Calcium in PDB 4wb3: Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin

The structure of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin, PDB code: 4wb3 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)	32.85 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.840, 282.630, 45.760, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.9

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

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin (pdb code 4wb3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin, PDB code: 4wb3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:17.2 occ:1.00 OP1 D:0G32 2.2 18.8 1.0 OP1 D:0U5 2.4 15.0 1.0 O D:HOH258 2.4 18.0 1.0 OD2 A:ASP705 2.5 18.6 1.0 O D:HOH253 2.5 13.7 1.0 OP2 D:0G6 2.5 15.0 1.0 O D:HOH254 2.6 12.6 1.0 CG A:ASP705 3.3 18.3 1.0 P D:0G32 3.6 16.2 1.0 P D:0U5 3.7 18.0 1.0 P D:0G6 3.7 16.8 1.0 O D:HOH255 3.7 16.4 1.0 OP1 D:0G6 3.9 15.2 1.0 O A:HOH914 4.0 20.4 1.0 NZ A:LYS701 4.0 17.6 1.0 CB A:ASP705 4.0 16.3 1.0 OD1 A:ASP705 4.1 17.2 1.0 OP2 D:0U5 4.2 17.2 1.0 OP2 D:0G32 4.3 18.2 1.0 O5' D:0U5 4.4 19.8 1.0 O A:HOH916 4.5 18.7 1.0 C3' D:0C31 4.5 13.2 1.0 O3' D:0C31 4.5 14.7 1.0 O5' D:0G32 4.6 17.6 1.0 MG D:MG103 4.7 16.0 1.0 O5' D:0G6 4.8 15.5 1.0 O D:HOH271 4.8 15.8 1.0 O3' D:0U5 4.8 17.0 1.0 C5' D:0U5 4.8 19.6 1.0 O3' D:0A4 4.8 16.4 1.0 NH2 A:ARG718 4.9 22.4 1.0 OP1 D:0C31 5.0 21.5 1.0 O2 D:3KA28 5.0 15.0 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:26.2 occ:1.00 OP2 E:0G32 2.3 38.1 1.0 OP2 E:0U5 2.4 26.1 1.0 O E:HOH247 2.4 28.2 1.0 O E:HOH227 2.4 39.2 1.0 OD2 C:ASP705 2.5 32.9 1.0 OP1 E:0G6 2.5 25.3 1.0 O E:HOH209 2.6 24.2 1.0 CG C:ASP705 3.4 34.2 1.0 O E:HOH206 3.7 20.6 1.0 P E:0U5 3.7 25.5 1.0 P E:0G6 3.7 27.1 1.0 P E:0G32 3.7 31.7 1.0 OP2 E:0G6 4.0 25.5 1.0 NZ C:LYS701 4.0 25.6 1.0 CB C:ASP705 4.1 31.9 1.0 OP1 E:0U5 4.2 33.2 1.0 OD1 C:ASP705 4.2 36.1 1.0 O C:HOH905 4.2 28.2 1.0 OP1 E:0G32 4.4 28.8 1.0 O5' E:0U5 4.4 28.1 1.0 O3' E:0C31 4.6 29.8 1.0 C3' E:0C31 4.6 29.9 1.0 O5' E:0G32 4.7 33.7 1.0 MG E:MG103 4.7 26.5 1.0 O C:HOH907 4.7 41.2 1.0 C5' E:0U5 4.8 24.3 1.0 O5' E:0G6 4.8 29.0 1.0 O3' E:0U5 4.8 27.5 1.0 OP1 E:0C31 4.8 52.8 1.0 O3' E:0A4 4.9 30.2 1.0 O2 E:3KA28 4.9 34.8 1.0 O E:HOH237 4.9 27.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca101 b:24.1 occ:1.00 O6 D:0G27 2.4 18.7 1.0 O6 D:0G26 2.4 23.5 1.0 O6 D:0G19 2.5 25.7 1.0 O6 D:0G32 2.5 22.6 1.0 O6 D:0G18 2.5 23.9 1.0 O6 D:0G22 2.5 25.3 1.0 O6 D:0G25 2.5 22.6 1.0 O6 D:0G17 2.6 23.6 1.0 C6 D:0G26 3.4 19.1 1.0 C6 D:0G19 3.4 28.6 1.0 C6 D:0G27 3.4 21.6 1.0 C6 D:0G22 3.5 26.4 1.0 C6 D:0G32 3.5 21.1 1.0 C6 D:0G25 3.5 26.4 1.0 C6 D:0G18 3.5 24.0 1.0 C6 D:0G17 3.5 25.6 1.0 N1 D:0G26 3.8 19.8 1.0 N1 D:0G19 3.8 28.8 1.0 N1 D:0G22 3.8 26.6 1.0 N1 D:0G18 3.8 25.2 1.0 N1 D:0G32 3.8 24.4 1.0 N1 D:0G27 3.9 18.6 1.0 N1 D:0G25 3.9 27.9 1.0 