Atomistry » Magnesium » PDB 3fps-3fzi » 3ftm
Atomistry »
  Magnesium »
    PDB 3fps-3fzi »
      3ftm »

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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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

Go back to Magnesium Binding Sites List in 3ftm
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: Sun Aug 10 21:04:24 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy