Magnesium in PDB 8t2t: Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State

Enzymatic activity of Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State

All present enzymatic activity of Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State:
2.7.7.49;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State (pdb code 8t2t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State, PDB code: 8t2t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8t2t

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Magnesium binding site 1 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:91.1
occ:1.00
 O3' A:U7 2.1 128.3 1.0
C3' A:U7 2.9 127.2 1.0
C4' A:U7 3.0 125.5 1.0
OP1 B:U579 3.0 67.1 1.0
O2' A:U7 3.2 126.7 1.0
MG B:MG701 3.2 98.2 1.0
P A:U8 3.3 144.5 1.0
OP1 A:U8 3.6 132.7 1.0
C5' A:U8 3.6 127.8 1.0
C2' A:U7 3.6 124.9 1.0
C5' A:U7 3.6 119.6 1.0
OP1 B:G563 3.7 78.6 1.0
OP2 B:C581 3.8 39.4 1.0
O5' A:U8 3.9 133.2 1.0
P B:U579 4.1 57.8 1.0
O4' A:U7 4.3 122.6 1.0
O3' B:U638 4.4 87.3 1.0
OP2 A:U8 4.5 132.4 1.0
O3' B:G578 4.5 62.1 1.0
OP1 B:C581 4.5 52.4 1.0
O2' B:U638 4.5 104.1 1.0
C1' A:U7 4.6 118.8 1.0
OP2 B:U579 4.6 52.6 1.0
O5' A:U7 4.6 122.0 1.0
C3' B:U638 4.6 93.2 1.0
P B:C581 4.7 53.2 1.0
C4' A:U8 4.8 128.3 1.0
P B:G563 4.9 64.2 1.0

Magnesium binding site 2 out of 10 in 8t2t

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Magnesium binding site 2 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:98.2
occ:1.00
 OP1 B:C581 2.0 52.4 1.0
O2' B:U638 2.0 104.1 1.0
O3' B:U638 2.0 87.3 1.0
C3' B:U638 2.7 93.2 1.0
C2' B:U638 2.8 100.5 1.0
P B:C581 3.0 53.2 1.0
MG A:MG101 3.2 91.1 1.0
OP1 B:C562 3.3 70.3 1.0
OP2 B:C581 3.3 39.4 1.0
OP2 B:G563 3.3 66.0 1.0
OP1 B:G563 3.7 78.6 1.0
C1' B:U638 3.9 94.3 1.0
P B:G563 4.0 64.2 1.0
O3' B:A580 4.1 68.5 1.0
OP1 A:U8 4.1 132.7 1.0
C4' B:U638 4.1 87.3 1.0
O5' B:C581 4.2 47.2 1.0
C5' A:U8 4.3 127.8 1.0
O3' A:U7 4.5 128.3 1.0
P B:C562 4.6 74.8 1.0
O4' B:U638 4.6 89.9 1.0
P A:U8 4.8 144.5 1.0
O5' B:C562 4.8 77.4 1.0
O5' A:U8 4.9 133.2 1.0
C5' B:C562 4.9 75.1 1.0
N B:NH4710 5.0 68.7 1.0
N1 B:U638 5.0 91.9 1.0

Magnesium binding site 3 out of 10 in 8t2t

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Magnesium binding site 3 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:82.5
occ:1.00
 OP2 B:A120 2.1 95.4 1.0
P B:A120 3.1 105.8 1.0
O5' B:A120 3.4 88.6 1.0
OP1 B:A120 3.8 96.5 1.0
N7 B:A120 4.2 87.2 1.0
C8 B:A120 4.2 89.2 1.0
OP2 B:G121 4.2 81.4 1.0
N7 B:G121 4.5 75.8 1.0
O3' B:A119 4.5 95.4 1.0
C5' B:A120 4.7 86.2 1.0
OP1 B:A119 4.7 97.3 1.0
C3' B:A119 4.9 90.8 1.0
O5' B:A119 4.9 92.9 1.0

Magnesium binding site 4 out of 10 in 8t2t

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Magnesium binding site 4 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:81.7
occ:1.00
 OP2 B:A323 2.4 88.9 1.0
P B:A323 3.8 95.3 1.0
O6 B:G324 4.3 83.3 1.0
OP1 B:A323 4.4 92.7 1.0
O5' B:A323 4.5 81.3 1.0
N7 B:G324 4.6 84.1 1.0
C6 B:G324 4.7 75.9 1.0
C5 B:G324 4.9 75.1 1.0
O3' B:A322 4.9 77.8 1.0
N7 B:A323 4.9 88.1 1.0
C8 B:A323 5.0 88.1 1.0
C3' B:A322 5.0 80.0 1.0

Magnesium binding site 5 out of 10 in 8t2t

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Magnesium binding site 5 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:69.6
occ:1.00
 OP2 B:A157 2.2 91.9 1.0
N7 B:G158 2.7 89.1 1.0
P B:A157 3.3 93.3 1.0
O6 B:G158 3.5 92.5 1.0
C5 B:G158 3.5 87.6 1.0
O5' B:A157 3.7 86.0 1.0
C8 B:G158 3.7 92.4 1.0
OP1 B:A157 3.7 87.7 1.0
C6 B:G158 3.8 90.5 1.0
N7 B:G159 4.2 91.0 1.0
O6 B:G159 4.3 88.9 1.0
O4 B:U229 4.3 81.0 1.0
O3' B:A156 4.7 100.0 1.0
C4 B:G158 4.7 88.2 1.0
N9 B:G158 4.8 88.3 1.0
C5 B:G159 4.9 85.1 1.0
C6 B:G159 4.9 84.2 1.0

