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Magnesium in PDB 3ftm: Class II Ligase Ribozyme Product-Template Duplex, Structure 1

Protein crystallography data

The structure of Class II Ligase Ribozyme Product-Template Duplex, Structure 1, PDB code: 3ftm 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) 29.60 / 2.70
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 31.550, 31.550, 171.066, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.8

Other elements in 3ftm:

The structure of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 also contains other interesting chemical elements:

Potassium (K) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1 (pdb code 3ftm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1, PDB code: 3ftm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3ftm

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Magnesium binding site 1 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:39.7
occ:1.00
 O A:HOH310 2.2 34.0 1.0
O A:HOH309 2.8 26.4 1.0
O6 A:G53 3.2 32.4 1.0
O4 A:U52 4.0 43.5 1.0
N7 A:G53 4.1 34.6 1.0
C6 A:G53 4.1 32.2 1.0
C4 A:U52 4.5 42.9 1.0
C5 A:G53 4.5 33.6 1.0
C5 A:U52 4.7 42.5 1.0

Magnesium binding site 2 out of 9 in 3ftm

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Magnesium binding site 2 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:45.4
occ:1.00
 O2' A:A48 2.2 50.9 1.0
C2' A:A48 3.0 47.6 1.0
C1' A:A48 3.2 45.3 1.0
O2' D:A4 3.2 49.2 1.0
N3 A:A48 3.6 41.3 1.0
O4' D:C5 3.7 39.1 1.0
N3 D:A4 3.7 47.5 1.0
C1' D:C5 3.9 38.9 1.0
C2' D:A4 3.9 49.0 1.0
C1' D:A4 4.1 49.1 1.0
N9 A:A48 4.1 43.1 1.0
O4' A:A48 4.2 47.0 1.0
N1 B:G2 4.2 37.2 1.0
C4 A:A48 4.3 42.0 1.0
C2 B:G2 4.4 36.9 1.0
C3' A:A48 4.4 49.0 1.0
N1 D:C5 4.4 39.2 1.0
C2 D:A4 4.5 48.1 1.0
N2 B:G2 4.5 36.4 1.0
O4' A:G49 4.6 48.2 1.0
C4 D:A4 4.6 48.1 1.0
C4' A:A48 4.7 48.4 1.0
C2 A:A48 4.7 40.1 1.0
C6 B:G2 4.7 37.5 1.0
N9 D:A4 4.8 48.5 1.0
O3' A:A48 4.9 50.7 1.0
O2 D:C5 4.9 42.1 1.0
C2 D:C5 4.9 41.6 1.0
C4' D:C5 4.9 40.3 1.0
N3 B:G2 4.9 35.2 1.0
C6 D:C5 5.0 39.5 1.0

Magnesium binding site 3 out of 9 in 3ftm

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Magnesium binding site 3 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:42.3
occ:1.00
 OP2 B:A3 1.9 38.7 1.0
O B:HOH315 2.1 40.6 1.0
P B:A3 3.3 38.9 1.0
O5' B:A3 3.8 41.2 1.0
OP1 B:A3 4.1 38.0 1.0
O5' B:G2 4.3 43.7 1.0
O3' B:G2 4.5 38.0 1.0
OP2 B:A4 4.5 45.0 1.0
N7 B:A4 4.5 38.3 1.0
N7 B:A3 4.7 34.5 1.0
OP1 B:G2 4.7 47.7 1.0
C3' B:G2 4.7 38.1 1.0
C8 B:A3 4.7 34.8 1.0
OP2 B:G2 4.8 45.3 1.0
P B:G2 4.8 46.7 1.0

Magnesium binding site 4 out of 9 in 3ftm

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Magnesium binding site 4 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:36.2
occ:1.00
 N1 B:A3 3.0 34.2 1.0
N6 B:A3 3.3 33.5 1.0
C2 B:A4 3.3 37.8 1.0
C6 B:A3 3.6 33.4 1.0
N1 B:A4 3.7 38.6 1.0
N3 B:A4 3.8 37.9 1.0
O2 A:U46 3.8 46.3 1.0
C2 B:A3 4.1 34.9 1.0
C1' A:G47 4.2 51.8 1.0
C2 A:U46 4.2 44.5 1.0
N3 A:U46 4.3 42.0 1.0
C6 B:A4 4.4 38.3 1.0
O4' A:G47 4.4 51.2 1.0
C4 B:A4 4.4 37.5 1.0
C5' D:A6 4.5 36.9 1.0
O6 B:G2 4.5 38.6 1.0
O2' A:G47 4.5 55.8 1.0
C4' D:A6 4.6 36.7 1.0
O2' D:C5 4.6 36.1 1.0
C5 B:A4 4.8 38.2 1.0
N3 A:G47 4.8 47.8 1.0
C5 B:A3 5.0 33.4 1.0
N9 A:G47 5.0 50.2 1.0

