Magnesium in PDB 6cih: Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State

The structure of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State, PDB code: 6cih was solved by R.T.Chan, J.K.Peters, A.R.Robart, T.Wiryaman, K.R.Rajashankar, N.Toor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.82 / 3.68
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	163.639, 255.361, 136.786, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.5

The structure of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State also contains other interesting chemical elements:

Sodium	(Na)	9 atoms
Iridium	(Ir)	41 atoms

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 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 86;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State (pdb code 6cih). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 86 binding sites of Magnesium where determined in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State, PDB code: 6cih:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg741 b:0.1 occ:1.00 OP1 A:A574 1.7 0.3 1.0 OP2 A:G552 2.5 0.4 1.0 OP2 B:C14 2.9 0.8 1.0 O5' A:A551 3.0 0.3 1.0 OP2 A:A551 3.0 0.2 1.0 P A:A574 3.1 0.9 1.0 O2' A:G550 3.1 0.2 1.0 P A:G552 3.1 0.9 1.0 O3' A:A551 3.1 0.7 1.0 O5' A:G552 3.2 0.8 1.0 O5' A:A574 3.4 0.2 1.0 C3' A:A551 3.5 0.8 1.0 MG A:MG742 3.6 0.9 1.0 P A:A551 3.6 0.0 1.0 NA A:NA822 3.8 93.5 1.0 O3' A:A573 4.0 0.9 1.0 P B:C14 4.1 0.4 1.0 OP2 A:A574 4.1 0.9 1.0 C2' A:G550 4.1 1.0 1.0 C5' A:A551 4.2 0.7 1.0 C5' A:G552 4.3 0.9 1.0 OP1 B:C14 4.3 0.9 1.0 C4' A:A551 4.4 0.4 1.0 C3' A:G550 4.4 0.4 1.0 O3' A:G550 4.5 0.5 1.0 OP1 A:G552 4.6 0.6 1.0 C2' A:A551 4.7 0.6 1.0 C8 A:A551 4.8 0.6 1.0 C5' A:A574 4.8 0.6 1.0 OP1 A:A551 4.9 0.1 1.0

Magnesium binding site 2 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg742 b:0.9 occ:1.00 OP2 A:A574 1.9 0.9 1.0 OP2 B:C14 2.5 0.8 1.0 O3' B:A13 2.5 0.2 1.0 OP2 A:G552 2.5 0.4 1.0 P A:A574 2.6 0.9 1.0 OP1 A:A574 2.7 0.3 1.0 OP1 A:C572 2.8 0.0 1.0 P B:C14 3.0 0.4 1.0 O5' A:A574 3.3 0.2 1.0 MG A:MG741 3.6 0.1 1.0 OP1 B:C14 3.7 0.9 1.0 C3' B:A13 3.8 0.8 1.0 P A:G552 4.0 0.9 1.0 O3' A:A573 4.0 0.9 1.0 P A:C572 4.0 86.9 1.0 O2' B:A13 4.1 0.3 1.0 C5' A:A574 4.2 0.6 1.0 C4' B:A13 4.2 0.4 1.0 O5' B:C14 4.4 0.1 1.0 OP2 A:C572 4.4 90.8 1.0 C2' B:A13 4.6 0.8 1.0 C3' A:A573 4.6 0.7 1.0 O5' A:G552 4.6 0.8 1.0 C5' B:A13 4.8 1.0 1.0 OP1 A:G552 4.8 0.6 1.0 O3' A:G571 4.8 0.9 1.0 O3' A:A551 5.0 0.7 1.0

Magnesium binding site 3 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg743 b:1.0 occ:1.00 OP1 A:U2 1.9 0.1 1.0 C5' A:C4 2.3 0.1 1.0 O5' A:C4 2.3 0.1 1.0 C3' A:C4 2.5 0.7 1.0 OP2 A:G5 2.7 0.7 1.0 O3' A:C4 2.7 0.9 1.0 C4' A:C4 2.8 0.5 1.0 P A:U2 3.0 0.1 1.0 C5' A:U2 3.1 0.7 1.0 O5' A:U2 3.1 0.1 1.0 OP1 A:C4 3.1 0.6 1.0 P A:C4 3.2 0.4 1.0 P A:G5 3.3 0.6 1.0 OP2 A:C4 3.8 0.5 1.0 OP2 A:U2 3.9 0.3 1.0 O4' A:C4 3.9 0.6 1.0 C2' A:C4 4.0 0.4 1.0 O3' A:G1 4.2 0.1 1.0 O5' A:G5 4.2 0.3 1.0 C1' A:C4 4.5 0.5 1.0 C4' A:U2 4.5 0.8 1.0 OP1 A:G5 4.6 97.1 1.0 O3' A:G3 4.6 0.5 1.0 C6 A:C4 4.7 0.7 1.0 C8 A:G5 4.7 0.7 1.0 N7 A:G5 4.7 0.9 1.0 O2' A:C4 4.9 0.8 1.0 N1 A:C4 4.9 0.8 1.0

