Magnesium in PDB 6mec: Structure of A Group II Intron Retroelement After Dna Integration

Other elements in 6mec:

The structure of Structure of A Group II Intron Retroelement After Dna Integration also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 51;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Group II Intron Retroelement After Dna Integration (pdb code 6mec). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 51 binding sites of Magnesium where determined in the Structure of A Group II Intron Retroelement After Dna Integration, PDB code: 6mec:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 51 in 6mec

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Magnesium binding site 1 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:32.0
occ:1.00
OP2 A:A792 2.1 43.2 1.0
OP2 A:A815 2.2 29.9 1.0
P A:A792 3.4 43.2 1.0
N6 A:A481 3.6 49.2 1.0
P A:A815 3.6 29.9 1.0
O5' A:A792 4.0 43.2 1.0
O6 A:G480 4.0 37.7 1.0
OP1 A:A792 4.1 43.2 1.0
N7 A:G480 4.1 37.7 1.0
OP2 A:G793 4.1 38.9 1.0
O4' A:A815 4.4 29.9 1.0
O5' A:A815 4.4 29.9 1.0
OP1 A:A815 4.4 29.9 1.0
C5' A:A815 4.4 29.9 1.0
C6 A:A481 4.4 49.2 1.0
O3' A:A814 4.4 31.4 1.0
N1 A:A481 4.5 49.2 1.0
O3' A:G791 4.6 53.0 1.0
C8 A:A815 4.7 29.9 1.0
C6 A:G480 4.8 37.7 1.0
C5 A:G480 4.9 37.7 1.0
C3' A:G791 4.9 53.0 1.0

Magnesium binding site 2 out of 51 in 6mec

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Magnesium binding site 2 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:21.3
occ:1.00
OP2 A:G5 2.1 33.6 1.0
OP2 A:A6 2.1 34.3 1.0
P A:G5 3.0 33.6 1.0
OP1 A:G5 3.2 33.6 1.0
P A:A6 3.5 34.3 1.0
O5' A:G5 3.9 33.6 1.0
O5' A:A6 3.9 34.3 1.0
OP1 A:A6 4.1 34.3 1.0
O3' A:C4 4.4 36.3 1.0
C5' A:G5 4.6 33.6 1.0
O3' A:G5 4.7 33.6 1.0
N4 A:C7 4.7 39.8 1.0
C3' A:G5 4.8 33.6 1.0
C4' A:A401 5.0 43.2 1.0

Magnesium binding site 3 out of 51 in 6mec

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Magnesium binding site 3 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:26.3
occ:1.00
OP1 A:C813 2.0 21.8 1.0
O3' A:A812 2.0 26.1 1.0
P A:C813 2.3 21.8 1.0
O3' B:DG14 2.4 22.6 1.0
C5' A:C813 2.6 21.8 1.0
C4' B:DG14 2.6 22.6 1.0
O5' A:C813 2.7 21.8 1.0
C3' B:DG14 2.7 22.6 1.0
C2' B:DG14 2.8 22.6 1.0
C3' A:A812 3.4 26.1 1.0
O4' B:DG14 3.5 22.6 1.0
C1' B:DG14 3.6 22.6 1.0
C5' B:DG14 3.7 22.6 1.0
OP2 A:C813 3.8 21.8 1.0
O2' A:A812 3.8 26.1 1.0
C4' A:C813 4.0 21.8 1.0
C4' A:A812 4.1 26.1 1.0
C2' A:A812 4.1 26.1 1.0
O4' A:C813 4.7 21.8 1.0
C5' A:A812 4.8 26.1 1.0
O5' B:DG14 4.8 22.6 1.0
OP2 A:A814 4.9 31.4 1.0
N9 B:DG14 4.9 22.6 1.0
OP1 A:A814 4.9 31.4 1.0

Magnesium binding site 4 out of 51 in 6mec

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Magnesium binding site 4 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg904

b:29.6
occ:1.00
OP1 A:U817 2.0 34.7 1.0
OP1 A:A815 2.1 29.9 1.0
P A:A815 3.5 29.9 1.0
P A:U817 3.5 34.7 1.0
C8 A:G479 3.9 39.9 1.0
OP2 A:G480 4.0 37.7 1.0
OP2 A:A815 4.1 29.9 1.0
O5' A:U817 4.2 34.7 1.0
O3' A:G816 4.3 28.2 1.0
N7 A:G479 4.3 39.9 1.0
O5' A:A815 4.3 29.9 1.0
OP2 A:U817 4.5 34.7 1.0
O3' A:A814 4.5 31.4 1.0
C2' A:A814 4.5 31.4 1.0
C3' A:G479 4.5 39.9 1.0
O2' A:A814 4.6 31.4 1.0
N7 A:A815 4.6 29.9 1.0
C8 A:A815 4.7 29.9 1.0
N9 A:G479 4.7 39.9 1.0
C5' A:U817 4.7 34.7 1.0
C2' A:G479 4.8 39.9 1.0
C3' A:A814 4.9 31.4 1.0

