Atomistry » Calcium » PDB 4wa3-4wn0 » 4wb3
Atomistry »
  Calcium »
    PDB 4wa3-4wn0 »
      4wb3 »

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

Protein crystallography data

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

Other elements in 4wb3:

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

Calcium Binding Sites:

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 4wb3

Go back to Calcium Binding Sites List in 4wb3
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 4wb3

Go back to Calcium Binding Sites List in 4wb3
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 4wb3

Go back to Calcium Binding Sites List in 4wb3
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 4wb3

Go back to Calcium Binding Sites List in 4wb3
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 4wb3

Go back to Calcium Binding Sites List in 4wb3
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 4wb3

Go back to Calcium Binding Sites List in 4wb3
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

Reference:

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
Page generated: Sun Jul 14 14:03:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy