Magnesium in PDB 3bo3: A Relaxed Active Site Following Exon Ligation By A Group I Intron

The structure of A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo3 was solved by S.V.Lipchock, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.73 / 3.40
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.608, 109.608, 242.138, 90.00, 90.00, 90.00
R / Rfree (%)	28.2 / 32.5

The structure of A Relaxed Active Site Following Exon Ligation By A Group I Intron also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the A Relaxed Active Site Following Exon Ligation By A Group I Intron (pdb code 3bo3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo3:
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 A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:0.9 occ:1.00 OP1 B:A172 2.0 0.1 1.0 OP2 D:A4 2.1 0.8 0.7 OP1 B:C88 2.2 0.4 1.0 O3' D:U3 2.4 0.8 0.7 OP1 B:G170 2.4 0.4 1.0 P B:A172 3.0 0.4 1.0 OP2 B:A172 3.4 1.0 1.0 C3' D:U3 3.4 0.9 0.7 O3' B:C171 3.4 0.4 1.0 P D:A4 3.5 0.6 0.7 P B:C88 3.7 0.9 1.0 P B:G170 3.7 0.3 1.0 MG B:MG2 3.8 0.9 1.0 C4' D:U3 4.0 0.2 0.7 OP1 D:A4 4.0 0.4 0.7 OP1 B:U173 4.0 0.6 1.0 O5' B:G170 4.1 0.5 1.0 O3' B:A87 4.2 0.7 1.0 O5' D:A4 4.3 0.5 0.7 O5' B:A172 4.4 1.0 1.0 O2' C:G206 4.4 0.9 1.0 O2' D:U3 4.5 0.8 0.3 O3' B:G169 4.5 0.1 1.0 C4' D:U3 4.5 0.6 0.3 O3' D:U3 4.5 0.2 0.3 O5' B:C88 4.6 0.2 1.0 O3' C:G206 4.6 0.4 1.0 C5' D:U3 4.7 0.5 0.7 C2' D:U3 4.7 0.3 0.7 OP2 B:C88 4.7 0.8 1.0 O2' D:U3 4.7 0.6 0.7 C3' B:C171 4.8 0.8 1.0 OP2 B:G170 4.8 0.5 1.0

Magnesium binding site 2 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:0.9 occ:1.00 OP1 B:G128 1.8 0.7 1.0 OP2 B:A172 2.0 1.0 1.0 O2' C:G206 2.2 0.9 1.0 OP2 D:A4 2.5 0.8 0.7 O3' C:G206 2.5 0.4 1.0 P D:A4 3.1 0.6 0.7 P B:G128 3.2 0.3 1.0 C2' C:G206 3.3 0.2 1.0 P B:A172 3.3 0.4 1.0 C3' C:G206 3.4 0.4 1.0 O3' B:A127 3.5 0.2 1.0 O2' B:C171 3.5 0.1 1.0 OP1 B:C88 3.7 0.4 1.0 OP1 B:A172 3.8 0.1 1.0 MG B:MG1 3.8 0.9 1.0 O5' D:A4 3.9 0.5 0.7 OP1 B:A87 3.9 0.1 1.0 O5' B:G128 4.2 0.5 1.0 C1' C:G206 4.2 0.0 1.0 C4' C:G206 4.2 0.4 1.0 OP2 B:C88 4.2 0.8 1.0 OP2 B:G128 4.2 0.2 1.0 O3' B:C171 4.2 0.4 1.0 OP1 D:A4 4.3 0.4 0.7 O5' B:A172 4.4 1.0 1.0 P B:C88 4.4 0.9 1.0 C5' B:A172 4.5 0.5 1.0 C5' B:A87 4.6 0.6 1.0 OP1 B:U173 4.7 0.6 1.0 C3' B:A127 4.8 0.1 1.0 C2' B:C171 4.8 0.9 1.0 O4' C:G206 4.8 0.6 1.0 O3' B:A87 4.9 0.7 1.0 C5' B:G128 5.0 0.5 1.0

Magnesium binding site 3 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:0.4 occ:1.00 OP2 B:A174 2.0 0.2 1.0 OP2 B:U173 2.2 0.0 1.0 P B:A174 3.3 0.8 1.0 P B:U173 3.5 0.9 1.0 N7 C:G206 3.6 0.8 1.0 OP1 B:A174 3.7 0.0 1.0 O3' B:A172 3.8 0.0 1.0 O2' B:A172 4.0 0.1 1.0 N7 B:A174 4.0 0.6 1.0 C8 C:G206 4.2 0.2 1.0 O3' B:U173 4.3 0.9 1.0 C3' B:U173 4.3 0.1 1.0 O5' B:A174 4.3 0.2 1.0 C8 B:A174 4.4 0.6 1.0 O5' B:U173 4.5 0.8 1.0 C5 C:G206 4.5 0.8 1.0 OP1 B:U173 4.6 0.6 1.0 N7 B:G175 4.6 0.6 1.0 C3' B:A172 4.8 0.2 1.0 O6 C:G206 4.8 0.5 1.0 C2' B:A172 5.0 0.1 1.0 C6 C:G206 5.0 1.0 1.0

