Magnesium in PDB 6chr: Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State)

The structure of Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State), PDB code: 6chr 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)	50.08 / 3.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	165.015, 256.893, 137.232, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.3

The structure of Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State) also contains other interesting chemical elements:

Sodium

(Na)

9 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 - 82;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State) (pdb code 6chr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 82 binding sites of Magnesium where determined in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S State), PDB code: 6chr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:0.5 occ:1.00 OP1 A:A574 1.9 0.3 1.0 OP2 A:G552 2.3 0.8 1.0 OP1 A:A551 2.4 0.9 1.0 P A:A551 2.4 0.1 1.0 OP2 A:A551 2.5 0.1 1.0 O5' A:A551 2.5 0.2 1.0 P A:G552 3.3 0.8 1.0 P A:A574 3.3 0.2 1.0 C5' A:A551 3.4 0.1 1.0 O5' A:G552 3.5 0.3 1.0 O3' A:A551 3.6 0.1 1.0 MG A:MG702 3.7 0.6 1.0 C3' A:A551 3.7 0.4 1.0 NA A:NA743 3.8 0.5 1.0 O5' A:A574 3.8 1.0 1.0 O3' A:G550 4.1 0.0 1.0 OP2 A:A574 4.1 0.9 1.0 C4' A:A551 4.1 0.1 1.0 O3' A:A573 4.4 0.7 1.0 O3' B:A16 4.6 0.5 1.0 OP1 A:G552 4.7 0.2 1.0 C5' A:G552 4.7 0.5 1.0 C3' A:G550 4.9 0.7 1.0

Magnesium binding site 2 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:0.6 occ:1.00 OP2 A:G552 2.2 0.8 1.0 OP2 A:A574 2.4 0.9 1.0 O3' B:A16 2.5 0.5 1.0 OP1 A:C572 2.8 0.5 1.0 P A:A574 2.9 0.2 1.0 O5' A:A574 3.1 1.0 1.0 OP1 A:A574 3.2 0.3 1.0 O2' B:A16 3.2 0.1 1.0 P A:G552 3.3 0.8 1.0 C3' B:A16 3.4 0.6 1.0 OP1 A:G552 3.6 0.2 1.0 C4' B:A16 3.6 0.1 1.0 MG A:MG701 3.7 0.5 1.0 C5' A:A574 3.9 0.8 1.0 C2' B:A16 3.9 0.8 1.0 P A:C572 3.9 1.0 1.0 O5' A:G552 4.2 0.3 1.0 OP2 A:C572 4.3 0.0 1.0 O3' A:A573 4.5 0.7 1.0 C5' B:A16 4.5 0.8 1.0 O3' A:A551 4.6 0.1 1.0 O3' A:G571 4.6 0.9 1.0 O4' B:A16 4.7 0.0 1.0 C5' A:G552 4.8 0.5 1.0 C1' B:A16 4.9 0.8 1.0 C4' A:A574 5.0 0.9 1.0

Magnesium binding site 3 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:0.6 occ:1.00 C1' A:G1 2.3 0.1 1.0 OP1 A:C4 2.8 0.1 1.0 O5' A:C4 2.9 0.3 1.0 OP2 A:C4 2.9 0.8 1.0 P A:C4 2.9 0.0 1.0 C2' A:G1 3.0 0.9 1.0 OP2 A:G5 3.4 0.1 1.0 O4' A:G1 3.6 0.3 1.0 O2' A:G1 3.7 0.1 1.0 O2' A:U2 3.9 0.4 1.0 C5' A:C4 3.9 0.6 1.0 C2' A:U2 4.0 0.7 1.0 C3' A:G1 4.2 0.8 1.0 C6 A:U2 4.4 0.8 1.0 O3' A:G3 4.5 0.5 1.0 C4' A:G1 4.6 0.8 1.0 OP1 A:A419 4.6 0.8 1.0 C3' A:U2 4.8 0.9 1.0 C3' A:C4 4.8 0.8 1.0 P A:G5 4.9 0.5 1.0 C4' A:C4 4.9 0.7 1.0

Magnesium binding site 4 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:0.4 occ:1.00 OP2 A:C7 2.0 0.5 1.0 OP1 A:A341 2.0 0.9 1.0 OP1 A:A6 2.4 0.2 1.0 P A:C7 3.1 0.6 1.0 P A:A341 3.2 0.9 1.0 O5' A:A341 3.3 0.5 1.0 OP1 A:C7 3.4 0.6 1.0 P A:A6 3.8 0.7 1.0 O3' A:A6 4.2 0.4 1.0 OP2 A:A341 4.2 0.0 1.0 O5' A:C7 4.2 0.1 1.0 O3' A:A340 4.3 0.3 1.0 OP2 A:A6 4.5 0.0 1.0 O5' A:A6 4.5 0.4 1.0 C3' A:A6 4.6 0.3 1.0 C5' A:A6 4.6 0.9 1.0 O2' A:C576 4.7 0.6 1.0 C5' A:A341 4.7 0.4 1.0 O3' A:G5 4.8 0.6 1.0

