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Magnesium in PDB 3fs0: Class II Ligase Ribozyme Product-Template Duplex, Structure 2

Protein crystallography data

The structure of Class II Ligase Ribozyme Product-Template Duplex, Structure 2, PDB code: 3fs0 was solved by J.N.Pitt, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.85 / 2.30
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 30.040, 30.040, 59.666, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2 (pdb code 3fs0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2, PDB code: 3fs0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3fs0

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Magnesium binding site 1 out of 5 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Class II Ligase Ribozyme Product-Template Duplex, Structure 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:40.6
occ:1.00
O2' A:A48 2.7 43.9 1.0
N3 A:A48 2.9 38.1 1.0
C2' A:A48 3.2 43.2 1.0
C1' A:A48 3.4 40.7 1.0
N2 B:G2 3.4 34.2 1.0
C2 B:G2 3.8 35.0 1.0
C4 A:A48 3.8 38.6 1.0
C2 A:A48 3.8 38.9 1.0
N1 B:G2 3.9 35.1 1.0
N9 A:A48 4.0 40.5 1.0
N3 B:G2 4.5 34.8 1.0
O4' A:A48 4.6 40.2 1.0
C3' A:A48 4.7 40.9 1.0
O4' A:G49 4.7 44.3 1.0
C6 B:G2 4.8 34.7 1.0

Magnesium binding site 2 out of 5 in 3fs0

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Magnesium binding site 2 out of 5 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Class II Ligase Ribozyme Product-Template Duplex, Structure 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg108

b:45.6
occ:1.00
O B:HOH137 3.0 40.9 1.0
OP2 B:U-2 3.1 39.8 1.0
C5 B:U-2 3.7 30.7 1.0
C6 B:U-2 3.8 31.9 1.0
C5 B:C-1 4.4 37.9 1.0
OP2 B:C-1 4.4 51.9 1.0
P B:U-2 4.4 42.5 1.0
C5' B:U-2 4.4 45.2 1.0
C4 B:U-2 4.6 30.9 1.0
O5' B:U-2 4.7 41.5 1.0
N1 B:U-2 4.8 34.7 1.0
C3' B:U-2 4.9 43.5 1.0

Magnesium binding site 3 out of 5 in 3fs0

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Magnesium binding site 3 out of 5 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Class II Ligase Ribozyme Product-Template Duplex, Structure 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg109

b:45.2
occ:1.00
OP2 B:A4 2.5 41.7 1.0
O5' B:A4 3.3 40.6 1.0
P B:A4 3.4 40.5 1.0
C8 B:A4 3.7 39.8 1.0
N7 B:A4 3.9 37.1 1.0
OP2 B:C5 4.0 52.8 1.0
OP1 B:A4 4.2 44.4 1.0
C5 B:C5 4.2 49.9 1.0
O B:HOH105 4.3 45.1 1.0
C3' B:A4 4.5 45.8 1.0
C5' B:A4 4.6 41.9 1.0
N9 B:A4 4.7 41.5 1.0
O3' B:A3 4.8 41.4 1.0
N4 B:C5 4.9 48.1 1.0
C5 B:A4 5.0 39.6 1.0

Magnesium binding site 4 out of 5 in 3fs0

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Magnesium binding site 4 out of 5 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Class II Ligase Ribozyme Product-Template Duplex, Structure 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg104

b:56.5
occ:1.00
C3' B:C5 2.4 53.4 1.0
C2' B:C5 2.6 53.8 1.0
O3' B:C5 2.8 54.1 1.0
N1 B:C5 3.4 50.5 1.0
C6 B:C5 3.5 50.8 1.0
C1' B:C5 3.5 52.4 1.0
O2' B:C5 3.7 55.1 1.0
C4' B:C5 3.8 53.3 1.0
O4' B:C5 4.1 51.6 1.0
C2 B:C5 4.1 49.5 1.0
C5 B:C5 4.2 49.9 1.0
O5' B:C5 4.3 55.2 1.0
C5' B:C5 4.5 54.4 1.0
O2 B:C5 4.7 47.5 1.0
N3 B:C5 4.7 49.7 1.0
C4 B:C5 4.7 49.9 1.0

Magnesium binding site 5 out of 5 in 3fs0

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Magnesium binding site 5 out of 5 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Class II Ligase Ribozyme Product-Template Duplex, Structure 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg140

b:48.0
occ:1.00
O B:HOH112 2.7 40.2 1.0
N6 B:A3 2.8 39.9 1.0
N6 B:A4 3.0 40.2 1.0
O4 A:U46 3.0 47.8 1.0
N7 A:G47 3.1 45.2 1.0
N7 B:A3 3.2 38.9 1.0
C6 B:A4 3.4 37.9 1.0
N7 B:G2 3.4 32.1 1.0
C8 A:G47 3.6 44.7 1.0
N1 B:A4 3.6 37.6 1.0
C6 B:A3 3.7 38.7 1.0
C4 A:U46 3.7 48.7 1.0
C5 B:A3 3.7 38.8 1.0
N3 A:U46 3.9 48.1 1.0
C5 A:G47 4.1 45.4 1.0
C8 B:G2 4.1 34.7 1.0
C5 B:G2 4.2 34.3 1.0
C5 B:A4 4.2 39.6 1.0
C8 B:A3 4.4 41.2 1.0
O6 B:G2 4.4 33.7 1.0
C2 B:A4 4.5 37.2 1.0
OP2 B:G2 4.6 37.2 1.0
C6 B:G2 4.6 34.7 1.0
O6 A:G47 4.7 48.8 1.0
N9 A:G47 4.7 44.0 1.0
C6 A:G47 4.7 45.4 1.0
N7 B:A4 4.9 37.1 1.0
C5 A:U46 4.9 49.0 1.0
N1 B:A3 4.9 38.4 1.0
C4 A:G47 5.0 44.5 1.0

Reference:

J.N.Pitt, A.R.Ferre-D'amare. Structure-Guided Engineering of the Regioselectivity of Rna Ligase Ribozymes. J.Am.Chem.Soc. V. 131 3532 2009.
ISSN: ISSN 0002-7863
PubMed: 19220054
DOI: 10.1021/JA8067325
Page generated: Mon Dec 14 08:09:12 2020

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