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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:

Zinc (Zn) 12 atoms

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

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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 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 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 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 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 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

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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

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