Magnesium in PDB 6me0: Structure of A Group II Intron Retroelement Prior to Dna Integration

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

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the Structure of A Group II Intron Retroelement Prior to Dna Integration (pdb code 6me0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the Structure of A Group II Intron Retroelement Prior to Dna Integration, PDB code: 6me0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in the Structure of A Group II Intron Retroelement Prior to Dna Integration


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 Retroelement Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:70.4 occ:1.00 OP1 A:A815 2.0 62.8 1.0 O3' A:C866 2.1 91.2 1.0 O2' A:C866 2.1 91.2 1.0 OP2 A:G793 2.2 61.1 1.0 OP1 B:DG15 2.6 64.2 1.0 C2' A:C866 2.7 91.2 1.0 C3' A:C866 2.8 91.2 1.0 P A:A815 3.1 62.8 1.0 OP2 A:A815 3.3 62.8 1.0 O5' B:DG15 3.5 64.2 1.0 MG A:MG933 3.5 65.1 1.0 OP1 A:A792 3.6 66.3 1.0 P B:DG15 3.6 64.2 1.0 P A:G793 3.7 61.1 1.0 C4' A:C866 4.0 91.2 1.0 O5' A:A815 4.1 62.8 1.0 C1' A:C866 4.2 91.2 1.0 C5' A:A792 4.2 66.3 1.0 O3' A:A814 4.3 66.3 1.0 OP1 A:G793 4.4 61.1 1.0 O5' A:A792 4.4 66.3 1.0 O5' A:G793 4.5 61.1 1.0 C5' B:DG15 4.6 64.2 1.0 P A:A792 4.6 66.3 1.0 O3' A:A792 4.6 66.3 1.0 OP2 B:DG15 4.6 64.2 1.0 O3' B:DG14 4.7 58.4 1.0 O4' A:C866 4.7 91.2 1.0

Magnesium binding site 2 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:57.9 occ:1.00 OP2 A:A6 2.1 60.1 1.0 OP1 A:A401 2.1 61.7 1.0 OP2 A:C7 2.1 56.7 1.0 OP1 A:A6 2.2 60.1 1.0 P A:A6 2.5 60.1 1.0 O5' A:A401 3.1 61.7 1.0 P A:A401 3.2 61.7 1.0 O5' A:A6 3.6 60.1 1.0 P A:C7 3.6 56.7 1.0 O3' A:G5 3.8 67.2 1.0 C5' A:A6 4.2 60.1 1.0 OP2 A:A401 4.2 61.7 1.0 O3' A:A400 4.3 61.0 1.0 O3' A:A6 4.3 60.1 1.0 C3' A:A6 4.4 60.1 1.0 O5' A:C7 4.5 56.7 1.0 C5' A:A401 4.5 61.7 1.0 OP1 A:C7 4.6 56.7 1.0 O4' A:A401 4.7 61.7 1.0 C4' A:A6 4.9 60.1 1.0

Magnesium binding site 3 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:66.1 occ:1.00 OP2 A:A492 2.1 71.8 1.0 P A:A492 3.2 71.8 1.0 O5' A:A492 3.4 71.8 1.0 N7 A:G493 3.5 83.2 1.0 N7 A:A492 3.9 71.8 1.0 C8 A:A492 4.0 71.8 1.0 OP1 A:A492 4.1 71.8 1.0 C8 A:G493 4.3 83.2 1.0 OP2 A:G493 4.4 83.2 1.0 O3' A:A491 4.5 65.1 1.0 O6 A:G493 4.5 83.2 1.0 C5 A:G493 4.6 83.2 1.0 C5' A:A492 4.6 71.8 1.0 C3' A:A491 4.7 65.1 1.0 O5' A:A491 4.8 65.1 1.0 C5 A:A492 4.8 71.8 1.0 OP2 A:A491 5.0 65.1 1.0 N9 A:A492 5.0 71.8 1.0 C6 A:G493 5.0 83.2 1.0

Magnesium binding site 4 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:69.0 occ:1.00 O3' A:G10 2.1 67.5 1.0 O2' A:G10 2.2 67.5 1.0 OP2 A:A11 2.4 79.5 1.0 P A:A11 2.5 79.5 1.0 C3' A:G10 2.8 67.5 1.0 OP1 A:A11 2.9 79.5 1.0 C2' A:G10 3.0 67.5 1.0 C1' A:G10 4.0 67.5 1.0 O5' A:A11 4.0 79.5 1.0 C4' A:G10 4.2 67.5 1.0 N6 A:A13 4.6 78.1 1.0 N7 A:A12 4.7 79.3 1.0 O4' A:G10 4.7 67.5 1.0 N7 A:A13 4.9 78.1 1.0 C8 A:A12 4.9 79.3 1.0

