Magnesium in PDB 3bo4: 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: 3bo4 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)	36.71 / 3.33
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	111.188, 111.188, 240.300, 90.00, 90.00, 90.00
R / Rfree (%)	28 / 29.6

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

Potassium

(K)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the A Relaxed Active Site Following Exon Ligation By A Group I Intron (pdb code 3bo4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 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:96.0 occ:1.00 OP1 B:A172 2.4 0.8 1.0 OP1 B:C88 2.4 0.7 1.0 OP1 B:G170 2.4 0.3 1.0 P B:A172 3.6 0.4 1.0 P B:G170 3.6 0.1 1.0 O3' B:G169 3.7 0.8 1.0 O5' B:A172 3.7 0.3 1.0 P B:C88 3.7 0.3 1.0 OP2 B:C88 4.3 0.3 1.0 C4' D:DT3 4.4 0.5 1.0 O3' B:A87 4.5 0.6 1.0 OP2 B:A172 4.5 0.9 1.0 OP1 B:U173 4.6 0.7 1.0 OP2 B:G170 4.7 1.0 1.0 O5' B:G170 4.7 0.3 1.0 O3' D:DT3 4.7 0.8 1.0 O3' B:C171 4.7 0.5 1.0 C5' B:G170 4.7 1.0 1.0 C3' B:C171 4.8 0.4 1.0 O4' D:DT3 4.8 0.9 1.0 O5' B:C88 4.8 0.9 1.0 O2' B:G169 4.9 0.0 1.0

Magnesium binding site 2 out of 12 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:0.1 occ:1.00 OP1 B:G128 1.9 0.3 1.0 O3' C:DG206 2.3 0.8 1.0 OP1 B:A87 2.7 0.4 1.0 P B:G128 3.0 0.3 1.0 O5' B:G128 3.2 0.8 1.0 OP2 B:A172 3.3 0.9 1.0 C3' C:DG206 3.6 0.9 1.0 O B:HOH1050 3.8 53.7 1.0 C5' B:A87 3.9 0.0 1.0 OP1 B:A172 3.9 0.8 1.0 P B:A172 4.0 0.4 1.0 P B:A87 4.0 0.5 1.0 O3' B:A127 4.1 0.6 1.0 OP2 B:G128 4.1 0.9 1.0 OP2 B:C88 4.2 0.3 1.0 O2' B:C171 4.3 0.5 1.0 O5' B:A87 4.3 0.9 1.0 C5' B:G128 4.4 0.9 1.0 C4' C:DG206 4.4 0.3 1.0 O3' B:C171 4.5 0.5 1.0 O3' B:A86 4.6 0.2 1.0 C2' C:DG206 4.7 0.3 1.0 C3' B:A127 5.0 1.0 1.0

Magnesium binding site 3 out of 12 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:87.5 occ:1.00 OP2 B:A174 2.1 0.2 1.0 OP2 B:U173 2.3 0.9 1.0 P B:A174 3.5 0.8 1.0 N7 C:DG206 3.6 0.0 1.0 P B:U173 3.7 0.7 1.0 C8 C:DG206 3.7 0.2 1.0 O3' B:A172 4.2 0.4 1.0 OP1 B:A174 4.3 0.0 1.0 O3' B:U173 4.4 0.1 1.0 OP1 B:U173 4.4 0.7 1.0 O5' B:A174 4.5 0.8 1.0 C3' B:U173 4.5 0.9 1.0 N7 B:A174 4.6 0.4 1.0 O5' B:U173 4.8 0.6 1.0 O2' B:A172 4.8 0.2 1.0 N7 B:G175 4.8 0.3 1.0 C5 C:DG206 4.9 0.9 1.0 C8 B:A174 4.9 0.2 1.0 N9 C:DG206 4.9 0.4 1.0

Magnesium binding site 4 out of 12 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:Mg1018 b:0.9 occ:1.00 OP2 B:U80 4.4 0.1 1.0 OP1 B:U80 4.8 0.2 1.0

