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Magnesium in PDB 2oiu: L1 Ribozyme Ligase Circular Adduct

Protein crystallography data

The structure of L1 Ribozyme Ligase Circular Adduct, PDB code: 2oiu was solved by M.P.Robertson, W.G.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.34 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.290, 100.018, 71.930, 90.00, 104.42, 90.00
R / Rfree (%) 20.3 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the L1 Ribozyme Ligase Circular Adduct (pdb code 2oiu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the L1 Ribozyme Ligase Circular Adduct, PDB code: 2oiu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 2oiu

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Magnesium binding site 1 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg72

b:71.7
occ:1.00
 OP1 Q:A39 2.2 75.2 1.0
OP2 Q:G40 2.2 70.5 1.0
OP1 Q:G1 2.2 69.3 1.0
O3' Q:U71 2.8 67.6 1.0
P Q:G1 3.1 68.6 1.0
O Q:HOH93 3.2 61.9 1.0
P Q:A39 3.4 74.2 1.0
P Q:G40 3.7 71.5 1.0
OP2 Q:A39 3.9 74.6 1.0
C3' Q:U71 3.9 64.8 1.0
C4' Q:U71 4.0 64.6 1.0
O5' Q:A39 4.0 70.2 1.0
OP2 Q:G1 4.0 71.2 1.0
O2' Q:U71 4.1 66.1 1.0
O5' Q:G1 4.3 68.4 1.0
C5' Q:G1 4.4 70.0 1.0
C5' Q:U71 4.4 64.7 1.0
O5' Q:G40 4.4 69.3 1.0
N7 Q:G40 4.5 70.3 1.0
O3' Q:A39 4.6 71.5 1.0
C2' Q:U71 4.6 65.1 1.0
OP1 Q:G40 4.6 71.2 1.0
C3' Q:A39 4.7 72.7 1.0
C5' Q:A39 4.7 70.8 1.0
O3' Q:U38 4.7 69.2 1.0
C8 Q:G40 4.8 70.3 1.0

Magnesium binding site 2 out of 7 in 2oiu

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Magnesium binding site 2 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg73

b:78.5
occ:1.00
 O6 Q:G1 2.2 76.5 1.0
O Q:HOH88 3.1 60.5 1.0
O Q:HOH91 3.2 54.1 1.0
C6 Q:G1 3.3 75.6 1.0
C5 Q:G1 4.1 75.9 1.0
N7 Q:G1 4.1 75.4 1.0
N1 Q:G1 4.4 75.7 1.0
O4 Q:U71 4.7 68.0 1.0
C5 Q:U71 4.8 67.1 1.0

Magnesium binding site 3 out of 7 in 2oiu

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Magnesium binding site 3 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg74

b:62.0
occ:1.00
 O Q:HOH91 3.1 54.1 1.0
N2 Q:G1 3.2 75.3 1.0
N1 Q:G1 3.3 75.7 1.0
O4 Q:U50 3.4 67.1 1.0
C4 Q:U50 3.5 66.8 1.0
C5 Q:U50 3.7 67.6 1.0
C2 Q:G1 3.8 75.5 1.0
N3 Q:U50 4.3 66.4 1.0
C6 Q:G1 4.4 75.6 1.0
O6 Q:G1 4.5 76.5 1.0
C6 Q:U50 4.5 67.3 1.0
O4 Q:U71 4.9 68.0 1.0

Magnesium binding site 4 out of 7 in 2oiu

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Magnesium binding site 4 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg75

b:91.6
occ:1.00
 O6 Q:G11 2.9 67.7 1.0
C6 Q:G11 3.6 65.9 1.0
N7 Q:G11 3.7 67.5 1.0
C5 Q:G11 3.9 67.3 1.0
OP1 Q:A13 4.3 69.3 1.0
N1 Q:G11 4.7 65.9 1.0
O Q:HOH87 4.8 54.3 1.0
C8 Q:G11 4.8 67.3 1.0
OP2 Q:A13 4.9 65.6 1.0

Magnesium binding site 5 out of 7 in 2oiu

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Magnesium binding site 5 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:

Magnesium binding site 6 out of 7 in 2oiu

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Magnesium binding site 6 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg77

b:80.5
occ:1.00
 O Q:HOH79 2.9 55.8 1.0
O4' Q:G53 3.0 69.0 1.0
O2' Q:G52 3.2 73.4 1.0
C4' Q:G53 3.6 69.8 1.0
C5' Q:G53 3.8 71.4 1.0
C2' Q:G52 3.9 73.2 1.0
C1' Q:G53 4.0 66.7 1.0
N3 Q:G52 4.2 71.4 1.0
O5' Q:G53 4.6 72.5 1.0
N2 Q:G52 4.6 72.6 1.0
C1' Q:G52 4.7 73.0 1.0
C2 Q:G52 4.9 72.6 1.0
C2' Q:G53 5.0 68.3 1.0
C3' Q:G53 5.0 69.2 1.0

Magnesium binding site 7 out of 7 in 2oiu

Go back to Magnesium Binding Sites List in 2oiu
Magnesium binding site 7 out of 7 in the L1 Ribozyme Ligase Circular Adduct


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of L1 Ribozyme Ligase Circular Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg78

b:81.7
occ:1.00
 O6 Q:G53 2.7 65.7 1.0
O Q:HOH83 2.8 60.6 1.0
O6 Q:G52 3.2 71.3 1.0
C6 Q:G53 3.5 65.7 1.0
N7 Q:G53 3.6 65.8 1.0
N7 Q:G52 3.7 72.9 1.0
C6 Q:G52 3.8 71.5 1.0
C5 Q:G53 3.9 66.1 1.0
N4 Q:C70 4.1 72.8 1.0
C5 Q:G52 4.1 71.2 1.0
O4 Q:U54 4.4 68.1 1.0
O4 Q:U71 4.5 68.0 1.0
O Q:HOH94 4.7 47.7 1.0
N3 Q:U71 4.8 67.5 1.0
C8 Q:G52 4.8 72.6 1.0
N1 Q:G53 4.8 66.7 1.0
C8 Q:G53 4.9 65.8 1.0
N2 Q:G1 5.0 75.3 1.0

Reference:

M.P.Robertson, W.G.Scott. The Structural Basis of Ribozyme-Catalyzed Rna Assembly. Science V. 315 1549 2007.
ISSN: ISSN 0036-8075
PubMed: 17363667
DOI: 10.1126/SCIENCE.1136231
Page generated: Sun Aug 10 12:28:15 2025

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