Magnesium in PDB 4p95: Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme)

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme), PDB code: 4p95 was solved by M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, B.Masquida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.82 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.630, 85.710, 108.530, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.6

The structure of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) (pdb code 4p95). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme), PDB code: 4p95:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:12.1 occ:1.00 O A:HOH797 1.8 3.8 1.0 O A:HOH793 1.8 5.5 1.0 O A:HOH794 1.8 5.0 1.0 O A:HOH795 1.8 1.7 1.0 O A:HOH796 1.9 0.0 1.0 OP1 A:G325 2.1 4.8 1.0 P A:G325 3.5 5.0 1.0 O6 A:G290 4.1 5.2 1.0 O3' A:C324 4.1 5.8 1.0 C8 A:G325 4.2 6.6 1.0 O6 A:G289 4.2 3.5 1.0 OP2 A:G325 4.2 23.9 1.0 O2' A:C324 4.2 0.0 1.0 N7 A:G289 4.2 5.5 1.0 N7 A:G325 4.3 7.2 1.0 C2' A:C324 4.4 4.6 1.0 O5' A:G325 4.6 7.6 1.0 C3' A:C324 4.8 6.0 1.0 C6 A:G289 4.8 7.3 1.0 C5 A:G289 4.9 7.6 1.0 N7 A:G290 5.0 6.1 1.0

Magnesium binding site 2 out of 3 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:8.2 occ:1.00 O A:HOH799 1.8 2.2 1.0 O A:HOH802 1.8 1.9 1.0 O A:HOH801 1.8 1.4 1.0 O A:HOH803 1.8 1.7 1.0 O A:HOH800 1.9 1.1 1.0 O A:HOH798 1.9 1.9 1.0 O A:HOH728 3.7 8.9 1.0 O4 A:U315 4.1 4.3 1.0 O6 A:G323 4.1 1.5 1.0 N3 A:C324 4.2 3.4 1.0 O A:HOH786 4.2 4.2 1.0 O6 A:G325 4.3 4.1 1.0 O2 A:C324 4.3 4.5 1.0 N7 A:G314 4.4 4.8 1.0 N4 A:C313 4.5 4.1 1.0 O6 A:G314 4.6 8.6 1.0 O A:HOH732 4.7 5.1 1.0 C2 A:C324 4.7 5.0 1.0 C5 A:C313 4.7 9.0 1.0 C4 A:C313 4.8 5.9 1.0 O A:HOH745 4.8 4.8 1.0

Magnesium binding site 3 out of 3 in the Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Speciation of A Group I Intron Into A Lariat Capping Ribozyme (Circularly Permutated Ribozyme) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:0.9 occ:1.00 O A:HOH710 1.8 37.5 1.0 O A:HOH720 1.8 40.9 1.0 O A:HOH805 1.8 43.1 1.0 O A:HOH804 1.8 31.1 1.0 O A:HOH719 1.8 29.2 1.0 O4' A:G548 4.0 8.2 1.0 O2 A:U547 4.1 20.1 1.0 O A:HOH708 4.2 4.5 1.0 C1' A:G548 4.3 20.5 1.0 O2' A:U547 4.7 10.1 1.0 O2' A:C272 4.8 12.2 1.0 C4' A:G548 5.0 9.9 1.0

M.Meyer, H.Nielsen, V.Olieric, P.Roblin, S.D.Johansen, E.Westhof, B.Masquida. Speciation of A Group I Intron Into A Lariat Capping Ribozyme. Proc.Natl.Acad.Sci.Usa V. 111 7659 2014.
ISSN: ESSN 1091-6490
PubMed: 24821772
DOI: 10.1073/PNAS.1322248111