Magnesium binding site 5 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg705 b:0.6 occ:1.00 O6 A:G434 2.5 0.2 1.0 OP2 A:A433 2.7 0.4 1.0 C6 A:G434 3.5 0.8 1.0 N7 A:G434 3.5 0.3 1.0 C5 A:G434 3.9 0.7 1.0 P A:A433 4.0 0.7 1.0 N7 A:A433 4.3 0.3 1.0 OP2 A:A432 4.4 0.6 1.0 O5' A:A433 4.5 0.5 1.0 O5' A:A432 4.6 0.6 1.0 C8 A:A433 4.6 0.1 1.0 N1 A:A492 4.7 0.5 1.0 C2 A:A492 4.8 0.5 1.0 N1 A:G434 4.8 0.0 1.0 C8 A:G434 4.8 0.5 1.0 OP1 A:A433 4.8 0.7 1.0

Magnesium binding site 6 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg706 b:0.6 occ:1.00 OP2 A:G430 2.5 0.1 1.0 P A:G430 3.7 0.5 1.0 N7 A:G431 3.9 0.1 1.0 O5' A:G430 4.0 0.5 1.0 N7 A:G430 4.1 0.1 1.0 O6 A:G431 4.1 0.7 1.0 OP2 A:A429 4.2 1.0 1.0 C8 A:G430 4.3 0.6 1.0 O5' A:A429 4.3 0.2 1.0 OP1 A:G430 4.5 0.9 1.0 P A:A429 4.6 1.0 1.0 OP1 A:A429 4.7 0.7 1.0 C5 A:G431 4.7 0.8 1.0 C6 A:G431 4.8 0.2 1.0 O A:HOH929 4.8 0.4 1.0 O3' A:A429 4.9 0.6 1.0 C8 A:G431 4.9 0.9 1.0 OP2 A:G431 5.0 0.9 1.0

Magnesium binding site 7 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg707 b:0.9 occ:1.00 C5 A:U520 3.2 0.5 1.0 C6 A:U520 3.3 0.5 1.0 C4 A:U520 3.4 0.1 1.0 N1 A:U520 3.8 0.5 1.0 N3 A:U520 3.8 0.7 1.0 O4 A:U520 4.0 0.5 1.0 C2 A:U520 4.0 0.5 1.0 O2' A:U520 4.6 0.1 1.0 C1' A:U520 4.7 0.4 1.0 O2 A:U520 4.9 0.4 1.0

Magnesium binding site 8 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg708 b:0.9 occ:1.00 OP1 A:C435 2.6 0.8 1.0 OP2 A:A436 2.6 0.7 1.0 P A:C435 3.4 0.9 1.0 O5' A:C435 3.6 0.3 1.0 OP2 A:C435 3.7 0.2 1.0 P A:A436 4.1 0.4 1.0 C5' A:C435 4.2 0.2 1.0 O3' A:C435 4.7 0.8 1.0 C3' A:C435 4.8 0.5 1.0 O5' A:A436 4.8 0.1 1.0 O3' A:G434 4.9 0.1 1.0 C5 A:U470 4.9 1.0 1.0

Magnesium binding site 9 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg709 b:0.2 occ:1.00 O2' A:A433 2.6 0.7 1.0 O2' A:A8 2.6 0.2 1.0 O4' A:A433 2.7 0.1 1.0 C1' A:A433 2.8 0.7 1.0 C1' A:A8 3.2 1.0 1.0 C2' A:A433 3.2 0.1 1.0 C4' A:A433 3.3 0.2 1.0 C2' A:A8 3.3 0.7 1.0 N3 A:A8 3.5 0.0 1.0 C3' A:A433 3.9 0.2 1.0 N9 A:A8 4.1 0.7 1.0 O4' A:A8 4.1 0.9 1.0 O4' A:A9 4.2 0.2 1.0 N9 A:A433 4.2 0.3 1.0 C4 A:A8 4.2 0.6 1.0 N3 A:A432 4.4 0.6 1.0 C2 A:A432 4.4 0.3 1.0 C1' A:A9 4.5 0.9 1.0 C5' A:A433 4.5 0.6 1.0 O3' A:A433 4.6 0.4 1.0 C2 A:A8 4.6 0.7 1.0 C3' A:A8 4.7 0.7 1.0 C4' A:A8 4.9 0.2 1.0

Magnesium binding site 10 out of 82 in the Crystal Structure of A Group II Intron Lariat with An Intact 3' Splice Site (Pre-2S 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 with An Intact 3' Splice Site (Pre-2S State) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg710 b:1.0 occ:1.00 O6 A:G99 2.7 0.9 1.0 O4 A:U100 2.8 0.7 1.0 N7 A:G99 3.5 0.9 1.0 C6 A:G99 3.6 0.5 1.0 C4 A:U100 3.7 0.5 1.0 C5 A:G99 3.9 0.8 1.0 O6 A:G98 4.0 0.7 1.0 N3 A:U100 4.3 0.5 1.0 C6 A:G98 4.4 0.8 1.0 O4 A:U78 4.5 0.2 1.0 C5 A:U100 4.7 0.1 1.0 C8 A:G99 4.8 0.1 1.0 C5 A:G98 4.8 0.4 1.0 N1 A:G99 4.8 0.7 1.0 N7 A:G98 5.0 0.3 1.0

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