Calcium in PDB 8avq: AO75L in Complex with Udp-Xylose

The structure of AO75L in Complex with Udp-Xylose, PDB code: 8avq was solved by M.E.Laugeri, I.Speciale, A.Gimeno, S.Lin, A.Poveda, T.Lowary, J.L.Vanetten, J.J.Barbero, C.De Castro, M.Tonetti, A.L.Rojas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.90 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.285, 130.427, 87.143, 90, 118.01, 90
R / Rfree (%)	19.6 / 22.7

The structure of AO75L in Complex with Udp-Xylose also contains other interesting chemical elements:

Magnesium

(Mg)

39 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the AO75L in Complex with Udp-Xylose (pdb code 8avq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the AO75L in Complex with Udp-Xylose, PDB code: 8avq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:28.6 occ:1.00 O22 A:BCN301 2.2 31.1 1.0 O A:GLU242 2.3 30.1 1.0 OD1 A:ASP240 2.4 33.6 1.0 O4 A:BCN301 2.4 30.5 1.0 O A:HOH501 2.4 37.7 1.0 O6 A:BCN301 2.6 27.2 1.0 N1 A:BCN301 2.7 30.5 1.0 C2 A:BCN301 3.2 31.6 1.0 CG A:ASP240 3.3 37.0 1.0 C4 A:BCN301 3.3 31.5 1.0 C6 A:BCN301 3.4 29.0 1.0 C5 A:BCN301 3.4 28.8 1.0 C3 A:BCN301 3.4 31.3 1.0 C1 A:BCN301 3.4 31.1 1.0 C A:GLU242 3.5 32.4 1.0 OD2 A:ASP240 3.7 41.5 1.0 N A:GLU242 4.1 30.9 1.0 O A:ASP240 4.2 31.4 1.0 CA A:GLU242 4.3 33.2 1.0 O21 A:BCN301 4.4 30.4 1.0 O A:HOH560 4.4 45.7 1.0 CB A:ASN243 4.4 32.1 1.0 C A:ASP240 4.5 31.1 1.0 N A:ASN243 4.6 32.1 1.0 CB A:GLU242 4.6 35.8 1.0 CB A:ASP240 4.7 34.7 1.0 N A:ASP240 4.8 31.7 1.0 CA A:ASN243 4.8 31.6 1.0 C A:ASN243 4.9 31.5 1.0 CA A:ASP240 4.9 32.0 1.0 OD1 A:ASN243 5.0 37.0 1.0

Calcium binding site 2 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:83.2 occ:1.00 O A:ILE149 3.5 28.8 1.0 N A:ILE149 3.7 29.7 1.0 CG A:MSE147 4.0 41.6 1.0 O A:GLY174 4.0 43.4 1.0 CA A:ASN148 4.1 32.4 1.0 O A:MSE147 4.2 31.9 1.0 CG2 A:ILE173 4.4 41.2 1.0 CG1 A:ILE149 4.4 29.1 1.0 C A:ASN148 4.4 31.2 1.0 N A:ASN148 4.4 31.8 1.0 C A:MSE147 4.5 32.5 1.0 C A:ILE149 4.5 28.8 1.0 SE A:MSE147 4.5 53.9 1.0 CG2 A:VAL162 4.5 31.8 1.0 CA A:ILE149 4.6 29.6 1.0 O A:HOH611 4.8 53.2 1.0 O A:HOH577 4.9 51.6 1.0

