Calcium in PDB 6ghv: Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.

The structure of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic., PDB code: 6ghv was solved by M.Thepaut, S.Achilli, L.Medve, A.Bernardi, F.Fieschi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	105.612, 57.507, 107.247, 90.00, 118.67, 90.00
R / Rfree (%)	17.6 / 23.4

The structure of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. also contains other interesting chemical elements:

Chlorine

(Cl)

20 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. (pdb code 6ghv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic., PDB code: 6ghv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:30.0 occ:1.00 OD1 A:ASP366 2.2 27.1 1.0 OE1 A:GLU347 2.4 34.7 1.0 OD1 A:ASN365 2.4 22.9 1.0 OE1 A:GLU354 2.4 32.5 1.0 O A:ASP366 2.4 25.7 1.0 OD1 A:ASN349 2.5 26.9 1.0 O3 A:EZ81001 2.6 29.4 1.0 O4 A:EZ81001 2.7 30.1 1.0 CG A:ASP366 3.2 28.1 1.0 CD A:GLU347 3.2 38.5 1.0 CD A:GLU354 3.3 32.8 1.0 CG A:ASN365 3.4 27.4 1.0 CG A:ASN349 3.4 28.4 1.0 C3 A:EZ81001 3.4 29.5 1.0 C4 A:EZ81001 3.5 30.8 1.0 C A:ASP366 3.5 27.2 1.0 OE2 A:GLU347 3.6 41.3 1.0 N A:ASP366 3.6 28.8 1.0 OE2 A:GLU354 3.7 37.1 1.0 ND2 A:ASN365 3.7 22.6 1.0 ND2 A:ASN349 3.9 28.0 1.0 CA A:ASP366 3.9 25.7 1.0 OD2 A:ASP366 4.0 32.3 1.0 CB A:ASP366 4.1 28.4 1.0 N A:ASN349 4.2 31.5 1.0 CG A:GLU347 4.5 35.6 1.0 CG A:GLU354 4.5 30.6 1.0 C A:ASN365 4.6 26.5 1.0 N A:ASN350 4.6 34.1 1.0 CG1 A:VAL351 4.6 40.1 1.0 N A:ASP367 4.6 26.6 1.0 CB A:GLU354 4.6 29.7 1.0 CB A:ASN349 4.6 31.9 1.0 CB A:ASN365 4.7 25.1 1.0 C2 A:EZ81001 4.8 28.1 1.0 CA A:ASN349 4.9 32.6 1.0 C5 A:EZ81001 4.9 29.8 1.0 CB A:GLU347 4.9 34.0 1.0 CA A:ASN365 4.9 27.7 1.0 N A:VAL351 5.0 37.2 1.0

Calcium binding site 2 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:30.0 occ:1.00 O A:HOH1129 2.1 30.0 1.0 OD1 A:ASP355 2.2 19.9 1.0 OE1 A:GLU324 2.4 34.7 1.0 OD2 A:ASP320 2.5 27.8 1.0 OD1 A:ASP320 2.5 29.3 1.0 OD1 A:ASN350 2.5 35.9 1.0 O A:GLU354 2.5 24.0 1.0 OE2 A:GLU324 2.6 30.8 1.0 CD A:GLU324 2.8 32.6 1.0 CG A:ASP320 2.9 27.6 1.0 CG A:ASN350 3.3 35.8 1.0 CG A:ASP355 3.4 22.1 1.0 C A:GLU354 3.4 25.3 1.0 CA A:ASP355 3.7 24.8 1.0 N A:ASP355 3.9 24.0 1.0 CB A:ASN350 3.9 34.3 1.0 O A:HOH1118 3.9 23.9 1.0 CB A:ASP355 4.0 24.1 1.0 ND2 A:ASN350 4.1 37.3 1.0 O A:HOH1102 4.2 35.6 1.0 O A:HOH1147 4.2 41.0 1.0 N A:GLU354 4.2 30.7 1.0 CZ2 A:TRP327 4.3 31.9 1.0 OD2 A:ASP355 4.3 22.1 1.0 CG A:GLU324 4.3 34.2 1.0 CA A:ASN350 4.4 34.9 1.0 CB A:ASP320 4.4 26.0 1.0 CA A:GLU354 4.5 28.7 1.0 OD2 A:ASP366 4.6 32.3 1.0 O A:ASP320 4.7 26.0 1.0 CH2 A:TRP327 4.9 29.3 1.0 O A:HOH1111 4.9 37.5 1.0 N A:GLY325 4.9 32.6 1.0 C A:ASP355 5.0 28.1 1.0 CA A:GLU324 5.0 34.1 1.0

