Magnesium in PDB 7qtt: Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Enzymatic activity of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
All present enzymatic activity of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region):
2.3.2.27;
3.6.4.13;
5.2.1.8;
Other elements in 7qtt:
The structure of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
(pdb code 7qtt). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region), PDB code: 7qtt:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 7qtt
Go back to
Magnesium Binding Sites List in 7qtt
Magnesium binding site 1 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Mg1501
b:103.9
occ:1.00
|
O1G
|
b:GTP1500
|
2.1
|
100.5
|
1.0
|
O3A
|
b:GTP1500
|
2.2
|
100.5
|
1.0
|
O3B
|
b:GTP1500
|
2.2
|
100.5
|
1.0
|
O2A
|
b:GTP1500
|
2.2
|
100.5
|
1.0
|
PB
|
b:GTP1500
|
2.4
|
100.5
|
1.0
|
OG1
|
b:THR143
|
2.5
|
105.9
|
1.0
|
PA
|
b:GTP1500
|
2.6
|
100.5
|
1.0
|
PG
|
b:GTP1500
|
2.6
|
100.5
|
1.0
|
O2B
|
b:GTP1500
|
2.9
|
100.5
|
1.0
|
CB
|
b:THR143
|
3.2
|
105.9
|
1.0
|
O2G
|
b:GTP1500
|
3.4
|
100.5
|
1.0
|
O1A
|
b:GTP1500
|
3.4
|
100.5
|
1.0
|
O3G
|
b:GTP1500
|
3.9
|
100.5
|
1.0
|
O1B
|
b:GTP1500
|
3.9
|
100.5
|
1.0
|
O5'
|
b:GTP1500
|
3.9
|
100.5
|
1.0
|
CG2
|
b:THR143
|
4.2
|
105.9
|
1.0
|
N
|
b:THR143
|
4.3
|
105.9
|
1.0
|
CA
|
b:THR143
|
4.4
|
105.9
|
1.0
|
OD2
|
b:ASP169
|
4.4
|
121.6
|
1.0
|
C5'
|
b:GTP1500
|
4.7
|
100.5
|
1.0
|
N
|
b:GLY180
|
4.9
|
111.6
|
1.0
|
ND1
|
b:HIS139
|
4.9
|
102.0
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 7qtt
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Magnesium Binding Sites List in 7qtt
Magnesium binding site 2 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
d:Mg201
b:94.4
occ:1.00
|
OP2
|
d:U74
|
2.1
|
93.8
|
1.0
|
OP1
|
d:G72
|
2.2
|
88.6
|
1.0
|
P
|
d:U74
|
3.3
|
93.8
|
1.0
|
OP1
|
d:G54
|
3.5
|
89.8
|
1.0
|
OP1
|
d:U74
|
3.6
|
93.8
|
1.0
|
P
|
d:G72
|
3.6
|
88.6
|
1.0
|
O5'
|
d:U74
|
4.1
|
93.8
|
1.0
|
O5'
|
d:G54
|
4.3
|
89.8
|
1.0
|
P
|
d:G54
|
4.4
|
89.8
|
1.0
|
C5'
|
d:U74
|
4.4
|
93.8
|
1.0
|
OP2
|
d:G72
|
4.4
|
88.6
|
1.0
|
O3'
|
g:G-1
|
4.4
|
102.2
|
1.0
|
O5'
|
d:G72
|
4.5
|
88.6
|
1.0
|
O3'
|
d:G71
|
4.5
|
83.0
|
1.0
|
O3'
|
d:A73
|
4.5
|
100.4
|
1.0
|
O5'
|
g:G1
|
4.8
|
107.5
|
1.0
|
OP2
|
d:G54
|
4.8
|
89.8
|
1.0
|
C5'
|
d:G72
|
4.8
|
88.6
|
1.0
|
C3'
|
d:A73
|
4.9
|
100.4
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 7qtt
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Magnesium Binding Sites List in 7qtt
Magnesium binding site 3 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
d:Mg202
b:97.2
occ:1.00
|
OP1
|
d:U74
|
2.1
|
93.8
|
1.0
|
OP2
|
d:G54
|
2.2
|
89.8
|
1.0
|
OP2
|
d:A53
|
2.3
|
93.8
|
1.0
|
OP1
|
d:A53
|
2.3
|
93.8
|
1.0
|
P
|
d:A53
|
2.5
|
93.8
|
1.0
|
NZ
|
I:LYS10
|
2.7
|
124.5
|
1.0
|
O5'
|
d:A53
|
3.2
|
93.8
|
1.0
|
P
|
d:U74
|
3.3
|
93.8
|
1.0
|
O5'
|
d:U74
|
3.4
|
93.8
|
1.0
|
P
|
d:G54
|
3.6
|
89.8
|
1.0
|
CE
|
I:LYS10
|
3.7
|
124.5
|
1.0
|
O3'
|
d:A73
|
4.0
|
100.4
|
1.0
|
O3'
|
d:U52
|
4.0
|
107.4
|
1.0
|
C5'
|
d:A53
|
4.2
|
93.8
|
1.0
|
C5'
|
d:G54
|
4.2
|
89.8
|
1.0
|
OP1
|
d:G54
|
4.3
|
89.8
|
1.0
|
O6
|
d:G46
|
4.3
|
102.6
|
1.0
|
O5'
|
d:G54
|
4.3
|
89.8
|
1.0
|
OP2
|
d:U74
|
4.5
|
93.8
|
1.0
|
C3'
|
d:A53
|
4.6
|
93.8
|
1.0
|
O3'
|
d:A53
|
4.6