Calcium binding site 3 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:27.5 occ:1.00 O B:HOH480 2.3 40.6 1.0 O B:GLU242 2.3 29.0 1.0 OD1 B:ASP240 2.4 30.1 1.0 O22 B:BCN301 2.4 32.1 1.0 O4 B:BCN301 2.4 32.9 1.0 O6 B:BCN301 2.5 34.5 1.0 O B:HOH499 2.6 35.8 1.0 N1 B:BCN301 2.7 33.1 1.0 CG B:ASP240 3.3 32.1 1.0 C2 B:BCN301 3.3 32.2 1.0 C4 B:BCN301 3.3 32.7 1.0 C6 B:BCN301 3.4 34.2 1.0 C5 B:BCN301 3.4 34.4 1.0 C3 B:BCN301 3.4 33.3 1.0 C1 B:BCN301 3.5 32.6 1.0 C B:GLU242 3.5 30.3 1.0 OD2 B:ASP240 3.6 35.4 1.0 N B:GLU242 4.1 29.5 1.0 O B:ASP240 4.2 27.7 1.0 CA B:GLU242 4.3 30.9 1.0 O B:HOH524 4.4 41.1 1.0 CB B:ASN243 4.5 30.2 1.0 O21 B:BCN301 4.5 29.2 1.0 C B:ASP240 4.5 28.7 1.0 N B:ASN243 4.5 29.7 1.0 CB B:ASP240 4.6 31.1 1.0 CB B:GLU242 4.7 33.2 1.0 N B:ASP240 4.8 29.5 1.0 OD1 B:ASN243 4.8 34.0 1.0 CA B:ASN243 4.8 30.3 1.0 C B:ASN243 4.9 31.4 1.0 CA B:ASP240 4.9 29.5 1.0

Calcium binding site 4 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:74.7 occ:1.00 O B:ILE149 3.7 31.7 1.0 N B:ILE149 3.8 32.3 1.0 CA B:ASN148 4.1 32.9 1.0 O B:MSE147 4.1 34.0 1.0 CG B:MSE147 4.1 42.4 1.0 O B:GLY174 4.1 49.3 1.0 CG1 B:ILE149 4.3 32.1 1.0 SE B:MSE147 4.4 55.5 1.0 CG2 B:VAL162 4.4 31.4 1.0 C B:MSE147 4.4 34.3 1.0 N B:ASN148 4.4 33.4 1.0 C B:ASN148 4.5 32.5 1.0 CG2 B:ILE173 4.6 46.9 1.0 C B:ILE149 4.6 31.4 1.0 CA B:ILE149 4.7 32.0 1.0

Calcium binding site 5 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca306 b:70.8 occ:1.00 O B:HOH587 3.2 57.5 1.0 O B:HOH573 3.3 54.1 1.0 O B:ARG41 3.9 29.6 1.0 N B:GLN44 4.0 32.6 1.0 C B:TYR43 4.0 32.2 1.0 O B:TYR43 4.2 33.7 1.0 CA B:GLN44 4.2 33.2 1.0 N B:TYR43 4.5 30.6 1.0 CA B:TYR43 4.5 31.7 1.0 C B:GLN42 4.5 30.0 1.0 CG B:ARG41 4.5 31.0 1.0 O B:HOH432 4.6 42.5 1.0 C B:ARG41 4.7 29.7 1.0 O B:GLN42 4.7 29.1 1.0 CB B:GLN44 4.8 34.9 1.0 O B:HOH472 4.9 41.9 1.0 CA B:GLN42 5.0 31.5 1.0

Calcium binding site 6 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca307 b:88.1 occ:1.00 OD2 B:ASP167 2.6 48.1 1.0 CG B:ASP167 3.5 45.9 1.0 OD1 B:ASP167 3.9 47.8 1.0 O B:HOH526 4.8 51.8 1.0 CB B:ASP167 4.8 41.3 1.0

Calcium binding site 7 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca308 b:78.2 occ:1.00 O B:HOH529 3.0 48.8 1.0 O B:ASP73 3.4 29.6 1.0 O B:ASN202 3.7 29.4 1.0 C B:ASP73 3.9 30.5 1.0 O B:HOH487 4.1 37.0 1.0 CD1 B:TYR74 4.2 31.9 1.0 OD1 B:ASN202 4.3 36.4 1.0 CA B:TYR74 4.3 30.2 1.0 CB B:ASP73 4.3 32.1 1.0 N B:TYR74 4.3 30.8 1.0 O B:HOH521 4.6 42.2 1.0 C B:ASN202 4.6 28.6 1.0 O B:HOH453 4.6 23.9 1.0 CA B:ASP73 4.8 30.7 1.0 CG B:ASN202 4.8 33.8 1.0 CE1 B:TYR74 4.8 32.1 1.0