Calcium binding site 3 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:49.0 occ:1.00 O A:HOH1139 1.9 38.0 1.0 OD2 A:ASP355 2.2 22.1 1.0 O A:HOH1118 2.2 23.9 1.0 O A:HOH1102 2.3 35.6 1.0 CG A:ASP355 3.2 22.1 1.0 OD1 A:ASP355 3.5 19.9 1.0 OE1 A:GLU324 3.9 34.7 1.0 O A:LEU321 4.3 35.5 1.0 CB A:ASP355 4.4 24.1 1.0 O A:HOH1171 4.4 57.5 1.0 O A:ASP320 4.5 26.0 1.0 CA A:LEU321 4.7 32.8 1.0 O A:HOH1144 4.7 32.0 1.0 C A:LEU321 4.9 37.4 1.0 OE1 A:GLU353 4.9 51.9 1.0

Calcium binding site 4 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:22.1 occ:1.00 OE1 B:GLU354 2.2 18.9 1.0 OD1 B:ASP366 2.3 20.6 1.0 OD1 B:ASN349 2.4 22.5 1.0 OE1 B:GLU347 2.5 26.2 1.0 O4 B:EZ81001 2.5 22.7 1.0 OD1 B:ASN365 2.5 27.4 1.0 O B:ASP366 2.5 16.9 1.0 O3 B:EZ81001 2.6 22.0 1.0 CD B:GLU354 3.2 23.8 1.0 CG B:ASP366 3.3 21.8 1.0 CD B:GLU347 3.3 26.3 1.0 C3 B:EZ81001 3.3 22.2 1.0 C4 B:EZ81001 3.3 23.6 1.0 CG B:ASN349 3.4 26.9 1.0 CG B:ASN365 3.5 26.7 1.0 OE2 B:GLU347 3.5 24.3 1.0 C B:ASP366 3.6 22.0 1.0 OE2 B:GLU354 3.7 23.3 1.0 ND2 B:ASN365 3.8 25.8 1.0 N B:ASP366 3.8 20.9 1.0 ND2 B:ASN349 3.8 25.9 1.0 OD2 B:ASP366 3.9 23.4 1.0 CA B:ASP366 4.1 20.4 1.0 N B:ASN349 4.2 27.7 1.0 CB B:ASP366 4.3 19.8 1.0 CG1 B:VAL351 4.3 25.6 1.0 CG B:GLU354 4.5 24.6 1.0 CG B:GLU347 4.5 25.7 1.0 CB B:ASN349 4.6 25.2 1.0 N B:ASN350 4.7 25.2 1.0 CB B:GLU354 4.7 24.6 1.0 C2 B:EZ81001 4.7 23.8 1.0 C5 B:EZ81001 4.7 25.1 1.0 N B:ASP367 4.8 21.0 1.0 CB B:ASN365 4.8 26.7 1.0 C B:ASN365 4.8 22.9 1.0 CA B:ASN349 4.9 26.2 1.0

Calcium binding site 5 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1003 b:25.6 occ:1.00 OD1 B:ASP355 2.3 28.7 1.0 O B:GLU354 2.3 26.9 1.0 O B:HOH1133 2.4 18.5 1.0 OD2 B:ASP320 2.4 28.1 1.0 OD1 B:ASP320 2.5 21.2 1.0 OE1 B:GLU324 2.6 32.6 1.0 OD1 B:ASN350 2.6 28.4 1.0 OE2 B:GLU324 2.8 29.5 1.0 CG B:ASP320 2.8 26.1 1.0 CD B:GLU324 3.0 29.6 1.0 C B:GLU354 3.3 27.1 1.0 CG B:ASN350 3.4 26.9 1.0 CG B:ASP355 3.4 28.7 1.0 CA B:ASP355 3.7 28.4 1.0 N B:ASP355 4.0 27.6 1.0 O B:HOH1164 4.1 36.4 1.0 CB B:ASP355 4.1 27.9 1.0 CB B:ASN350 4.1 25.6 1.0 N B:GLU354 4.2 28.9 1.0 CZ2 B:TRP327 4.2 25.8 1.0 CB B:ASP320 4.3 25.2 1.0 O B:HOH1155 4.3 23.3 1.0 ND2 B:ASN350 4.3 23.1 1.0 CA B:GLU354 4.4 25.2 1.0 O B:HOH1126 4.4 28.2 1.0 OD2 B:ASP355 4.5 32.3 1.0 CA B:ASN350 4.5 25.1 1.0 CG B:GLU324 4.5 27.8 1.0 CH2 B:TRP327 4.5 27.0 1.0 OD2 B:ASP366 4.5 23.4 1.0 O B:ASP320 4.8 24.7 1.0 N B:GLY325 4.9 30.2 1.0 C B:ASP355 4.9 28.9 1.0

