Magnesium in PDB 7uim: Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)

Enzymatic activity of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)

All present enzymatic activity of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex):
2.7.7.49;

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) (pdb code 7uim). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex), PDB code: 7uim:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 7uim

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Magnesium binding site 1 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:21.9
occ:1.00
 OP1 B:C581 1.9 17.4 1.0
O3' B:U638 1.9 26.3 1.0
O2' B:U638 2.0 26.3 1.0
C3' B:U638 2.7 26.3 1.0
C2' B:U638 2.8 26.3 1.0
P B:C581 2.9 17.4 1.0
OP1 B:G563 3.0 14.9 1.0
OP2 B:C581 3.0 17.4 1.0
OP1 B:C562 3.4 16.5 1.0
OP2 B:G563 3.4 14.9 1.0
P B:G563 3.7 14.9 1.0
C1' B:U638 3.7 26.3 1.0
O5' B:C581 3.8 17.4 1.0
C4' B:U638 4.1 26.3 1.0
O3' B:A580 4.1 21.2 1.0
O5' B:C562 4.1 16.5 1.0
P B:C562 4.4 16.5 1.0
O4' B:U638 4.5 26.3 1.0
O5' B:G563 4.8 14.9 1.0
O3' B:C562 4.8 16.5 1.0
N1 B:U638 4.9 26.3 1.0

Magnesium binding site 2 out of 13 in 7uim

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Magnesium binding site 2 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:22.0
occ:1.00
 OP2 B:C564 3.3 13.5 1.0
P B:C564 3.7 13.5 1.0
O5' B:G563 3.8 14.9 1.0
OP1 B:C564 3.8 13.5 1.0
O3' B:C581 3.8 17.4 1.0
O3' B:G563 3.8 14.9 1.0
C5' B:G578 3.9 26.8 1.0
OP2 B:U579 3.9 24.1 1.0
C4' B:C581 4.0 17.4 1.0
C5' B:G563 4.1 14.9 1.0
O2' B:C581 4.4 17.4 1.0
C5' B:C581 4.4 17.4 1.0
C3' B:C581 4.4 17.4 1.0
O5' B:G578 4.4 26.8 1.0
OP1 B:G578 4.5 26.8 1.0
C3' B:G563 4.7 14.9 1.0
O5' B:C581 4.8 17.4 1.0
OP2 B:G578 4.8 26.8 1.0
P B:G578 4.8 26.8 1.0
OP1 B:G563 4.8 14.9 1.0
C4' B:G563 4.8 14.9 1.0
P B:G563 4.9 14.9 1.0

Magnesium binding site 3 out of 13 in 7uim

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Magnesium binding site 3 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:48.1
occ:1.00
 OP1 B:C564 2.9 13.5 1.0
OP2 B:G578 3.4 26.8 1.0
OP2 B:C577 3.8 30.0 1.0
P B:C564 4.0 13.5 1.0
OP2 B:C565 4.3 12.7 1.0
O5' B:C564 4.4 13.5 1.0
OP2 B:C564 4.4 13.5 1.0
C5' B:C564 4.5 13.5 1.0
P B:C577 4.6 30.0 1.0
P B:G578 4.7 26.8 1.0
O5' B:G578 4.7 26.8 1.0
OP1 B:C565 4.7 12.7 1.0
OP1 B:C577 4.8 30.0 1.0
P B:C565 4.8 12.7 1.0
O5' B:C577 4.8 30.0 1.0
O3' B:C564 4.9 13.5 1.0
MG B:MG704 4.9 31.6 1.0

