4.5
|
43.5
|
1.0
|
CG
|
A:ASN692
|
4.5
|
41.3
|
1.0
|
OP1
|
C:DC43
|
4.5
|
42.3
|
1.0
|
CB
|
A:ASP10
|
4.6
|
34.8
|
1.0
|
CA
|
A:ASP10
|
4.7
|
34.8
|
1.0
|
MG
|
A:MG1502
|
4.8
|
34.8
|
1.0
|
N
|
A:MET11
|
4.9
|
35.4
|
1.0
|
C
|
A:ASP10
|
5.0
|
34.8
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 8umf
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Magnesium Binding Sites List in 8umf
Magnesium binding site 2 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1502
b:34.8
occ:1.00
|
OD2
|
A:ASP10
|
2.1
|
34.8
|
1.0
|
OP1
|
C:DC43
|
2.1
|
42.3
|
1.0
|
ND1
|
A:HIS944
|
2.3
|
39.0
|
1.0
|
CE1
|
A:HIS944
|
3.1
|
39.0
|
1.0
|
P
|
C:DC43
|
3.3
|
42.3
|
1.0
|
CG
|
A:ASP10
|
3.3
|
34.8
|
1.0
|
CG
|
A:HIS944
|
3.3
|
39.0
|
1.0
|
O
|
A:TYR15
|
3.5
|
38.9
|
1.0
|
OP2
|
C:DC43
|
3.5
|
42.3
|
1.0
|
CB
|
A:HIS944
|
3.7
|
39.0
|
1.0
|
OD1
|
A:ASP10
|
4.0
|
34.8
|
1.0
|
OP2
|
C:DT44
|
4.1
|
46.1
|
1.0
|
O
|
A:MET11
|
4.2
|
35.4
|
1.0
|
OE1
|
A:GLN939
|
4.2
|
44.3
|
1.0
|
CA
|
A:HIS944
|
4.2
|
39.0
|
1.0
|
O5'
|
C:DC43
|
4.2
|
42.3
|
1.0
|
C5'
|
C:DC43
|
4.2
|
42.3
|
1.0
|
NE2
|
A:HIS944
|
4.3
|
39.0
|
1.0
|
O
|
A:ASP10
|
4.3
|
34.8
|
1.0
|
CB
|
A:ASP10
|
4.4
|
34.8
|
1.0
|
CD2
|
A:HIS944
|
4.4
|
39.0
|
1.0
|
C
|
A:TYR15
|
4.6
|
38.9
|
1.0
|
CA
|
A:GLY12
|
4.7
|
35.8
|
1.0
|
OD2
|
A:ASP947
|
4.7
|
43.0
|
1.0
|
C
|
A:MET11
|
4.8
|
35.4
|
1.0
|
C
|
A:ASP10
|
4.8
|
34.8
|
1.0
|
MG
|
A:MG1501
|
4.8
|
41.1
|
1.0
|
N
|
A:GLY17
|
4.9
|
31.4
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 8umf
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Magnesium Binding Sites List in 8umf
Magnesium binding site 3 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1503
b:34.7
occ:1.00
|
OD1
|
A:ASP756
|
2.1
|
33.4
|
1.0
|
OP2
|
D:DT34
|
2.2
|
31.4
|
1.0
|
OD1
|
A:ASN786
|
2.2
|
37.8
|
1.0
|
O3'
|
E:DC35
|
2.3
|
34.0
|
1.0
|
CG
|
A:ASP756
|
3.3
|
33.4
|
1.0
|
CG
|
A:ASN786
|
3.4
|
37.8
|
1.0
|
P
|
D:DT34
|
3.5
|
31.4
|
1.0
|
C3'
|
E:DC35
|
3.6
|
34.0
|
1.0
|
O
|
A:LYS789
|
3.7
|
42.4
|
1.0
|
O
|
A:ASN786
|
3.8
|
37.8
|
1.0
|
O5'
|
D:DT34
|
3.9
|
31.4
|
1.0
|
CB
|
A:ASP756
|
4.1
|
33.4
|
1.0
|
ND2
|
A:ASN786
|
4.1
|
37.8
|
1.0
|
OD2
|
A:ASP756
|
4.2
|
33.4
|
1.0
|
C4'
|
E:DC35
|
4.2
|
34.0
|
1.0
|
O
|
A:HIS757
|
4.2
|
29.5
|
1.0
|
CD
|
A:LYS789
|
4.4
|
42.4
|
1.0
|
CA
|
A:ASP756
|
4.4
|
33.4
|
1.0
|
C5'
|
E:DC35
|
4.4
|
34.0
|
1.0
|
NZ
|
A:LYS789
|
4.4
|
42.4
|
1.0
|
N
|
A:HIS757
|
4.5
|
29.5
|
1.0
|
CA
|
A:ASN786
|
4.5
|
37.8
|
1.0
|
CG
|
A:LYS789
|
4.5
|
42.4
|
1.0
|
CB
|
A:ASN786
|
4.6
|
37.8
|
1.0
|
C
|
A:ASN786
|
4.6
|
37.8
|
1.0
|
CB
|
A:LYS789
|
4.7
|
42.4
|
1.0
|
C2'
|
E:DC35
|
4.7
|
34.0
|
1.0
|
OP1
|
D:DT34
|
4.7
|
31.4
|
1.0
|
C
|
A:LYS789
|
4.8
|
42.4
|
1.0
|
C
|