Calcium binding site 6 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:54.3 occ:1.00 OD2 B:ASP355 2.1 32.3 1.0 O B:HOH1148 2.1 29.9 1.0 O B:HOH1212 2.1 29.1 1.0 O B:HOH1155 2.2 23.3 1.0 O B:HOH1108 2.2 28.6 1.0 O B:HOH1126 2.3 28.2 1.0 CG B:ASP355 3.1 28.7 1.0 OD1 B:ASP355 3.5 28.7 1.0 OE1 B:GLU324 4.0 32.6 1.0 O B:HOH1171 4.3 34.0 1.0 O B:LEU321 4.3 34.0 1.0 CB B:ASP355 4.4 27.9 1.0 OE2 B:GLU353 4.4 39.6 1.0 O B:HOH1191 4.4 28.9 1.0 O B:ASP320 4.7 24.7 1.0 CA B:LEU321 4.7 25.9 1.0 CD B:GLU353 4.8 39.2 1.0 C B:LEU321 5.0 28.5 1.0

Calcium binding site 7 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1002 b:25.7 occ:1.00 OE1 C:GLU354 2.3 24.8 1.0 OD1 C:ASN365 2.3 21.1 1.0 O C:ASP366 2.4 23.2 1.0 OD1 C:ASP366 2.4 24.5 1.0 O3 C:EZ81001 2.5 23.9 1.0 O4 C:EZ81001 2.5 24.4 1.0 OE1 C:GLU347 2.5 33.4 1.0 OD1 C:ASN349 2.7 25.4 1.0 CD C:GLU354 3.2 26.9 1.0 C3 C:EZ81001 3.3 23.9 1.0 CG C:ASN365 3.3 23.6 1.0 CD C:GLU347 3.3 33.2 1.0 CG C:ASP366 3.3 25.5 1.0 C4 C:EZ81001 3.4 23.8 1.0 C C:ASP366 3.5 23.9 1.0 OE2 C:GLU354 3.5 25.1 1.0 CG C:ASN349 3.6 27.8 1.0 OE2 C:GLU347 3.6 31.3 1.0 ND2 C:ASN365 3.6 20.7 1.0 N C:ASP366 3.8 25.1 1.0 ND2 C:ASN349 3.9 26.7 1.0 CA C:ASP366 4.0 24.7 1.0 OD2 C:ASP366 4.0 30.5 1.0 CB C:ASP366 4.2 25.3 1.0 N C:ASN349 4.3 28.9 1.0 CG1 C:VAL351 4.5 33.7 1.0 CG C:GLU354 4.5 27.3 1.0 CG C:GLU347 4.5 32.0 1.0 N C:ASP367 4.6 23.3 1.0 CB C:ASN365 4.6 24.6 1.0 C C:ASN365 4.7 25.6 1.0 C2 C:EZ81001 4.7 23.9 1.0 CB C:GLU354 4.7 27.9 1.0 C5 C:EZ81001 4.7 26.3 1.0 N C:ASN350 4.8 26.8 1.0 CB C:ASN349 4.8 28.5 1.0 CA C:ASN365 4.9 25.1 1.0 CB C:GLU347 4.9 31.0 1.0 CA C:ASN349 5.0 30.6 1.0

Calcium binding site 8 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1003 b:27.9 occ:1.00 O C:HOH1121 2.2 24.9 1.0 OD1 C:ASP355 2.4 28.4 1.0 O C:GLU354 2.5 23.0 1.0 OD1 C:ASN350 2.5 28.5 1.0 OE1 C:GLU324 2.5 29.8 1.0 OD1 C:ASP320 2.5 29.7 1.0 OD2 C:ASP320 2.5 27.7 1.0 OE2 C:GLU324 2.8 29.5 1.0 CG C:ASP320 2.9 29.4 1.0 CD C:GLU324 3.0 30.8 1.0 CG C:ASN350 3.2 26.4 1.0 C C:GLU354 3.4 26.1 1.0 CG C:ASP355 3.5 26.3 1.0 CA C:ASP355 3.8 26.8 1.0 CB C:ASN350 3.9 26.6 1.0 O C:HOH1126 4.0 31.9 1.0 ND2 C:ASN350 4.0 28.7 1.0 N C:ASP355 4.0 27.7 1.0 O C:HOH1183 4.1 32.6 1.0 N C:GLU354 4.2 28.5 1.0 CB C:ASP355 4.2 26.0 1.0 O C:HOH1112 4.3 31.8 1.0 CA C:GLU354 4.4 26.4 1.0 CZ2 C:TRP327 4.4 29.0 1.0 CA C:ASN350 4.4 27.7 1.0 CB C:ASP320 4.5 27.7 1.0 OD2 C:ASP355 4.5 28.3 1.0 OD2 C:ASP366 4.5 30.5 1.0 CG C:GLU324 4.6 30.7 1.0 O C:ASP320 4.8 28.8 1.0 CH2 C:TRP327 4.8 31.3 1.0 O C:HOH1101 4.8 38.7 1.0 N C:GLY325 4.9 30.1 1.0 CA C:CA1004 5.0 51.4 1.0 CB C:GLU354 5.0 27.9 1.0 C C:ASP355 5.0 27.1 1.0