Calcium binding site 8 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca307 b:27.9 occ:1.00 O C:GLU242 2.3 28.5 1.0 OD1 C:ASP240 2.3 28.9 1.0 O22 C:BCN301 2.3 29.5 1.0 O C:HOH481 2.4 33.5 1.0 O C:HOH499 2.5 32.7 1.0 O6 C:BCN301 2.5 28.1 1.0 O4 C:BCN301 2.6 30.5 1.0 N1 C:BCN301 2.8 30.6 1.0 CG C:ASP240 3.3 32.2 1.0 C2 C:BCN301 3.3 29.6 1.0 C4 C:BCN301 3.3 32.1 1.0 C6 C:BCN301 3.4 29.1 1.0 C5 C:BCN301 3.4 29.3 1.0 C3 C:BCN301 3.4 31.8 1.0 C C:GLU242 3.5 29.4 1.0 C1 C:BCN301 3.5 30.7 1.0 OD2 C:ASP240 3.6 35.5 1.0 N C:GLU242 4.0 28.5 1.0 O C:ASP240 4.1 28.1 1.0 CA C:GLU242 4.2 29.4 1.0 O C:HOH541 4.3 37.2 1.0 C C:ASP240 4.5 28.6 1.0 O21 C:BCN301 4.5 29.3 1.0 O C:HOH506 4.5 41.2 1.0 CB C:GLU242 4.5 30.7 1.0 CB C:ASN243 4.6 28.5 1.0 N C:ASN243 4.6 30.1 1.0 CB C:ASP240 4.6 31.3 1.0 N C:ASP240 4.8 30.8 1.0 CA C:ASP240 4.9 30.1 1.0 CA C:ASN243 4.9 28.8 1.0 OD1 C:ASN243 4.9 30.6 1.0 C C:ASN243 4.9 28.8 1.0

Calcium binding site 9 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca308 b:56.7 occ:0.50 O C:HOH467 2.1 35.2 0.5 O C:HOH435 2.3 46.5 1.0 OD2 C:ASP167 3.3 49.4 1.0 O C:HOH485 3.6 63.2 1.0 OD1 C:ASP167 3.8 49.5 1.0 CG C:ASP167 3.9 45.8 1.0 O C:HOH478 4.1 46.9 1.0 O C:ASP163 4.3 31.3 1.0 O C:LEU164 4.5 33.0 1.0

Calcium binding site 10 out of 13 in the AO75L in Complex with Udp-Xylose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of AO75L in Complex with Udp-Xylose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca305 b:29.4 occ:1.00 O D:GLU242 2.2 28.9 1.0 O22 D:BCN301 2.3 30.4 1.0 O D:HOH462 2.4 36.0 1.0 OD1 D:ASP240 2.4 28.8 1.0 O4 D:BCN301 2.5 31.1 1.0 O6 D:BCN301 2.5 30.6 1.0 O D:HOH485 2.6 28.9 1.0 N1 D:BCN301 2.7 30.2 1.0 C2 D:BCN301 3.3 29.7 1.0 C4 D:BCN301 3.3 31.7 1.0 C5 D:BCN301 3.4 30.6 1.0 C6 D:BCN301 3.4 30.6 1.0 CG D:ASP240 3.4 32.4 1.0 C3 D:BCN301 3.4 32.2 1.0 C D:GLU242 3.4 29.1 1.0 C1 D:BCN301 3.5 30.0 1.0 OD2 D:ASP240 3.8 34.9 1.0 N D:GLU242 4.0 28.8 1.0 CA D:GLU242 4.2 29.6 1.0 O D:ASP240 4.2 28.1 1.0 O D:HOH549 4.3 35.7 1.0 O21 D:BCN301 4.5 31.6 1.0 N D:ASN243 4.5 30.5 1.0 CB D:ASN243 4.5 30.0 1.0 CB D:GLU242 4.5 31.5 1.0 C D:ASP240 4.5 29.3 1.0 O D:HOH552 4.6 49.0 1.0 CB D:ASP240 4.7 30.1 1.0 OD1 D:ASN243 4.8 34.1 1.0 N D:ASP240 4.8 28.8 1.0 CA D:ASN243 4.8 30.1 1.0 C D:ASN243 4.9 30.1 1.0 CA D:ASP240 4.9 29.3 1.0 C D:TRP241 5.0 28.6 1.0

M.E.Laugeri, I.Speciale, A.Gimeno, S.Lin, A.Poveda, T.Lowary, J.L.Van Etten, J.J.Barbero, C.De Castro, M.Tonetti, A.L.Rojas. AO75L in Complex with Udp-Xylose To Be Published.