Magnesium binding site 4 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1016 b:0.3 occ:1.00 OP1 B:U126 2.3 0.4 1.0 O6 B:G53 3.3 1.0 1.0 P B:U126 3.5 0.5 1.0 C6 B:G53 4.0 0.1 1.0 O2' B:G125 4.1 0.3 1.0 O3' B:G125 4.1 0.7 1.0 OP2 B:U126 4.1 0.7 1.0 N7 B:G53 4.2 0.1 1.0 C5 B:G53 4.4 0.1 1.0 C2' B:G125 4.4 0.4 1.0 N7 B:G54 4.6 0.1 1.0 O5' B:U126 4.8 0.6 1.0 O6 B:G54 4.8 0.4 1.0 C3' B:G125 4.8 0.1 1.0

Magnesium binding site 5 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1017 b:0.8 occ:1.00 OP2 B:U80 4.3 0.4 1.0 OP1 B:U80 4.7 0.4 1.0 P B:U80 4.9 0.3 1.0

Magnesium binding site 6 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1018 b:0.3 occ:1.00 O6 B:G67 3.3 0.1 1.0 O B:HOH1042 3.3 0.8 1.0 N4 B:C66 3.5 0.5 1.0 C4 B:C66 4.1 0.5 1.0 C6 B:G67 4.4 0.8 1.0 C5 B:C66 4.4 0.6 1.0 N4 B:C68 4.4 0.5 1.0 N7 B:G67 4.6 0.6 1.0 O6 B:G77 4.7 0.7 1.0 C5 B:G67 4.9 0.6 1.0 N3 B:C66 5.0 0.7 1.0

Magnesium binding site 7 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1019 b:95.2 occ:1.00 O B:HOH1034 2.9 64.6 1.0 OP2 B:A58 4.0 0.6 1.0 O2' B:A81 4.1 0.3 1.0 O6 B:G84 4.3 0.9 1.0 N7 B:G84 4.5 0.8 1.0 C2' B:A81 4.9 0.9 1.0

Magnesium binding site 8 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1020 b:0.7 occ:1.00 OP1 B:U124 2.0 0.1 1.0 OP2 B:C171 2.6 0.2 1.0 O3' B:G170 3.3 0.0 1.0 P B:U124 3.4 0.2 1.0 P B:C171 3.6 1.0 1.0 OP2 B:A127 3.7 0.9 1.0 O2' B:G170 3.8 0.2 1.0 O5' B:U124 4.1 0.9 1.0 C5' B:U124 4.2 0.9 1.0 OP2 B:U124 4.2 0.1 1.0 OP2 B:G125 4.3 0.8 1.0 O3' B:G123 4.5 0.7 1.0 C3' B:G170 4.5 0.8 1.0 OP1 B:C171 4.5 0.6 1.0 O2' B:U126 4.6 0.2 1.0 C2' B:G170 4.7 0.3 1.0 O5' B:C171 4.8 0.2 1.0

Magnesium binding site 9 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1021 b:0.0 occ:1.00 OP2 B:A39 2.0 0.3 1.0 OP2 B:G38 2.3 0.8 1.0 O5' D:C1 2.4 0.3 1.0 O2' B:G37 3.3 0.4 1.0 P B:G38 3.3 0.9 1.0 P B:A39 3.4 0.7 1.0 OP1 B:G38 3.6 0.9 1.0 C5' D:C1 3.7 0.1 1.0 O4' D:C1 4.0 0.9 1.0 C4' D:C1 4.1 0.3 1.0 N7 B:A39 4.2 0.9 1.0 OP1 B:A39 4.2 0.7 1.0 O5' B:A39 4.3 0.1 1.0 O3' B:G37 4.3 0.3 1.0 O3' B:G38 4.4 0.1 1.0 C3' B:G38 4.5 0.4 1.0 C2' B:G37 4.5 0.3 1.0 O5' B:G38 4.5 0.9 1.0 C8 B:A39 4.6 0.7 1.0 C1' B:G37 4.7 0.5 1.0 C3' B:G37 4.9 0.9 1.0

Magnesium binding site 10 out of 13 in the A Relaxed Active Site Following Exon Ligation By A Group I Intron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of A Relaxed Active Site Following Exon Ligation By A Group I Intron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1022 b:0.4 occ:1.00 O4 B:U50 2.9 0.2 1.0 OP2 B:A49 3.6 0.8 1.0 C4 B:U50 4.0 0.2 1.0 OP2 B:A48 4.3 0.3 1.0 O5' B:A48 4.5 0.5 1.0 C5 B:U50 4.7 0.1 1.0 P B:A49 4.8 0.0 1.0 OP1 B:U133 4.8 0.1 1.0 P B:A48 5.0 0.1 1.0

S.V.Lipchock, S.A.Strobel. A Relaxed Active Site After Exon Ligation By the Group I Intron Proc.Natl.Acad.Sci.Usa V. 105 5699 2008.
ISSN: ISSN 0027-8424
PubMed: 18408159
DOI: 10.1073/PNAS.0712016105