Magnesium binding site 5 out of 12 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:Mg1019 b:0.1 occ:1.00 OP1 B:U126 2.1 0.5 1.0 P B:U126 3.5 0.5 1.0 O6 B:G53 3.5 0.2 1.0 O2' B:G125 3.9 0.3 1.0 N7 B:G53 4.0 1.0 1.0 O3' B:G125 4.1 0.3 1.0 OP2 B:U126 4.1 0.7 1.0 C6 B:G53 4.2 0.1 1.0 N7 B:G54 4.2 0.5 1.0 C2' B:G125 4.2 0.3 1.0 O6 B:G54 4.3 1.0 1.0 C5 B:G53 4.4 0.0 1.0 O5' B:U126 4.7 0.1 1.0 C3' B:G125 4.7 0.1 1.0 C5 B:U126 4.7 0.3 1.0 C6 B:U126 4.9 0.5 1.0

Magnesium binding site 6 out of 12 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:Mg1020 b:0.9 occ:1.00 O6 B:G77 4.1 0.0 1.0 N4 B:C66 4.5 0.5 1.0 N4 B:C78 4.6 0.5 1.0 O6 B:G67 4.8 0.7 1.0 N4 B:C68 4.9 0.9 1.0 N7 B:G77 5.0 0.5 1.0

Magnesium binding site 7 out of 12 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:Mg1021 b:85.0 occ:1.00 O B:HOH1045 1.9 84.9 1.0 OP2 B:A58 4.0 0.1 1.0 O6 B:G84 4.4 0.7 1.0 O2' B:A81 4.5 0.4 1.0 N7 B:G84 4.6 0.3 1.0 OP2 B:G83 5.0 0.0 1.0 P B:A58 5.0 0.0 1.0 C2' B:A81 5.0 0.3 1.0

Magnesium binding site 8 out of 12 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:Mg1022 b:79.7 occ:1.00 OP2 B:C171 2.1 0.3 1.0 K B:K1016 2.1 0.2 1.0 OP1 B:U124 2.4 0.7 1.0 O3' B:G170 2.9 0.4 1.0 O2' B:G170 3.0 0.6 1.0 P B:C171 3.1 0.1 1.0 P B:U124 3.8 0.8 1.0 C2' B:G170 3.9 0.6 1.0 C3' B:G170 3.9 0.2 1.0 OP1 B:C171 4.1 1.0 1.0 O5' B:C171 4.2 0.1 1.0 OP2 B:A127 4.3 0.8 1.0 C1' B:G170 4.3 0.6 1.0 O3' B:G123 4.6 0.3 1.0 OP2 B:U124 4.7 0.3 1.0 O5' B:U124 4.7 0.6 1.0 C5' B:U124 4.8 0.4 1.0 C4' B:G170 4.9 0.8 1.0 OP2 B:G125 5.0 0.8 1.0 O4' B:G170 5.0 0.2 1.0

Magnesium binding site 9 out of 12 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:Mg1023 b:0.5 occ:1.00 OP2 B:A39 2.0 0.7 1.0 OP2 B:G38 2.2 0.1 1.0 O5' D:C1 2.8 0.1 1.0 P B:G38 3.2 0.3 1.0 P B:A39 3.4 0.7 1.0 O5' B:G38 3.4 0.1 1.0 O3' B:G37 3.6 0.4 1.0 O4' D:C1 3.9 0.4 1.0 C5' D:C1 3.9 0.4 1.0 N7 B:A39 4.0 0.3 1.0 O2' B:G37 4.0 0.4 1.0 OP1 B:A39 4.0 0.7 1.0 C4' D:C1 4.2 0.7 1.0 O5' B:A39 4.2 0.1 1.0 C8 B:A39 4.4 0.1 1.0 O3' B:G38 4.4 0.4 1.0 C3' B:G38 4.5 0.1 1.0 OP1 B:G38 4.6 0.3 1.0 C3' B:G37 4.8 0.5 1.0 C5' B:G38 4.8 0.1 1.0 C2' B:G37 4.9 1.0 1.0

Magnesium binding site 10 out of 12 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:Mg1024 b:0.2 occ:1.00 O B:HOH1046 2.4 0.6 1.0 O B:HOH1030 2.8 0.4 1.0 O4 B:U50 3.4 0.7 1.0 OP2 B:A48 3.5 0.3 1.0 O5' B:A48 3.7 0.0 1.0 OP2 B:U133 4.0 0.8 1.0 P B:A48 4.0 0.1 1.0 OP2 B:A49 4.1 0.3 1.0 OP1 B:U133 4.2 0.9 1.0 OP1 B:A48 4.3 0.4 1.0 C5' B:A48 4.4 0.1 1.0 C4 B:U50 4.6 0.6 1.0 P B:U133 4.6 0.8 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