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Magnesium in PDB 3skw: Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak

Protein crystallography data

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak, PDB code: 3skw was solved by O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.65 / 2.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.376, 35.414, 119.269, 90.00, 95.18, 90.00
R / Rfree (%) 21.7 / 28.7

Other elements in 3skw:

The structure of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak also contains other interesting chemical elements:

Caesium (Cs) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak (pdb code 3skw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak, PDB code: 3skw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3skw

Go back to Magnesium Binding Sites List in 3skw
Magnesium binding site 1 out of 2 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:51.2
occ:1.00
O6 A:G45 3.0 43.3 1.0
N7 A:G46 3.3 42.6 1.0
N7 A:G45 3.3 47.0 1.0
O6 A:G46 3.4 38.0 1.0
C6 A:G45 3.5 45.8 1.0
C5 A:G45 3.6 46.7 1.0
C5 A:G46 4.0 39.0 1.0
C6 A:G46 4.0 40.8 1.0
C8 A:G46 4.3 39.9 1.0
C8 A:G45 4.3 51.0 1.0
N1 A:G45 4.6 47.3 1.0
C4 A:G45 4.7 49.7 1.0
N4 A:C69 5.0 28.8 1.0

Magnesium binding site 2 out of 2 in 3skw

Go back to Magnesium Binding Sites List in 3skw
Magnesium binding site 2 out of 2 in the Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 2'- Deoxyguanosine Riboswitch Bound to 2'- Deoxyguanosine, Cesium Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:53.7
occ:1.00
O4 A:U63 2.6 42.5 1.0
O6 A:G76 2.7 47.4 1.0
O6 A:G75 3.3 50.5 1.0
N7 A:G76 3.6 66.1 1.0
C6 A:G76 3.7 54.3 1.0
C4 A:U63 3.8 38.0 1.0
C5 A:G76 4.0 62.1 1.0
C6 A:G75 4.1 50.6 1.0
N6 A:A77 4.1 61.1 1.0
N4 A:C64 4.3 35.3 1.0
N3 A:U63 4.4 40.7 1.0
OP1 A:G33 4.7 51.3 1.0
C5 A:G75 4.7 55.1 1.0
N7 A:G75 4.8 62.6 1.0
C8 A:G76 4.9 66.9 1.0
C6 A:A77 4.9 55.4 1.0
O4 A:U62 4.9 44.9 1.0
C5 A:U63 5.0 30.1 1.0
N1 A:G76 5.0 55.3 1.0

Reference:

O.Pikovskaya, A.Polonskaia, D.J.Patel, A.Serganov. Structural Principles of Nucleoside Selectivity in A 2'-Deoxyguanosine Riboswitch. Nat.Chem.Biol. V. 7 748 2011.
ISSN: ISSN 1552-4450
PubMed: 21841796
DOI: 10.1038/NCHEMBIO.631
Page generated: Mon Dec 14 08:51:16 2020

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