A:ASP756
|
4.9
|
33.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 8umf
Go back to
Magnesium Binding Sites List in 8umf
Magnesium binding site 4 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg201
b:15.6
occ:1.00
|
O4
|
B:U69
|
3.6
|
28.9
|
1.0
|
C4
|
B:U69
|
4.4
|
28.9
|
1.0
|
O6
|
B:G70
|
4.5
|
28.6
|
1.0
|
O4
|
B:U26
|
4.6
|
40.0
|
1.0
|
C5
|
B:U69
|
4.6
|
28.9
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 8umf
Go back to
Magnesium Binding Sites List in 8umf
Magnesium binding site 5 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg202
b:20.3
occ:1.00
|
OP1
|
B:A114
|
3.7
|
29.3
|
1.0
|
OP2
|
B:A114
|
4.0
|
29.3
|
1.0
|
OP2
|
B:C97
|
4.1
|
27.7
|
1.0
|
O5'
|
B:A114
|
4.1
|
29.3
|
1.0
|
P
|
B:A114
|
4.1
|
29.3
|
1.0
|
OP2
|
B:U115
|
4.2
|
28.3
|
1.0
|
O6
|
B:G99
|
4.2
|
30.2
|
1.0
|
N7
|
B:G98
|
4.4
|
28.8
|
1.0
|
O6
|
B:G98
|
4.4
|
28.8
|
1.0
|
C5
|
B:C97
|
4.5
|
27.7
|
1.0
|
NH2
|
A:ARG279
|
4.5
|
22.2
|
1.0
|
N4
|
B:C116
|
4.8
|
27.5
|
1.0
|
C5'
|
B:A114
|
4.8
|
29.3
|
1.0
|
N4
|
B:C97
|
4.9
|
27.7
|
1.0
|
C4
|
B:C97
|
4.9
|
27.7
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 8umf
Go back to
Magnesium Binding Sites List in 8umf
Magnesium binding site 6 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg203
b:33.6
occ:1.00
|
O6
|
B:G105
|
3.6
|
31.9
|
1.0
|
N7
|
B:G105
|
4.2
|
31.9
|
1.0
|
O4
|
B:U104
|
4.2
|
27.3
|
1.0
|
C6
|
B:G105
|
4.4
|
31.9
|
1.0
|
C4
|
B:U104
|
4.5
|
27.3
|
1.0
|
C5
|
B:G105
|
4.7
|
31.9
|
1.0
|
N6
|
B:A106
|
4.7
|
37.0
|
1.0
|
C5
|
B:U104
|
4.9
|
27.3
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 8umf
Go back to
Magnesium Binding Sites List in 8umf
Magnesium binding site 7 out
of 7 in the Structure of PSCAS9 in Complex with Grna and Dna in Product State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of PSCAS9 in Complex with Grna and Dna in Product State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg204
b:23.1
occ:1.00
|
OP2
|
B:A94
|
3.7
|
32.6
|
1.0
|
OP2
|
B:C95
|
3.8
|
31.4
|
1.0
|
NH2
|
A:ARG329
|
4.0
|
25.7
|
1.0
|
OP2
|
B:C116
|
4.1
|
27.5
|
1.0
|
O5'
|
B:A94
|
4.3
|
32.6
|
1.0
|
P
|
B:A94
|
4.3
|
32.6
|
1.0
|
CZ
|
A:ARG329
|
4.3
|
25.7
|
1.0
|
C4'
|
B:U115
|
4.3
|
28.3
|
1.0
|
OP1
|
B:C116
|
4.4
|
27.5
|
1.0
|
NE
|
A:ARG329
|
4.5
|
25.7
|
1.0
|
OP1
|
B:A94
|
4.5
|
32.6
|
1.0
|
C5
|
B:C95
|
4.5
|
31.4
|
1.0
|
P
|
B:C116
|
4.5
|
27.5
|
1.0
|
O3'
|
B:U115
|
4.5
|
28.3
|
1.0
|
C5'
|
B:U115
|
4.8
|
28.3
|
1.0
|
C3'
|
B:U115
|
5.0
|
28.3
|
1.0
|
NH1
|
A:ARG329
|
5.0
|
25.7
|
1.0
|
|
Reference:
J.P.K.Bravo,
D.W.Taylor.
Structure-Guided Engineering of PSCAS9 Yields A High Fidelity and Activity Enzyme For in Vivo Gene Editing To Be Published.
Page generated: Thu Oct 31 22:12:51 2024
|