Magnesium binding site 4 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg744 b:0.7 occ:1.00 OP2 A:C7 2.0 0.9 1.0 OP1 A:A6 2.1 0.2 1.0 OP1 A:A341 2.2 0.3 1.0 O5' A:A341 3.2 0.6 1.0 P A:C7 3.2 0.3 1.0 P A:A341 3.3 0.3 1.0 P A:A6 3.5 0.9 1.0 OP1 A:C7 3.7 95.8 1.0 C5' A:A6 4.0 1.0 1.0 O3' A:A6 4.1 0.3 1.0 O5' A:A6 4.2 0.4 1.0 O3' A:G5 4.3 73.8 1.0 O3' A:A340 4.3 0.6 1.0 C3' A:A6 4.4 0.2 1.0 OP2 A:A341 4.4 95.1 1.0 O5' A:C7 4.4 91.3 1.0 C5' A:A341 4.5 0.9 1.0 O4' A:A341 4.5 85.4 1.0 OP2 A:A6 4.5 77.9 1.0 O2' A:C576 4.6 0.3 1.0 C4' A:A341 4.8 0.5 1.0 C4' A:A6 4.8 0.2 1.0

Magnesium binding site 5 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg745 b:0.6 occ:0.50 O2' A:A359 4.0 0.6 1.0

Magnesium binding site 6 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg748 b:73.3 occ:1.00 C5 A:C554 4.2 0.9 1.0 O4 A:U556 4.6 0.9 1.0 N7 A:G555 4.6 1.0 1.0 C6 A:C554 4.8 0.4 1.0 C4 A:C554 5.0 0.6 1.0

Magnesium binding site 7 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg749 b:0.6 occ:1.00 N4 A:C527 2.4 0.6 1.0 O6 A:G524 2.7 0.8 1.0 C6 A:G524 3.5 0.1 1.0 C4 A:C527 3.5 0.0 1.0 N7 A:G524 3.8 1.0 1.0 C5 A:G524 3.9 0.2 1.0 C5 A:C527 4.2 0.3 1.0 N3 A:C527 4.3 0.1 1.0 N1 A:G524 4.5 0.1 1.0 C8 A:G524 5.0 0.1 1.0

Magnesium binding site 8 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg752 b:0.5 occ:1.00 O A:HOH1037 3.8 0.8 1.0 N7 A:A410 4.1 0.8 1.0 OP2 A:A410 4.1 0.9 1.0 C8 A:A410 4.4 0.5 1.0 O6 A:G411 4.5 0.6 1.0 N7 A:G411 4.6 0.2 1.0 O5' A:A410 5.0 0.0 1.0 C5 A:A410 5.0 1.0 1.0

Magnesium binding site 9 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg756 b:0.7 occ:1.00 O3' A:U14 2.1 0.4 1.0 C4' A:U14 2.3 1.0 1.0 O2' A:U14 2.4 0.9 1.0 C3' A:U14 2.4 0.9 1.0 C2' A:U14 2.9 0.2 1.0 C5' A:U14 3.2 0.0 1.0 O4' A:U14 3.4 0.9 1.0 P A:U15 3.6 0.5 1.0 C1' A:U14 3.6 0.6 1.0 OP1 A:U15 4.0 0.3 1.0 OP2 A:U15 4.5 0.9 1.0 O5' A:U14 4.5 1.0 1.0 O5' A:U15 4.5 94.3 1.0 OP1 A:U108 4.5 0.8 1.0 C5' A:U15 4.7 91.7 1.0 OP1 A:C109 4.8 0.6 1.0

Magnesium binding site 10 out of 86 in the Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of A Group II Intron Lariat in the Post-Catalytic State within 5.0Å range:

R.T.Chan, J.K.Peters, A.R.Robart, T.Wiryaman, K.R.Rajashankar, N.Toor. Structural Basis For the Second Step of Group II Intron Splicing. Nat Commun V. 9 4676 2018.
ISSN: ESSN 2041-1723
PubMed: 30410046
DOI: 10.1038/S41467-018-06678-0