N1 D:0G17 3.9 28.1 1.0 N1 D:0A16 4.5 33.4 1.0 C6 D:0A16 4.6 33.5 1.0 C5 D:0G25 4.7 25.7 1.0 C5 D:0G26 4.7 20.0 1.0 C5 D:0G27 4.7 19.4 1.0 C5 D:0G22 4.7 30.9 1.0 C5 D:0G32 4.7 22.7 1.0 C5 D:0G19 4.7 30.1 1.0 C5 D:0G18 4.7 24.6 1.0 C5 D:0G17 4.7 27.0 1.0 C2 D:0A16 4.7 31.8 1.0 N6 D:0A16 4.9 32.1 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:20.4 occ:0.89 OP1 D:0C34 2.3 21.3 1.0 O D:HOH290 2.3 25.3 1.0 O D:HOH256 2.4 22.2 1.0 O D:HOH260 2.4 21.9 1.0 O D:HOH265 2.5 21.8 1.0 O D:HOH261 2.5 24.4 1.0 O D:HOH262 2.5 18.2 1.0 P D:0C34 3.7 22.6 1.0 O5' D:0C34 4.2 24.7 1.0 OP2 D:0A33 4.3 20.1 1.0 O6 D:0G6 4.3 19.8 1.0 O D:HOH274 4.3 18.3 1.0 C5 D:0C34 4.4 19.3 1.0 N4 D:0C36 4.4 22.6 1.0 OP2 D:0C34 4.5 20.9 1.0 O D:HOH259 4.5 15.4 1.0 O D:HOH273 4.5 21.8 1.0 O D:HOH292 4.6 34.8 1.0 OP1 D:0A33 4.7 18.0 1.0 C6 D:0C34 4.7 19.4 1.0 O D:HOH315 4.7 31.5 1.0 O D:HOH334 4.8 39.1 1.0 N7 D:0G35 4.8 19.8 1.0 O3' D:0A33 4.8 21.2 1.0 O D:HOH266 4.9 19.4 1.0 OP1 D:0A4 4.9 24.2 1.0 P D:0A33 5.0 17.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca101 b:36.7 occ:1.00 O6 E:0G19 2.4 45.0 1.0 O6 E:0G22 2.4 39.7 1.0 O6 E:0G27 2.4 42.8 1.0 O6 E:0G17 2.5 38.4 1.0 O6 E:0G32 2.5 36.4 1.0 O6 E:0G26 2.5 40.1 1.0 O6 E:0G18 2.5 37.0 1.0 O6 E:0G25 2.6 43.3 1.0 C6 E:0G27 3.4 41.0 1.0 C6 E:0G19 3.4 45.3 1.0 C6 E:0G22 3.4 45.8 1.0 C6 E:0G32 3.4 37.4 1.0 C6 E:0G17 3.4 38.9 1.0 C6 E:0G18 3.5 37.9 1.0 C6 E:0G26 3.5 40.5 1.0 C6 E:0G25 3.6 53.6 1.0 N1 E:0G27 3.7 37.6 1.0 N1 E:0G32 3.7 36.8 1.0 N1 E:0G19 3.8 45.7 1.0 N1 E:0G22 3.8 41.4 1.0 N1 E:0G26 3.8 36.5 1.0 N1 E:0G18 3.9 41.8 1.0 N1 E:0G17 3.9 39.8 1.0 N1 E:0G25 3.9 53.9 1.0 N1 E:0A16 4.4 57.7 1.0 C6 E:0A16 4.6 53.6 1.0 C5 E:0G22 4.6 48.8 1.0 C5 E:0G27 4.6 44.4 1.0 C5 E:0G19 4.6 46.5 1.0 C5 E:0G17 4.6 38.7 1.0 C5 E:0G32 4.6 37.5 1.0 C2 E:0A16 4.7 57.0 1.0 C5 E:0G18 4.7 37.8 1.0 C5 E:0G26 4.8 43.4 1.0 C5 E:0G25 4.8 51.9 1.0 N6 E:0A16 4.9 52.5 1.0 C2 E:0G27 5.0 36.7 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Mirror-Image L-Rna/L-Dna Aptamer Nox-D20 in Complex with Mouse C5A-Desarg Complement Anaphylatoxin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca102 b:28.9 occ:0.84 O E:HOH231 2.3 31.5 1.0 O E:HOH216 2.4 29.5 1.0 OP2 E:0C34 2.4 39.2 1.0 O E:HOH229 2.5 32.4 1.0 O E:HOH217 2.5 27.5 1.0 O E:HOH222 2.5 32.2 1.0 O E:HOH230 2.5 29.3 1.0 P E:0C34 3.8 38.4 1.0 OP1 E:0A33 4.1 35.0 1.0 O E:HOH228 4.2 30.9 1.0 O E:HOH208 4.3 25.3 1.0 O6 E:0G6 4.3 30.1 1.0 O5' E:0C34 4.3 36.8 1.0 C5 E:0C34 4.4 35.0 1.0 O E:HOH226 4.4 38.7 1.0 N4 E:0C36 4.5 30.6 1.0 O E:HOH255 4.5 37.0 1.0 OP1 E:0C34 4.6 38.7 1.0 OP2 E:0A33 4.7 29.6 1.0 N7 E:0G35 4.8 38.0 1.0 O E:HOH220 4.8 27.6 1.0 OP2 E:0A4 4.8 25.9 1.0 C6 E:0C34 4.8 38.3 1.0 O E:HOH213 4.9 21.7 1.0 O4 E:0U5 4.9 25.8 1.0 P E:0A33 4.9 32.8 1.0 O3' E:0A33 5.0 33.8 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