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Magnesium in PDB 3bo2: A Relaxed Active Site Following Exon Ligation By A Group I Intron

Protein crystallography data

The structure of A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo2 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) 50.00 / 3.31
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.960, 108.960, 249.495, 90.00, 90.00, 90.00
R / Rfree (%) 29.1 / 32.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A Relaxed Active Site Following Exon Ligation By A Group I Intron (pdb code 3bo2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the A Relaxed Active Site Following Exon Ligation By A Group I Intron, PDB code: 3bo2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3bo2

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Magnesium binding site 1 out of 10 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:0.7
occ:1.00
 OP1 B:A172 1.9 0.9 1.0
OP1 B:G170 2.3 0.8 1.0
OP1 B:C88 2.3 0.4 1.0
O C:HOH26 2.4 93.6 1.0
O3' E:U3 2.8 0.9 1.0
P B:A172 2.9 0.0 1.0
OP2 B:A172 3.3 0.4 1.0
O5' B:A172 3.5 0.0 1.0
P B:C88 3.5 0.7 1.0
P B:G170 3.6 0.3 1.0
O5' B:G170 3.9 0.8 1.0
OP2 B:C88 3.9 0.4 1.0
C3' E:U3 3.9 0.4 1.0
C4' E:U3 4.0 0.7 1.0
C5' B:G170 4.2 0.6 1.0
O3' B:C171 4.3 0.5 1.0
MG B:MG2 4.4 0.0 1.0
O2' E:U3 4.4 0.6 1.0
O3' B:A87 4.4 0.3 1.0
OP1 B:U173 4.5 0.4 1.0
OP2 B:G170 4.5 0.2 1.0
O3' B:G169 4.6 0.7 1.0
O5' B:C88 4.6 0.7 1.0
C5' E:U3 4.7 0.7 1.0
C3' B:C171 4.8 1.0 1.0
C2' E:U3 4.8 0.3 1.0
C5' B:A172 4.9 0.8 1.0
O3' C:G206 5.0 0.4 1.0

Magnesium binding site 2 out of 10 in 3bo2

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Magnesium binding site 2 out of 10 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:0.0
occ:1.00
 OP1 B:G128 1.8 0.5 1.0
OP2 B:A172 2.1 0.4 1.0
O2' C:G206 2.2 0.7 1.0
O3' C:G206 2.5 0.4 1.0
O C:HOH26 2.6 93.6 1.0
P B:G128 2.9 0.7 1.0
O3' B:A127 3.2 0.2 1.0
C2' C:G206 3.3 0.0 1.0
P B:A172 3.4 0.0 1.0
O5' B:G128 3.4 0.2 1.0
C3' C:G206 3.5 0.8 1.0
OP1 B:A87 3.8 0.7 1.0
OP2 B:C88 3.9 0.4 1.0
O2' B:C171 3.9 0.6 1.0
O3' B:C171 4.1 0.5 1.0
OP1 B:A172 4.1 0.9 1.0
C3' B:A127 4.2 0.7 1.0
OP2 B:G128 4.3 0.1 1.0
C4' B:A127 4.3 0.8 1.0
MG B:MG1 4.4 0.7 1.0
C1' C:G206 4.5 0.2 1.0
C5' B:G128 4.5 0.5 1.0
C4' C:G206 4.5 0.3 1.0
C5' B:A87 4.5 0.1 1.0
O5' B:A172 4.6 0.0 1.0
O B:HOH1022 4.8 67.5 1.0
P B:C88 4.9 0.7 1.0
C5' B:A127 5.0 0.6 1.0

Magnesium binding site 3 out of 10 in 3bo2

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Magnesium binding site 3 out of 10 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:97.5
occ:1.00
 OP2 B:A174 1.9 0.7 1.0
OP2 B:U173 2.1 0.8 1.0
P B:A174 3.0 0.6 1.0
OP1 B:A174 3.3 0.1 1.0
P B:U173 3.5 0.8 1.0
N7 C:G206 3.8 0.7 1.0
O3' B:A172 4.0 1.0 1.0
O3' B:U173 4.1 0.4 1.0
O5' B:A174 4.2 0.0 1.0
C3' B:U173 4.3 0.6 1.0
N7 B:A174 4.3 0.7 1.0
OP1 B:U173 4.3 0.4 1.0
C8 C:G206 4.4 0.3 1.0
O5' B:U173 4.5 0.6 1.0
C8 B:A174 4.6 0.8 1.0
C5 C:G206 4.8 0.5 1.0
N7 B:G175 4.8 0.9 1.0
O2' B:A172 4.9 0.4 1.0
C5' B:U173 5.0 0.8 1.0
O6 C:G206 5.0 0.4 1.0

