Magnesium in PDB 1u6b: Crystal Structure of A Self-Splicing Group I Intron with Both Exons

The structure of Crystal Structure of A Self-Splicing Group I Intron with Both Exons, PDB code: 1u6b was solved by P.L.Adams, M.R.Stahley, A.B.Kosek, J.Wang, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.22 / 3.10
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	108.541, 108.541, 249.158, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 27.9

The structure of Crystal Structure of A Self-Splicing Group I Intron with Both Exons also contains other interesting chemical elements:

Potassium

(K)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons (pdb code 1u6b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons, PDB code: 1u6b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1018 b:16.1 occ:1.00 OP1 B:A172 2.1 36.0 1.0 OP1 B:C88 2.3 31.1 1.0 OP2 C:A1 2.3 30.3 1.0 O3' D:5MU1 2.4 21.1 1.0 OP1 B:G170 2.5 31.6 1.0 OP2 B:A172 2.8 41.9 1.0 P B:A172 2.8 40.0 1.0 P B:C88 3.2 33.4 1.0 OP2 B:C88 3.3 32.7 1.0 O C:HOH101 3.6 33.0 1.0 P B:G170 3.7 32.5 1.0 P C:A1 3.8 30.0 1.0 O3' B:C171 3.8 40.8 1.0 C3' D:5MU1 3.8 20.0 1.0 O2' D:5MU1 4.0 2.0 0.0 C3' B:C171 4.1 42.1 1.0 O3' B:A87 4.1 28.0 1.0 O2' C:G206 4.2 2.0 0.0 O5' B:G170 4.2 33.6 1.0 O5' B:A172 4.2 42.3 1.0 O5' C:A1 4.3 27.2 1.0 OP2 B:G170 4.4 35.2 1.0 C4' D:5MU1 4.4 20.1 1.0 OP1 B:U173 4.4 35.5 1.0 O5' B:C88 4.5 33.9 1.0 O3' C:G206 4.6 36.1 1.0 C2' D:5MU1 4.6 18.9 1.0 O2' B:C171 4.6 44.4 1.0 OP1 C:A1 4.8 23.4 1.0 C2' B:C171 4.8 43.1 1.0 C5' B:G170 4.8 37.4 1.0 C5' B:A172 4.9 42.6 1.0 C2' C:G206 4.9 41.9 1.0

Magnesium binding site 2 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:12.0 occ:1.00 OP2 B:A174 2.1 40.1 1.0 OP2 B:U173 2.3 39.1 1.0 P B:A174 3.4 42.3 1.0 P B:U173 3.5 35.4 1.0 O3' B:A172 3.6 37.0 1.0 N7 C:G206 3.7 37.4 1.0 OP1 B:A174 3.9 41.5 1.0 C8 C:G206 4.1 38.1 1.0 O3' B:U173 4.3 42.2 1.0 O5' B:U173 4.4 36.0 1.0 C3' B:U173 4.4 40.4 1.0 O5' B:A174 4.5 45.4 1.0 N7 B:A174 4.6 50.4 1.0 OP1 B:U173 4.6 35.5 1.0 O2' B:A172 4.6 48.8 1.0 C5 C:G206 4.7 37.6 1.0 C8 B:A174 4.8 50.4 1.0 C3' B:A172 4.9 41.2 1.0

Magnesium binding site 3 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1019 b:27.3 occ:1.00 OP1 B:U126 1.8 38.0 1.0 P B:U126 2.9 40.9 1.0 O3' B:G125 3.5 42.8 1.0 OP2 B:U126 3.6 37.5 1.0 N7 B:G53 4.0 82.3 1.0 O2' B:G125 4.0 46.9 1.0 C2' B:G125 4.2 45.9 1.0 O5' B:U126 4.3 37.8 1.0 C3' B:G125 4.3 44.9 1.0 O6 B:G53 4.4 83.3 1.0 O6 B:G54 4.5 92.0 1.0 N7 B:G54 4.5 91.5 1.0 C5 B:G53 4.7 81.8 1.0 C8 B:G53 4.9 82.7 1.0 C6 B:G53 4.9 82.2 1.0

Magnesium binding site 4 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1020 b:38.7 occ:1.00 O B:HOH1071 2.0 41.9 1.0 OP2 B:U80 4.6 50.6 1.0 OP2 B:A81 4.7 38.7 1.0 O4 B:U62 4.9 59.4 1.0 OP1 B:U80 5.0 50.9 1.0