Magnesium binding site 5 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:54.9 occ:1.00 OP1 A:G480 2.5 70.5 1.0 OP1 A:C818 2.6 59.7 1.0 C5' A:G479 3.4 79.0 1.0 C4' A:G479 3.6 79.0 1.0 P A:G480 3.9 70.5 1.0 P A:C818 4.0 59.7 1.0 C3' A:G479 4.3 79.0 1.0 O3' A:G479 4.4 79.0 1.0 OP2 A:C818 4.6 59.7 1.0 OP2 A:G480 4.8 70.5 1.0 O5' A:G479 4.8 79.0 1.0 O3' A:U817 4.9 59.0 1.0 O5' A:G480 4.9 70.5 1.0 O4' A:G479 4.9 79.0 1.0 C5' A:G480 4.9 70.5 1.0 O5' A:C818 5.0 59.7 1.0

Magnesium binding site 6 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg906 b:39.3 occ:1.00 OP2 A:C131 2.4 55.2 1.0 P A:C131 3.6 55.2 1.0 N3 A:A210 3.7 46.9 1.0 O5' A:C131 3.8 55.2 1.0 O3' A:A130 4.0 57.9 1.0 O2' A:A210 4.1 46.9 1.0 C5' A:C131 4.2 55.2 1.0 C2 A:A210 4.3 46.9 1.0 O3' A:A210 4.4 46.9 1.0 C1' A:A210 4.6 46.9 1.0 C4 A:A210 4.8 46.9 1.0 C2' A:A210 4.9 46.9 1.0 OP1 A:C131 4.9 55.2 1.0

Magnesium binding site 7 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg907 b:76.2 occ:1.00 OP2 A:A143 2.1 93.2 1.0 OP2 A:U183 2.1 79.8 1.0 P A:U183 3.5 79.8 1.0 P A:A143 3.6 93.2 1.0 O2' A:C182 3.8 76.2 1.0 O3' A:C182 4.1 76.2 1.0 O3' A:G142 4.2 73.2 1.0 O5' A:A143 4.3 93.2 1.0 C2' A:C182 4.3 76.2 1.0 C8 A:A143 4.3 93.2 1.0 OP1 A:U183 4.3 79.8 1.0 C5' A:A143 4.5 93.2 1.0 O5' A:U183 4.5 79.8 1.0 OP1 A:A143 4.6 93.2 1.0 C3' A:C182 4.8 76.2 1.0 OP2 A:U184 4.8 89.9 1.0 N7 A:A143 4.8 93.2 1.0

Magnesium binding site 8 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:59.7 occ:1.00 OP1 A:U258 2.2 52.0 1.0 O2' A:C259 3.5 52.1 1.0 P A:U258 3.5 52.0 1.0 O5' A:U258 4.2 52.0 1.0 OP2 A:U258 4.2 52.0 1.0 C5' A:U258 4.4 52.0 1.0 C2' A:C259 4.5 52.1 1.0 O3' A:G257 4.7 51.2 1.0 C4' A:G257 4.9 51.2 1.0 C3' A:G257 4.9 51.2 1.0

Magnesium binding site 9 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:51.9 occ:1.00 OP2 A:A400 2.0 61.0 1.0 P A:A400 3.4 61.0 1.0 O5' A:A400 3.8 61.0 1.0 N7 A:G10 4.2 67.5 1.0 C8 A:A400 4.3 61.0 1.0 O6 A:G10 4.3 67.5 1.0 C3' A:G399 4.4 66.9 1.0 O3' A:G399 4.4 66.9 1.0 OP1 A:A400 4.4 61.0 1.0 N7 A:A400 4.5 61.0 1.0 O5' A:G399 4.9 66.9 1.0 C5 A:G10 5.0 67.5 1.0

Magnesium binding site 10 out of 32 in the Structure of A Group II Intron Retroelement Prior to 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 Prior to Dna Integration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg910 b:0.8 occ:1.00 OP1 A:G479 3.1 79.0 1.0 OP2 A:U2 3.9 91.9 1.0 N7 A:G479 4.4 79.0 1.0 P A:G479 4.5 79.0 1.0 N1 A:A814 4.6 66.3 1.0 OP1 A:G478 5.0 71.6 1.0

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