Magnesium binding site 4 out of 13 in 7uim

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Magnesium binding site 4 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:31.6
occ:1.00
 OP2 B:C577 2.3 30.0 1.0
P B:C577 3.2 30.0 1.0
O3' B:C576 3.4 30.7 1.0
C5' B:C576 3.6 30.7 1.0
OP1 B:C577 3.7 30.0 1.0
OP1 B:C576 3.9 30.7 1.0
C3' B:C576 4.0 30.7 1.0
O5' B:C576 4.0 30.7 1.0
C4' B:C576 4.2 30.7 1.0
MG B:MG712 4.3 14.6 1.0
OP1 B:C135 4.4 15.1 1.0
P B:C576 4.5 30.7 1.0
OP1 B:C565 4.5 12.7 1.0
O5' B:C577 4.6 30.0 1.0
C5' B:C135 4.7 15.1 1.0
MG B:MG713 4.9 48.1 1.0
MG B:MG703 4.9 48.1 1.0

Magnesium binding site 5 out of 13 in 7uim

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Magnesium binding site 5 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:48.1
occ:1.00
 OP2 B:A560 2.0 22.2 1.0
OP2 B:A559 2.3 25.4 1.0
P B:A560 3.4 22.2 1.0
P B:A559 3.7 25.4 1.0
OP1 B:C330 4.1 29.0 1.0
O5' B:A559 4.1 25.4 1.0
O5' B:A560 4.2 22.2 1.0
OP1 B:A560 4.2 22.2 1.0
MG B:MG710 4.2 26.9 1.0
O2' B:C329 4.4 20.6 1.0
O3' B:A559 4.4 25.4 1.0
C2' B:C329 4.5 20.6 1.0
N7 B:A560 4.5 22.2 1.0
C5' B:A559 4.5 25.4 1.0
OP1 B:A559 4.5 25.4 1.0
C8 B:A560 4.7 22.2 1.0
C3' B:A559 4.7 25.4 1.0
C3' B:C329 4.7 20.6 1.0
O3' B:G558 4.8 38.2 1.0
O5' B:C329 4.8 20.6 1.0

Magnesium binding site 6 out of 13 in 7uim

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Magnesium binding site 6 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:48.1
occ:1.00
 OP2 B:G139 2.7 12.5 1.0
OP2 B:C138 3.6 11.3 1.0
N7 B:G139 3.8 12.5 1.0
C8 B:G139 3.9 12.5 1.0
OP1 B:C138 4.0 11.3 1.0
P B:G139 4.0 12.5 1.0
P B:C138 4.2 11.3 1.0
C5' B:C138 4.2 11.3 1.0
N3 B:A141 4.2 15.2 1.0
O5' B:G139 4.3 12.5 1.0
OP2 B:U233 4.6 22.5 1.0
OP2 B:G140 4.6 16.0 1.0
C3' B:C138 4.6 11.3 1.0
O5' B:C138 4.7 11.3 1.0
C2 B:A141 4.8 15.2 1.0
O3' B:C138 4.9 11.3 1.0
C1' B:A141 4.9 15.2 1.0

Magnesium binding site 7 out of 13 in 7uim

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Magnesium binding site 7 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg707

b:48.1
occ:1.00
 OP1 B:G123 2.8 27.4 1.0
OP1 B:G247 2.9 21.4 1.0
OP1 B:U246 3.5 22.1 1.0
OP2 B:G247 3.7 21.4 1.0
P B:G247 3.7 21.4 1.0
P B:G123 3.9 27.4 1.0
OP2 B:G123 4.2 27.4 1.0
O5' B:G247 4.8 21.4 1.0
P B:U246 4.8 22.1 1.0
OP2 B:G248 4.8 23.3 1.0
O5' B:G123 4.9 27.4 1.0
O2' B:A245 4.9 28.5 1.0
O3' B:U246 4.9 22.1 1.0
O3' B:C122 5.0 28.7 1.0

