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Magnesium in PDB 3bo3: 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: 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

Other elements in 3bo3:

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

Magnesium Binding Sites:

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 3bo3

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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 3bo3

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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 3bo3

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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 3bo3

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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 3bo3

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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 3bo3

Go back to Magnesium Binding Sites List in 3bo3
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 3bo3

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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 3bo3

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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 3bo3

Go back to Magnesium Binding Sites List in 3bo3
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 3bo3

Go back to Magnesium Binding Sites List in 3bo3
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

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 17:52:06 2025

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