Magnesium binding site 4 out of 10 in 3bo2

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Magnesium binding site 4 out of 10 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:Mg1015

b:0.2
occ:1.00
 OP2 B:U80 4.7 0.4 1.0
OP2 B:C61 4.9 0.4 1.0
O4 B:U62 5.0 0.9 1.0

Magnesium binding site 5 out of 10 in 3bo2

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Magnesium binding site 5 out of 10 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:Mg1016

b:0.0
occ:1.00
 OP1 B:U124 2.2 0.5 1.0
OP2 B:C171 2.2 0.7 1.0
OP2 B:A127 3.3 0.8 1.0
P B:C171 3.5 0.2 1.0
P B:U124 3.6 0.0 1.0
C5' B:U124 3.8 0.6 1.0
O5' B:C171 3.9 0.6 1.0
OP2 B:G125 4.1 0.7 1.0
O5' B:U124 4.1 0.8 1.0
O3' B:G170 4.1 0.3 1.0
O3' B:G123 4.4 0.2 1.0
O2' B:U126 4.5 0.1 1.0
OP2 B:U124 4.6 0.0 1.0
P B:A127 4.7 0.5 1.0
OP1 B:C171 4.8 1.0 1.0
O2' B:G170 4.9 0.1 1.0

Magnesium binding site 6 out of 10 in 3bo2

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Magnesium binding site 6 out of 10 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:Mg1017

b:0.0
occ:1.00
 OP1 B:G125 2.3 1.0 1.0
P B:G125 3.7 0.8 1.0
OP1 B:A127 3.7 0.5 1.0
N6 B:A172 3.8 0.4 1.0
N7 B:A127 4.1 0.9 1.0
N7 B:A172 4.2 0.5 1.0
OP2 B:G125 4.5 0.7 1.0
O2' B:U50 4.5 0.1 1.0
OP2 B:A131 4.5 0.2 1.0
C8 B:A127 4.5 0.1 1.0
O3' B:U124 4.6 1.0 1.0
O5' B:G125 4.6 0.4 1.0
C5' B:G125 4.7 0.9 1.0
C6 B:A172 4.7 0.3 1.0
OP2 B:U51 4.8 0.3 1.0
C5 B:A172 4.8 0.5 1.0
C5 B:A127 4.9 0.2 1.0

Magnesium binding site 7 out of 10 in 3bo2

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Magnesium binding site 7 out of 10 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:Mg1018

b:0.7
occ:1.00
 OP2 B:A39 2.2 0.8 1.0
OP2 B:G38 2.3 0.3 1.0
O5' E:C1 2.5 0.8 1.0
O2' B:G37 2.9 0.1 1.0
OP1 B:G38 3.1 0.4 1.0
P B:G38 3.1 0.4 1.0
P B:A39 3.6 0.9 1.0
C5' E:C1 3.7 0.8 1.0
O3' B:G37 4.0 0.8 1.0
C4' E:C1 4.2 0.6 1.0
O4' E:C1 4.2 0.1 1.0
C2' B:G37 4.2 0.9 1.0
OP1 B:A39 4.3 1.0 1.0
O3' B:G38 4.5 0.3 1.0
O5' B:G38 4.5 0.2 1.0
C3' B:G38 4.5 0.0 1.0
O5' B:A39 4.6 0.2 1.0
C3' B:G37 4.6 0.1 1.0
N7 B:A39 4.7 0.4 1.0

Magnesium binding site 8 out of 10 in 3bo2

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Magnesium binding site 8 out of 10 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:Mg1019

b:0.4
occ:1.00
 OP2 B:A48 2.2 0.4 1.0
OP2 B:U133 2.9 0.3 1.0
OP1 B:U133 3.2 1.0 1.0
P B:U133 3.4 0.4 1.0
OP2 B:A134 3.4 0.8 1.0
P B:A48 3.6 0.1 1.0
O5' B:U133 3.9 0.3 1.0
O2' B:A47 4.0 0.4 1.0
OP1 B:A48 4.1 0.9 1.0
O3' B:A47 4.5 0.3 1.0
O5' B:A48 4.6 0.2 1.0
O B:HOH1037 4.7 0.6 1.0
C5' B:U133 4.8 0.7 1.0
O3' B:C132 4.9 0.5 1.0
P B:A134 4.9 0.9 1.0

Magnesium binding site 9 out of 10 in 3bo2

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Magnesium binding site 9 out of 10 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:Mg1020

b:0.6
occ:1.00
 OP1 B:U126 2.2 0.7 1.0
N7 B:G53 3.1 0.8 1.0
P B:U126 3.4 0.1 1.0
O2' B:G125 3.5 0.2 1.0
O3' B:G125 3.9 0.9 1.0
C8 B:G53 4.0 0.0 1.0
C5 B:G53 4.1 0.8 1.0
O6 B:G53 4.1 0.7 1.0
OP2 B:U126 4.1 0.2 1.0
C2' B:G125 4.2 0.9 1.0
N7 B:G54 4.2 0.9 1.0
C6 B:G53 4.5 0.7 1.0
O6 B:G54 4.5 0.9 1.0
C3' B:G125 4.7 1.0 1.0
O5' B:U126 4.7 0.2 1.0
N4 B:C52 4.8 0.4 1.0

Magnesium binding site 10 out of 10 in 3bo2

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Magnesium binding site 10 out of 10 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:Mg1021

b:0.2
occ:1.00
 N4 B:C66 3.9 0.1 1.0
O6 B:G67 4.5 0.2 1.0
C5 B:C66 4.6 0.7 1.0
C4 B:C66 4.7 0.7 1.0
O6 B:G77 4.7 0.8 1.0
OP2 B:G65 4.9 0.6 1.0
N4 B:C68 5.0 0.7 1.0

Reference:

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
Page generated: Sun Aug 10 17:51:48 2025

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