Magnesium binding site 8 out of 13 in 7uim

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Magnesium binding site 8 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg708

b:37.8
occ:1.00
 OP2 B:G158 2.0 34.2 1.0
N7 B:G158 2.4 34.2 1.0
C8 B:G158 2.4 34.2 1.0
P B:G158 3.2 34.2 1.0
C5' B:A157 3.3 29.4 1.0
O5' B:A157 3.4 29.4 1.0
C3' B:A157 3.4 29.4 1.0
O3' B:A157 3.6 29.4 1.0
C5 B:G158 3.8 34.2 1.0
N9 B:G158 3.8 34.2 1.0
O5' B:G158 3.9 34.2 1.0
C4' B:A157 3.9 29.4 1.0
C5' B:G158 4.3 34.2 1.0
O4' B:G158 4.4 34.2 1.0
C4 B:G158 4.4 34.2 1.0
OP1 B:G158 4.5 34.2 1.0
P B:A157 4.6 29.4 1.0
C1' B:G158 4.7 34.2 1.0
C2' B:A157 4.7 29.4 1.0
O4' B:A157 4.7 29.4 1.0
C4' B:G158 4.8 34.2 1.0
C6 B:G158 4.8 34.2 1.0
OP1 B:A157 4.8 29.4 1.0
C3' B:G158 4.8 34.2 1.0
O6 B:G158 5.0 34.2 1.0
OP2 B:A157 5.0 29.4 1.0

Magnesium binding site 9 out of 13 in 7uim

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Magnesium binding site 9 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg709

b:24.4
occ:1.00
 OP2 B:A323 2.0 27.5 1.0
P B:A323 3.4 27.5 1.0
O5' B:A323 3.9 27.5 1.0
OP1 B:A323 4.2 27.5 1.0
N7 B:A323 4.4 27.5 1.0
O3' B:A322 4.5 29.1 1.0
C8 B:A323 4.5 27.5 1.0
N7 B:G324 4.5 22.1 1.0
O6 B:G324 4.5 22.1 1.0
C3' B:A322 4.6 29.1 1.0
O5' B:A322 4.6 29.1 1.0
OP2 B:A322 4.8 29.1 1.0
C6 B:G324 5.0 22.1 1.0

Magnesium binding site 10 out of 13 in 7uim

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Magnesium binding site 10 out of 13 in the Cryoem Structure of An Group II Intron Retroelement (Apo-Complex)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryoem Structure of An Group II Intron Retroelement (Apo-Complex) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg710

b:26.9
occ:1.00
 OP2 B:G331 2.8 29.6 1.0
O5' B:C329 3.5 20.6 1.0
C3' B:C330 3.7 29.0 1.0
C5' B:C329 3.8 20.6 1.0
C6 B:C330 3.9 29.0 1.0
C3' B:C329 3.9 20.6 1.0
P B:G331 3.9 29.6 1.0
C8 B:G331 4.0 29.6 1.0
O5' B:C330 4.0 29.0 1.0
N7 B:G331 4.2 29.6 1.0
MG B:MG705 4.2 48.1 1.0
C5 B:C330 4.2 29.0 1.0
O3' B:C330 4.3 29.0 1.0
C4' B:C329 4.3 20.6 1.0
OP1 B:C329 4.4 20.6 1.0
OP1 B:G331 4.4 29.6 1.0
C2' B:C330 4.4 29.0 1.0
OP1 B:C330 4.5 29.0 1.0
N1 B:C330 4.5 29.0 1.0
C5' B:C330 4.6 29.0 1.0
C4' B:C330 4.6 29.0 1.0
O3' B:C329 4.6 20.6 1.0
P B:C329 4.7 20.6 1.0
P B:C330 4.7 29.0 1.0
C1' B:C330 4.8 29.0 1.0
OP2 B:A559 4.9 25.4 1.0
C2' B:C329 4.9 20.6 1.0
O4' B:C330 5.0 29.0 1.0

Reference:

K.Chung, L.Xu, P.Chai, J.Peng, S.C.Devarkar, A.M.Pyle. Structures of A Mobile Intron Retroelement Poised to Attack Its Structured Dna Target Science V. 378 627 2022.
ISSN: ESSN 1095-9203
PubMed: 36356138
DOI: 10.1126/SCIENCE.ABQ2844
Page generated: Thu Apr 6 23:47:28 2023

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