Calcium binding site 9 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1004 b:51.4 occ:1.00 O C:HOH1126 2.0 31.9 1.0 O C:HOH1112 2.0 31.8 1.0 O C:HOH1130 2.0 37.8 1.0 OD2 C:ASP355 2.1 28.3 1.0 O C:HOH1221 2.1 34.0 1.0 O C:HOH1128 2.3 34.6 1.0 CG C:ASP355 3.0 26.3 1.0 OD1 C:ASP355 3.3 28.4 1.0 OE1 C:GLU324 3.7 29.8 1.0 CB C:ASP355 4.3 26.0 1.0 O C:HOH1119 4.4 47.0 1.0 O C:LEU321 4.4 34.6 1.0 O C:HOH1168 4.4 42.0 1.0 O C:ASP320 4.5 28.8 1.0 CA C:LEU321 4.6 29.6 1.0 O C:HOH1161 4.8 22.4 0.5 OE2 C:GLU353 4.8 66.7 1.0 CD C:GLU324 4.9 30.8 1.0 CD2 C:LEU321 4.9 32.5 1.0 O C:HOH1161 4.9 23.9 0.5 C C:LEU321 4.9 32.6 1.0 CA C:CA1003 5.0 27.9 1.0

Calcium binding site 10 out of 18 in the Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of A Dc-Sign Crd in Complex with High Affinity Glycomimetic. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca503 b:26.6 occ:1.00 OE1 D:GLU354 2.2 22.0 1.0 OD1 D:ASP366 2.4 23.6 1.0 OE1 D:GLU347 2.5 32.9 1.0 O D:ASP366 2.5 27.4 1.0 O3 D:EZ8502 2.5 27.1 1.0 OD1 D:ASN349 2.5 30.2 1.0 O4 D:EZ8502 2.5 30.2 1.0 OD1 D:ASN365 2.7 25.6 1.0 CG D:ASP366 3.3 25.5 1.0 CD D:GLU354 3.3 27.8 1.0 C3 D:EZ8502 3.3 28.4 1.0 C4 D:EZ8502 3.4 28.6 1.0 CG D:ASN349 3.4 29.7 1.0 CD D:GLU347 3.4 33.5 1.0 C D:ASP366 3.5 26.2 1.0 CG D:ASN365 3.6 28.6 1.0 OE2 D:GLU354 3.7 30.6 1.0 ND2 D:ASN349 3.7 27.1 1.0 ND2 D:ASN365 3.8 30.2 1.0 OE2 D:GLU347 3.9 40.4 1.0 N D:ASP366 3.9 25.9 1.0 OD2 D:ASP366 4.0 25.2 1.0 CA D:ASP366 4.0 24.5 1.0 CB D:ASP366 4.2 25.5 1.0 N D:ASN349 4.3 31.2 1.0 CG1 D:VAL351 4.3 46.3 1.0 CG D:GLU354 4.5 28.1 1.0 N D:ASN350 4.6 26.8 1.0 CB D:GLU354 4.6 28.5 1.0 CG D:GLU347 4.6 34.4 1.0 CB D:ASN349 4.7 29.7 1.0 N D:ASP367 4.7 27.5 1.0 C2 D:EZ8502 4.7 25.9 1.0 C5 D:EZ8502 4.7 30.1 1.0 C D:ASN365 4.8 26.3 1.0 N D:VAL351 4.8 38.0 1.0 CA D:ASN349 4.9 31.5 1.0 CB D:ASN365 4.9 25.2 1.0 CB D:GLU347 4.9 37.2 1.0

L.Medve, S.Achilli, J.Guzman-Caldentey, M.Thepaut, L.Senaldi, A.Le Roy, S.Sattin, C.Ebel, C.Vives, S.Martin-Santamaria, A.Bernardi, F.Fieschi. Enhancing Potency and Selectivity of A Dc-Sign Glycomimetic Ligand By Fragment-Based Design: Structural Basis. Chemistry V. 25 14659 2019.
ISSN: ISSN 0947-6539
PubMed: 31469191
DOI: 10.1002/CHEM.201903391