Magnesium in PDB 4wb2: Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin

The structure of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin, PDB code: 4wb2 was solved by L.Yatime, C.Maasch, K.Hoehlig, S.Klussmann, A.Vater, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.88 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.470, 282.254, 45.899, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.3

The structure of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin (pdb code 4wb2). 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 Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin, PDB code: 4wb2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin


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 Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg103 b:17.4 occ:1.00 OP1 D:0U5 2.0 17.7 1.0 O D:HOH315 2.0 18.4 1.0 OP1 D:0G32 2.1 16.0 1.0 O D:HOH250 2.1 15.6 1.0 O D:HOH249 2.1 16.2 1.0 O D:HOH259 2.2 16.9 1.0 P D:0G32 3.4 15.9 1.0 P D:0U5 3.4 18.1 1.0 OP2 D:0G32 3.9 16.4 1.0 O2' D:0C31 4.0 15.2 1.0 O5' D:0U5 4.1 19.6 1.0 OP2 D:0U5 4.1 18.2 1.0 OP1 D:0G6 4.3 13.9 1.0 OP2 D:0A33 4.4 18.1 1.0 O5' D:0G32 4.4 16.9 1.0 O D:HOH255 4.4 18.0 1.0 O3' D:0C31 4.4 15.4 1.0 O4 D:3KA7 4.4 15.2 1.0 N7 D:0G6 4.4 18.8 1.0 O D:HOH267 4.5 24.9 1.0 O3' D:0A4 4.5 17.5 1.0 C4' D:0A4 4.7 16.8 1.0 C3' D:0C31 4.7 13.0 1.0 CA A:CA802 4.7 15.9 1.0 C5' D:0A4 4.7 18.8 1.0 C3' D:0A4 4.8 18.0 1.0 C4' D:0G32 4.8 15.9 1.0 C2' D:0C31 4.8 13.8 1.0 C5' D:0G32 4.8 18.3 1.0 O D:HOH258 4.8 15.1 1.0 O D:HOH272 4.9 22.2 1.0 C8 D:0G6 4.9 17.4 1.0 O D:HOH248 5.0 15.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin


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 Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg103 b:19.5 occ:0.99 OP2 E:0U5 2.0 22.0 1.0 OP2 E:0G32 2.0 21.1 1.0 O E:HOH225 2.0 21.6 1.0 O E:HOH224 2.1 20.0 1.0 O E:HOH227 2.1 21.1 1.0 O E:HOH230 2.2 21.2 1.0 P E:0G32 3.4 24.1 1.0 P E:0U5 3.4 20.4 1.0 OP1 E:0G32 3.9 23.6 1.0 O2' E:0C31 4.0 21.8 1.0 O5' E:0U5 4.1 21.4 1.0 OP1 E:0U5 4.1 19.3 1.0 O5' E:0G32 4.3 24.5 1.0 OP2 E:0G6 4.3 21.2 1.0 OP1 E:0A33 4.4 27.6 1.0 O3' E:0C31 4.4 22.2 1.0 O4 E:3KA7 4.5 24.7 1.0 O E:HOH234 4.5 22.3 1.0 N7 E:0G6 4.5 24.4 1.0 O3' E:0A4 4.5 23.0 1.0 C4' E:0A4 4.6 23.6 1.0 C5' E:0A4 4.7 23.7 1.0 C3' E:0A4 4.7 21.1 1.0 C4' E:0G32 4.7 23.2 1.0 O E:HOH236 4.7 28.9 1.0 CA C:CA802 4.7 20.7 1.0 C5' E:0G32 4.8 24.9 1.0 C3' E:0C31 4.8 22.4 1.0 C2' E:0C31 4.8 23.8 1.0 O E:HOH243 4.9 25.4 1.0 O E:HOH229 4.9 21.7 1.0 C8 E:0G6 5.0 23.6 1.0 O E:HOH261 5.0 27.4 1.0

L.Yatime, C.Maasch, K.Hoehlig, S.Klussmann, G.R.Andersen, A.Vater. Structural Basis For the Targeting of Complement Anaphylatoxin C5A Using A Mixed L-Rna/L-Dna Aptamer. Nat Commun V. 6 6481 2015.
ISSN: ESSN 2041-1723
PubMed: 25901944
DOI: 10.1038/NCOMMS7481