Magnesium binding site 6 out of 10 in 8t2t

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Magnesium binding site 6 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:32.7
occ:1.00
 OP1 B:G247 2.1 72.3 1.0
P B:G247 3.4 66.8 1.0
OP2 B:G248 3.7 68.6 1.0
OP2 B:G247 4.0 67.4 1.0
OP1 B:G123 4.0 66.9 1.0
OP2 B:G123 4.1 69.6 1.0
O5' B:G247 4.2 56.7 1.0
OP1 B:U246 4.4 72.6 1.0
OP1 B:C122 4.5 81.2 1.0
O3' B:U246 4.5 69.2 1.0
P B:G123 4.5 75.0 1.0
C5' B:G247 4.7 67.8 1.0

Magnesium binding site 7 out of 10 in 8t2t

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Magnesium binding site 7 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) 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 A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:44.9
occ:1.00
 OP2 B:G139 2.4 67.8 1.0
OP2 B:C138 3.7 70.0 1.0
P B:G139 3.7 64.6 1.0
OP1 B:C138 3.8 60.5 1.0
O5' B:C138 3.9 64.7 1.0
P B:C138 4.0 65.9 1.0
O5' B:G139 4.1 80.4 1.0
OP2 B:U233 4.1 82.4 1.0
N7 B:G139 4.2 67.6 1.0
C8 B:G139 4.2 63.5 1.0
N3 B:A141 4.2 82.1 1.0
C5' B:C138 4.5 58.2 1.0
C2 B:A141 4.6 84.1 1.0
C3' B:C138 4.6 54.3 1.0
O3' B:C138 4.7 51.6 1.0
OP2 B:G140 4.7 68.0 1.0
OP1 B:G139 4.8 65.4 1.0

Magnesium binding site 8 out of 10 in 8t2t

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Magnesium binding site 8 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg707

b:25.1
occ:1.00
 OP2 B:A560 2.2 73.4 1.0
OP2 B:A559 2.4 78.3 1.0
P B:A560 3.2 81.3 1.0
OP1 B:A560 3.5 82.7 1.0
P B:A559 3.6 63.5 1.0
O3' B:A559 3.8 78.5 1.0
O5' B:A559 4.2 71.5 1.0
OP1 B:A559 4.2 69.2 1.0
C3' B:A559 4.3 74.1 1.0
C5' B:A559 4.4 70.1 1.0
O5' B:A560 4.5 69.2 1.0
C8 B:A560 4.6 72.1 1.0
N7 B:A560 4.7 68.5 1.0
C3' B:C329 4.9 69.3 1.0
OP1 B:C330 4.9 87.9 1.0
C2' B:C329 4.9 69.9 1.0
O5' B:C329 4.9 74.8 1.0
O3' B:G558 4.9 86.3 1.0
C5' B:A560 4.9 73.0 1.0
C4' B:A559 4.9 73.9 1.0

Magnesium binding site 9 out of 10 in 8t2t

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Magnesium binding site 9 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg708

b:39.9
occ:1.00
 OP2 B:G578 2.0 66.9 1.0
O5' B:G578 2.5 60.0 1.0
P B:G578 2.8 83.5 1.0
OP2 B:C564 3.1 63.6 1.0
C3' B:C577 3.5 69.2 1.0
O3' B:C577 3.6 74.2 1.0
C5' B:G578 3.7 59.9 1.0
C5' B:C577 3.8 69.1 1.0
OP1 B:G578 4.1 71.3 1.0
OP2 B:C577 4.1 63.3 1.0
P B:C564 4.2 84.0 1.0
C4' B:C577 4.2 64.2 1.0
OP1 B:C564 4.5 77.1 1.0
O4' B:G578 4.6 60.1 1.0
C8 B:G578 4.6 52.1 1.0
O5' B:C564 4.6 67.7 1.0
C2' B:C577 4.7 66.7 1.0
O5' B:C577 4.7 67.2 1.0
C4' B:G578 4.8 59.7 1.0
P B:C577 4.8 72.2 1.0
C5' B:C564 4.9 59.7 1.0
C6 B:C577 4.9 63.1 1.0
O4' B:C577 5.0 74.2 1.0

Magnesium binding site 10 out of 10 in 8t2t

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Magnesium binding site 10 out of 10 in the Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A Group II Intron Ribonucleoprotein in the Post-Ligation (Post-2F) State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg709

b:73.7
occ:1.00
 OP2 B:G136 2.0 73.7 1.0
P B:G136 2.9 72.6 1.0
OP1 B:G136 3.0 81.6 1.0
O3' B:C135 3.7 60.4 1.0
O3' B:A137 3.9 51.5 1.0
OP1 B:C135 4.0 61.1 1.0
O5' B:C135 4.1 64.2 1.0
O5' B:G136 4.2 66.6 1.0
C5' B:C135 4.2 59.2 1.0
C3' B:C135 4.2 62.2 1.0
OP1 B:C138 4.3 60.5 1.0
P B:C135 4.6 69.8 1.0
C4' B:A137 4.6 47.2 1.0
P B:C138 4.6 65.9 1.0
C4' B:C135 4.8 57.5 1.0
C5' B:A137 4.8 43.0 1.0
C3' B:A137 4.9 52.7 1.0

Reference:

L.Xu, T.Liu, K.Chung, A.M.Pyle. Structural Insights Into Intron Catalysis and Dynamics During Splicing Nature 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06746-6
Page generated: Fri Oct 4 20:18:19 2024

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