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Magnesium in PDB 7qua: Duplex Rna Containing Xanthosine-Cytosine Base Pairs

Protein crystallography data

The structure of Duplex Rna Containing Xanthosine-Cytosine Base Pairs, PDB code: 7qua was solved by E.Ennifar, R.Micura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.80 / 1.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 41.07, 35.15, 31.93, 90, 129.05, 90
R / Rfree (%) 13.7 / 15.8

Other elements in 7qua:

The structure of Duplex Rna Containing Xanthosine-Cytosine Base Pairs also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs (pdb code 7qua). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs, PDB code: 7qua:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7qua

Go back to Magnesium Binding Sites List in 7qua
Magnesium binding site 1 out of 2 in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Duplex Rna Containing Xanthosine-Cytosine Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1103

b:22.8
occ:0.41
O A:HOH1285 2.0 37.8 0.7
O A:HOH1239 2.1 19.1 1.0
O A:HOH1303 2.2 33.4 0.6
H4' A:G1010 3.8 12.9 1.0
O A:HOH1269 4.0 31.2 0.9
O2' A:G1010 4.3 11.5 1.0
HO2' A:G1010 4.4 13.8 1.0
O A:HOH1210 4.6 25.8 1.0
C4' A:G1010 4.8 10.7 1.0

Magnesium binding site 2 out of 2 in 7qua

Go back to Magnesium Binding Sites List in 7qua
Magnesium binding site 2 out of 2 in the Duplex Rna Containing Xanthosine-Cytosine Base Pairs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Duplex Rna Containing Xanthosine-Cytosine Base Pairs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1104

b:33.5
occ:0.60
O A:HOH1224 1.8 14.6 0.7
O A:HOH1240 2.1 32.1 1.0
O A:HOH1304 2.3 33.2 1.0
O A:HOH1201 2.6 35.8 1.0
O A:HOH1277 3.0 30.0 1.0
N7 A:XMP1005 3.8 9.8 1.0
O A:HOH1260 3.8 19.1 1.0
O A:HOH1234 4.2 26.6 1.0
O3P A:XMP1005 4.4 12.4 1.0
O A:HOH1233 4.4 21.7 1.0
O6 A:XMP1005 4.5 9.2 1.0
H8 A:G1004 4.5 10.2 1.0
N7 A:G1004 4.6 8.2 1.0
H3' A:G1004 4.7 11.1 1.0
OP2 A:G1004 4.7 12.0 1.0
C8 A:G1004 4.7 8.6 1.0
C8 A:XMP1005 4.8 9.7 1.0
O A:HOH1238 4.8 55.6 1.0
C5 A:XMP1005 4.8 9.3 1.0
O A:HOH1255 4.9 20.3 1.0
H8 A:XMP1005 4.9 11.6 1.0

Reference:

S.Mair, K.Erharter, E.Renard, K.Brillet, M.Brunner, A.Lusser, C.Kreutz, E.Ennifar, R.Micura. Synthesis and Properties of Xanthosine-Modified Rna To Be Published.
Page generated: Thu Oct 3 07:01:17 2024

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