Magnesium binding site 5 out of 51 in 6mec

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Magnesium binding site 5 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg905

b:50.2
occ:1.00
OP2 A:A157 2.1 49.2 1.0
N7 A:G158 2.2 57.0 1.0
C8 A:G158 3.2 57.0 1.0
C5 A:G158 3.2 57.0 1.0
P A:A157 3.3 49.2 1.0
O6 A:G158 3.4 57.0 1.0
C6 A:G158 3.7 57.0 1.0
OP1 A:A157 3.7 49.2 1.0
O3' A:A156 4.2 55.8 1.0
C3' A:A156 4.3 55.8 1.0
N9 A:G158 4.4 57.0 1.0
N1 A:A180 4.4 60.3 1.0
C4 A:G158 4.4 57.0 1.0
O5' A:A157 4.5 49.2 1.0
C5' A:A157 4.8 49.2 1.0
O5' A:A156 4.9 55.8 1.0
N6 A:A180 4.9 60.3 1.0

Magnesium binding site 6 out of 51 in 6mec

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Magnesium binding site 6 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg906

b:43.3
occ:1.00
OP2 A:U30 2.1 69.6 1.0
P A:U30 3.2 69.6 1.0
O5' A:U30 3.3 69.6 1.0
C6 A:U30 3.9 69.6 1.0
C3' A:G29 4.0 60.2 1.0
C5 A:U30 4.0 69.6 1.0
O3' A:G29 4.1 60.2 1.0
OP1 A:G29 4.2 60.2 1.0
OP1 A:U30 4.5 69.6 1.0
C5' A:U30 4.7 69.6 1.0
O5' A:G29 4.8 60.2 1.0
C2' A:G29 4.8 60.2 1.0
OP2 A:C31 5.0 82.8 1.0

Magnesium binding site 7 out of 51 in 6mec

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Magnesium binding site 7 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg907

b:45.8
occ:1.00
OP1 A:G486 2.7 66.9 1.0
C5' A:G486 2.8 66.9 1.0
O5' A:G486 3.1 66.9 1.0
O3' A:G486 3.4 66.9 1.0
P A:G486 3.5 66.9 1.0
OP2 A:G487 3.5 61.4 1.0
C4' A:G486 3.7 66.9 1.0
P A:G487 3.7 61.4 1.0
C3' A:G486 3.8 66.9 1.0
OP1 A:G487 3.9 61.4 1.0
OP2 A:G486 4.4 66.9 1.0
O3' A:A485 4.7 74.0 1.0
O4' A:G486 5.0 66.9 1.0

Magnesium binding site 8 out of 51 in 6mec

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Magnesium binding site 8 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg908

b:43.4
occ:1.00
OP1 A:U215 2.1 64.3 1.0
O4 A:U28 2.5 56.4 1.0
C4 A:U28 3.2 56.4 1.0
C5 A:U28 3.3 56.4 1.0
P A:U215 3.6 64.3 1.0
O2' A:U27 4.2 57.0 1.0
O5' A:U215 4.3 64.3 1.0
OP2 A:U215 4.4 64.3 1.0
C3' A:U214 4.4 41.5 1.0
O3' A:U214 4.5 41.5 1.0
N3 A:U28 4.5 56.4 1.0
C6 A:U28 4.6 56.4 1.0
C2' A:U214 4.6 41.5 1.0
C5' A:U215 4.7 64.3 1.0

Magnesium binding site 9 out of 51 in 6mec

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Magnesium binding site 9 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg909

b:41.5
occ:1.00
OP1 A:U292 2.2 46.9 1.0
C5' A:U292 3.0 46.9 1.0
P A:U292 3.3 46.9 1.0
O5' A:U292 3.4 46.9 1.0
C4' A:U292 4.2 46.9 1.0
O3' A:C291 4.3 59.4 1.0
OP2 A:U292 4.5 46.9 1.0
O3' A:U292 4.5 46.9 1.0
OP2 A:G293 4.6 46.0 1.0
O6 A:G303 4.7 66.5 1.0
C3' A:U292 4.8 46.9 1.0
P A:G293 4.9 46.0 1.0
OP1 A:G293 4.9 46.0 1.0

Magnesium binding site 10 out of 51 in 6mec

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Magnesium binding site 10 out of 51 in the Structure of A Group II Intron Retroelement After Dna Integration


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 Retroelement After Dna Integration within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg910

b:61.3
occ:1.00
OP2 A:A340 2.1 54.9 1.0
P A:A340 3.5 54.9 1.0
O5' A:A340 4.0 54.9 1.0
O5' A:U339 4.2 48.4 1.0
OP2 A:U339 4.4 48.4 1.0
C3' A:U339 4.4 48.4 1.0
O3' A:U339 4.4 48.4 1.0
OP1 A:A340 4.5 54.9 1.0
C8 A:A340 4.6 54.9 1.0
N7 A:A340 4.6 54.9 1.0
P A:U339 4.7 48.4 1.0
OP1 A:U339 4.8 48.4 1.0
C5' A:U339 4.9 48.4 1.0

Reference:

D.B.Haack, X.Yan, C.Zhang, J.Hingey, D.Lyumkis, T.S.Baker, N.Toor. Cryo-Em Structures of A Group II Intron Reverse Splicing Into Dna. Cell V. 178 612 2019.
ISSN: ISSN 1097-4172
PubMed: 31348888
DOI: 10.1016/J.CELL.2019.06.035
Page generated: Mon Dec 14 23:36:58 2020

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