|
93.8
|
1.0
|
C5'
|
d:U74
|
4.8
|
93.8
|
1.0
|
O4'
|
d:U74
|
4.8
|
93.8
|
1.0
|
C3'
|
d:U52
|
4.9
|
107.4
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 7qtt
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Magnesium Binding Sites List in 7qtt
Magnesium binding site 4 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
d:Mg203
b:86.5
occ:1.00
|
OP1
|
d:G75
|
2.2
|
92.2
|
1.0
|
P
|
d:G75
|
3.6
|
92.2
|
1.0
|
O5'
|
d:G75
|
4.1
|
92.2
|
1.0
|
N7
|
d:G75
|
4.4
|
92.2
|
1.0
|
O4
|
d:U57
|
4.4
|
97.8
|
1.0
|
OP2
|
d:A76
|
4.4
|
96.5
|
1.0
|
OP2
|
d:G75
|
4.5
|
92.2
|
1.0
|
C8
|
d:G75
|
4.5
|
92.2
|
1.0
|
O3'
|
d:U74
|
4.6
|
93.8
|
1.0
|
C2'
|
d:U74
|
4.6
|
93.8
|
1.0
|
N7
|
d:A76
|
4.8
|
96.5
|
1.0
|
C3'
|
d:U74
|
4.8
|
93.8
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 7qtt
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Magnesium Binding Sites List in 7qtt
Magnesium binding site 5 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
d:Mg204
b:80.8
occ:1.00
|
OP2
|
d:G75
|
2.1
|
92.2
|
1.0
|
P
|
d:G75
|
3.4
|
92.2
|
1.0
|
OP1
|
d:G75
|
3.9
|
92.2
|
1.0
|
O3'
|
d:U74
|
4.0
|
93.8
|
1.0
|
OP2
|
d:G71
|
4.1
|
83.0
|
1.0
|
OP2
|
d:A56
|
4.2
|
91.4
|
1.0
|
OP2
|
d:G72
|
4.4
|
88.6
|
1.0
|
O5'
|
d:G75
|
4.6
|
92.2
|
1.0
|
N7
|
d:G72
|
4.7
|
88.6
|
1.0
|
OP2
|
d:C55
|
4.7
|
87.6
|
1.0
|
N7
|
d:G71
|
4.9
|
83.0
|
1.0
|
C5'
|
d:G71
|
5.0
|
83.0
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 7qtt
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Magnesium Binding Sites List in 7qtt
Magnesium binding site 6 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
d:Mg205
b:78.4
occ:1.00
|
OP1
|
d:C55
|
2.1
|
87.6
|
1.0
|
OP1
|
d:G71
|
2.1
|
83.0
|
1.0
|
P
|
d:C55
|
3.4
|
87.6
|
1.0
|
P
|
d:G71
|
3.4
|
83.0
|
1.0
|
O3'
|
d:G54
|
3.6
|
89.8
|
1.0
|
O5'
|
d:G71
|
3.7
|
83.0
|
1.0
|
OE1
|
a:GLN675
|
4.0
|
84.1
|
1.0
|
O5'
|
d:C55
|
4.2
|
87.6
|
1.0
|
C5'
|
d:G71
|
4.2
|
83.0
|
1.0
|
OP2
|
d:G71
|
4.4
|
83.0
|
1.0
|
O3'
|
d:A70
|
4.5
|
83.1
|
1.0
|
OP2
|
d:C55
|
4.6
|
87.6
|
1.0
|
C5'
|
d:C55
|
4.8
|
87.6
|
1.0
|
C3'
|
d:G54
|
5.0
|
89.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 7qtt
Go back to
Magnesium Binding Sites List in 7qtt
Magnesium binding site 7 out
of 7 in the Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structural Organization of A Late Activated Human Spliceosome (Baqr, Core Region) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
d:Mg206
b:104.7
occ:1.00
|
OP1
|
d:A48
|
2.1
|
113.8
|
1.0
|
OP2
|
d:A50
|
3.3
|
111.5
|
1.0
|
P
|
d:A48
|
3.5
|
113.8
|
1.0
|
OP1
|
d:G49
|
4.0
|
116.2
|
1.0
|
OP2
|
d:A48
|
4.2
|
113.8
|
1.0
|
O5'
|
d:A48
|
4.2
|
113.8
|
1.0
|
C5'
|
d:A48
|
4.3
|
113.8
|
1.0
|
O4
|
d:U52
|
4.4
|
107.4
|
1.0
|
O5'
|
d:A47
|
4.4
|
101.8
|
1.0
|
OP2
|
d:A47
|
4.5
|
101.8
|
1.0
|
P
|
d:A50
|
4.6
|
111.5
|
1.0
|
O3'
|
d:A47
|
4.6
|
101.8
|
1.0
|
OP1
|
d:A47
|
4.6
|
101.8
|
1.0
|
O4
|
d:U51
|
4.7
|
110.1
|
1.0
|
P
|
d:A47
|
4.7
|
101.8
|
1.0
|
C3'
|
d:A47
|
4.8
|
101.8
|
1.0
|
O5'
|
d:A50
|
4.9
|
111.5
|
1.0
|
N7
|
d:A50
|
5.0
|
111.5
|
1.0
|
|
Reference:
J.Schmitzova,
C.Cretu,
C.Dienemann,
H.Urlaub,
V.Pena.
Structural Basis of Catalytic Activation in Human Splicing Nature 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06049-W
Page generated: Thu Oct 3 07:01:39 2024
|