Magnesium binding site 5 out of 9 in 3ftm

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Magnesium binding site 5 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:48.1
occ:1.00
 O2' B:U-2 2.6 45.1 1.0
O2 A:C51 3.7 40.8 1.0
C2' B:U-2 3.7 46.3 1.0
O4' B:C-1 3.7 43.1 1.0
N2 A:G50 3.8 39.4 1.0
C4' B:C-1 4.0 44.0 1.0
C5' B:C-1 4.1 45.3 1.0
O2 B:U-2 4.4 42.1 1.0
C1' B:U-2 4.4 45.8 1.0
C2 A:C51 4.7 38.4 1.0
N2 B:G-3 4.7 30.6 1.0
C1' A:C51 4.9 42.9 1.0
C3' B:U-2 5.0 47.4 1.0

Magnesium binding site 6 out of 9 in 3ftm

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Magnesium binding site 6 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg312

b:44.0
occ:1.00
 N1 B:G1 2.6 43.2 1.0
N2 B:G1 2.9 43.9 1.0
C2 B:G1 3.2 42.3 1.0
OP2 A:A48 3.6 55.1 1.0
C8 A:G47 3.6 49.6 1.0
C6 B:G1 3.7 44.1 1.0
N7 A:G47 3.7 49.8 1.0
O6 B:G1 3.8 45.8 1.0
C3' A:G47 4.3 53.3 1.0
N9 A:G47 4.4 50.2 1.0
C5 A:G47 4.4 49.4 1.0
N3 B:G1 4.5 42.4 1.0
O5' A:G47 4.5 54.5 1.0
OP2 A:G47 4.7 54.9 1.0
C4 A:G47 4.8 49.0 1.0
C2' A:G47 4.8 53.5 1.0
C5 B:G1 4.8 43.4 1.0
P A:A48 4.9 56.8 1.0

Magnesium binding site 7 out of 9 in 3ftm

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Magnesium binding site 7 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg205

b:53.6
occ:1.00
 O6 C:G53 3.1 31.4 1.0
N7 C:G53 3.9 34.5 1.0
O4 C:U52 3.9 39.1 1.0
C6 C:G53 4.0 34.7 1.0
C5 C:G53 4.3 35.2 1.0
O D:HOH302 4.5 34.0 1.0
C4 C:U52 4.5 39.3 1.0
C5 C:U52 4.7 37.6 1.0

Magnesium binding site 8 out of 9 in 3ftm

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Magnesium binding site 8 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg316

b:49.4
occ:1.00
 OP2 C:U46 1.7 50.7 1.0
P C:U46 2.7 51.1 1.0
OP1 C:U46 3.1 51.4 1.0
O5' C:U46 3.3 50.4 1.0
O3' C:G45 4.1 49.1 1.0
OP2 C:G47 4.2 53.6 1.0
N7 C:G47 4.4 49.6 1.0
C3' C:G45 4.6 46.6 1.0
C5' C:U46 4.7 49.4 1.0
OP1 C:G45 4.8 44.0 1.0
O6 D:G1 4.8 55.6 1.0
O5' C:G45 4.9 42.5 1.0

Magnesium binding site 9 out of 9 in 3ftm

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Magnesium binding site 9 out of 9 in the Class II Ligase Ribozyme Product-Template Duplex, Structure 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Class II Ligase Ribozyme Product-Template Duplex, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg322

b:50.0
occ:1.00
 O4 C:U46 3.0 43.7 1.0
O2' D:G1 3.2 50.6 1.0
OP2 D:G2 3.3 53.6 1.0
N1 C:G47 3.5 49.6 1.0
O6 C:G47 3.7 50.1 1.0
C6 C:G47 3.8 48.9 1.0
N6 D:A4 4.0 48.8 1.0
C4 C:U46 4.1 43.4 1.0
C2 C:G47 4.3 50.7 1.0
C2' D:G1 4.5 50.6 1.0
N2 C:G47 4.5 50.9 1.0
P D:G2 4.5 53.2 1.0
O6 C:G45 4.5 36.4 1.0
C5 C:U46 4.8 43.0 1.0
OP1 D:G2 4.9 52.4 1.0
C5 C:G47 4.9 49.2 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: Wed Aug 14 13:53:21 2024

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