Magnesium in PDB 1zzn: Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands.

The structure of Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands., PDB code: 1zzn was solved by M.R.Stahley, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.04 / 3.37
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.466, 108.466, 246.400, 90.00, 90.00, 90.00
R / Rfree (%)	26.9 / 30.7

The structure of Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. (pdb code 1zzn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands., PDB code: 1zzn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands.


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 I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1015 b:33.2 occ:1.00 O3' D:5MU1 2.1 43.3 1.0 OP1 B:G170 2.1 43.0 1.0 OP1 B:A172 2.2 43.3 1.0 OP2 C:A1 2.2 41.2 1.0 OP1 B:C88 2.2 39.9 1.0 C3' D:5MU1 3.2 43.9 1.0 P B:A172 3.3 61.9 1.0 P C:A1 3.4 49.0 1.0 P B:G170 3.4 45.9 1.0 P B:C88 3.5 49.4 1.0 C4' D:5MU1 3.6 43.1 1.0 OP2 B:A172 3.8 49.1 1.0 O5' B:A172 3.8 61.5 1.0 OP1 C:A1 3.9 30.1 1.0 O5' B:G170 3.9 41.2 1.0 OP2 B:C88 3.9 33.5 1.0 MG C:MG207 3.9 29.0 1.0 C5' D:5MU1 3.9 41.4 1.0 O2' D:5MU1 3.9 42.1 0.0 O5' C:A1 4.0 48.5 1.0 C2' D:5MU1 4.1 38.3 1.0 OP2 B:G170 4.2 46.3 1.0 O3' B:A87 4.3 45.1 1.0 OP1 B:U173 4.4 51.3 1.0 O3' B:G169 4.5 29.9 1.0 C5' B:G170 4.6 47.5 1.0 O5' B:C88 4.6 44.0 1.0 O3' B:C171 4.7 61.1 1.0 O3' C:G206 4.7 48.1 1.0 O4' D:5MU1 4.9 51.3 1.0 O2' C:G206 5.0 43.4 1.0 O5' D:5MU1 5.0 40.8 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands.


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 I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:27.6 occ:1.00 OP2 B:A174 1.9 55.8 1.0 OP2 B:U173 2.1 56.3 1.0 P B:A174 3.2 62.3 1.0 P B:U173 3.4 52.7 1.0 O3' B:A172 3.6 52.3 1.0 OP1 B:A174 3.6 66.7 1.0 N7 C:G206 3.8 46.1 1.0 O2' B:A172 4.0 71.1 1.0 O3' B:U173 4.1 62.8 1.0 N7 B:A174 4.2 69.0 1.0 O5' B:A174 4.2 62.8 1.0 C3' B:U173 4.3 61.9 1.0 O5' B:U173 4.4 55.9 1.0 C8 C:G206 4.4 49.7 1.0 OP1 B:U173 4.5 51.3 1.0 C8 B:A174 4.6 68.7 1.0 C5 C:G206 4.7 47.1 1.0 C3' B:A172 4.7 58.7 1.0 N7 B:G175 4.9 79.1 1.0 O6 C:G206 4.9 55.4 1.0 C2' B:A172 5.0 63.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands.


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 I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1016 b:45.1 occ:1.00 OP2 B:C171 2.2 58.7 1.0 OP2 B:A127 2.4 68.1 1.0 OP1 B:U124 2.9 69.8 1.0 O2' B:U126 3.0 63.0 1.0 O5' B:C171 3.0 50.2 1.0 P B:C171 3.1 56.3 1.0 P B:A127 3.3 69.5 1.0 OP1 B:A127 3.4 69.0 1.0 OP2 B:G125 3.4 83.4 1.0 O3' B:G170 3.9 52.5 1.0 P B:U124 3.9 70.9 1.0 C2' B:U126 4.1 62.8 1.0 O5' B:U124 4.2 68.2 1.0 C5' B:C171 4.3 54.8 1.0 C5' B:U124 4.3 65.9 1.0 OP2 B:U124 4.4 71.9 1.0 O3' B:U126 4.4 60.6 1.0 C4' B:C171 4.4 62.4 1.0 OP1 B:C171 4.5 50.7 1.0 O5' B:A127 4.5 65.1 1.0 C3' B:U126 4.6 59.0 1.0 O4' B:C171 4.7 64.7 1.0 O2' B:G170 4.8 58.0 1.0 P B:G125 4.8 84.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands.


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 I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1017 b:55.2 occ:1.00 O B:HOH1065 2.2 18.5 1.0 OP1 B:U15 2.5 75.9 1.0 P B:U15 3.9 66.4 1.0 OP1 B:C29 4.4 51.0 1.0 O2' B:U165 4.4 84.7 1.0 OP2 B:U15 4.5 65.5 1.0 OP2 B:C29 4.7 58.7 1.0 OP2 B:U16 4.7 85.7 1.0 O5' B:U15 4.7 56.0 1.0 O3' B:C14 4.9 61.0 1.0 C5' B:U15 4.9 67.1 1.0 P B:C29 5.0 63.6 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of A Group I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands.


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 I Intron/Two Exon Complex That Includes All Catalytic Metal Ion Ligands. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg207 b:29.0 occ:1.00 OP2 C:A1 2.0 41.2 1.0 OP1 B:G128 2.0 43.7 1.0 O3' C:G206 2.1 48.1 1.0 O2' C:G206 2.2 43.4 1.0 OP2 B:A172 2.2 49.1 1.0 P C:A1 2.3 49.0 1.0 C2' C:G206 3.0 54.7 1.0 C3' C:G206 3.1 54.7 1.0 O5' C:A1 3.1 48.5 1.0 P B:G128 3.1 58.5 1.0 O3' B:A127 3.2 59.6 1.0 P B:A172 3.3 61.9 1.0 O5' B:A172 3.7 61.5 1.0 OP1 C:A1 3.8 30.1 1.0 MG B:MG1015 3.9 33.2 1.0 OP1 B:A172 3.9 43.3 1.0 O5' B:G128 4.0 63.4 1.0 OP1 B:A87 4.1 30.7 1.0 OP2 B:C88 4.1 33.5 1.0 C4' C:G206 4.1 58.1 1.0 C5' C:A1 4.3 45.3 1.0 C1' C:G206 4.3 53.1 1.0 OP2 B:G128 4.4 52.0 1.0 OP1 B:C88 4.5 39.9 1.0 C5' B:G128 4.5 70.9 1.0 C5' B:A87 4.5 37.5 1.0 C3' B:A127 4.5 66.2 1.0 P B:C88 4.6 49.4 1.0 O3' B:C171 4.7 61.1 1.0 O3' B:A87 4.7 45.1 1.0 O3' D:5MU1 4.8 43.3 1.0 O4' C:G206 4.9 52.2 1.0 O2' B:C171 5.0 59.7 1.0 OP1 B:U173 5.0 51.3 1.0

M.R.Stahley, S.A.Strobel. Structural Evidence For A Two-Metal-Ion Mechanism of Group I Intron Splicing. Science V. 309 1587 2005.
ISSN: ISSN 0036-8075
PubMed: 16141079
DOI: 10.1126/SCIENCE.1114994