Magnesium binding site 5 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1021 b:27.5 occ:1.00 N4 B:C66 4.3 45.0 1.0 O6 B:G77 4.3 43.7 1.0 O6 B:G67 4.6 25.3 1.0 N4 B:C68 4.8 21.5 1.0

Magnesium binding site 6 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1022 b:64.2 occ:1.00 O2' B:A81 4.0 38.9 1.0 O6 B:G84 4.1 45.6 1.0 N7 B:G84 4.3 42.6 1.0 C2' B:A81 4.4 34.7 1.0 O B:HOH1068 4.6 18.1 1.0 OP2 B:A58 4.7 47.8 1.0 OP2 B:U82 4.8 38.4 1.0 OP2 B:G83 5.0 40.4 1.0 C3' B:A81 5.0 32.9 1.0 C6 B:G84 5.0 45.2 1.0

Magnesium binding site 7 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1023 b:54.0 occ:1.00 OP1 B:U124 2.1 41.0 1.0 OP2 B:C171 2.3 40.1 1.0 P B:U124 3.5 40.0 1.0 P B:C171 3.7 38.2 1.0 K B:K1015 3.9 92.2 1.0 C5' B:U124 4.0 43.6 1.0 O3' B:G170 4.1 39.5 1.0 O3' B:G123 4.1 41.2 1.0 O5' B:U124 4.2 41.3 1.0 OP1 B:C171 4.6 39.4 1.0 OP2 B:U124 4.6 40.1 1.0 O5' B:C171 4.6 37.8 1.0 O2' B:G170 4.8 44.9 1.0 OP2 B:G125 4.8 50.6 1.0 OP2 B:A127 4.9 52.1 1.0

Magnesium binding site 8 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1024 b:30.9 occ:1.00 OP2 B:G38 1.8 59.8 1.0 OP2 B:A39 2.4 71.6 1.0 O2' B:G37 2.9 57.6 1.0 P B:G38 3.1 59.4 1.0 O5' B:G38 3.4 62.4 1.0 C5' D:C3 3.8 35.4 1.0 O4' D:C3 3.8 25.9 1.0 P B:A39 3.9 72.0 1.0 OP1 B:G38 4.0 60.9 1.0 C4' D:C3 4.1 29.5 1.0 C2' B:G37 4.2 52.0 1.0 O3' B:G37 4.3 53.6 1.0 O5' D:C3 4.4 41.5 1.0 C3' B:G38 4.5 72.1 1.0 O3' B:G38 4.6 72.0 1.0 O5' B:A39 4.7 70.3 1.0 N7 B:A39 4.7 71.5 1.0 OP1 B:A39 4.7 71.6 1.0 C3' B:G37 4.7 52.9 1.0 C5' B:G38 4.8 68.2 1.0 C1' D:C3 5.0 22.9 1.0

Magnesium binding site 9 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1025 b:74.0 occ:1.00 OP2 B:A48 2.6 64.5 1.0 OP2 B:U133 2.7 86.0 1.0 O B:HOH1054 3.0 50.3 1.0 OP1 B:U133 3.5 86.8 1.0 P B:U133 3.6 83.6 1.0 P B:A48 3.8 63.8 1.0 O5' B:A48 4.1 62.4 1.0 O4 B:U50 4.3 97.1 1.0 O5' B:U133 4.5 78.7 1.0 O2' B:A47 4.5 62.9 1.0 OP1 B:A48 4.5 64.3 1.0 OP2 B:A134 4.5 62.5 1.0 O3' B:C132 4.8 84.7 1.0 O3' B:A47 5.0 61.2 1.0

Magnesium binding site 10 out of 13 in the Crystal Structure of A Self-Splicing Group I Intron with Both Exons


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 Self-Splicing Group I Intron with Both Exons within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1026 b:56.7 occ:1.00 OP2 B:C74 2.3 0.3 1.0 OP1 B:C73 3.6 79.5 1.0 P B:C74 3.8 0.5 1.0 N7 B:G75 4.3 75.9 1.0 O6 B:G75 4.3 69.9 1.0 P B:C73 4.4 79.8 1.0 OP1 B:C74 4.5 0.6 1.0 O5' B:C74 4.5 0.2 1.0 O5' B:C73 4.5 84.8 1.0 OP2 B:C73 4.5 79.2 1.0 O3' B:C73 4.8 0.1 1.0

P.L.Adams, M.R.Stahley, A.B.Kosek, J.Wang, S.A.Strobel. Crystal Structure of A Self-Splicing Group I Intron with Both Exons. Nature V. 430 45 2004.
ISSN: ISSN 0028-0836
PubMed: 15175762
DOI: 10.1038/NATURE02642