Calcium in PDB 1g5n: Annexin V Complex with Heparin Oligosaccharides

The structure of Annexin V Complex with Heparin Oligosaccharides, PDB code: 1g5n was solved by I.Capila, M.J.Heraiz, Y.D.Mo, T.R.Mealy, B.Campos, J.R.Dedman, R.J.Linhardt, B.A.Seaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	155.874, 155.874, 37.344, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 23.8

The binding sites of Calcium atom in the Annexin V Complex with Heparin Oligosaccharides (pdb code 1g5n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Annexin V Complex with Heparin Oligosaccharides, PDB code: 1g5n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:21.4 occ:1.00 O A:HOH537 2.2 23.2 1.0 O A:HOH562 2.3 20.6 1.0 O A:MET26 2.3 16.7 1.0 OE1 A:GLU70 2.4 17.6 1.0 O A:GLY28 2.4 24.7 1.0 OE2 A:GLU70 2.5 17.4 1.0 O A:GLY30 2.5 22.9 1.0 CD A:GLU70 2.7 15.9 1.0 C A:MET26 3.5 20.3 1.0 C A:GLY28 3.6 25.6 1.0 C A:GLY30 3.7 23.5 1.0 N A:GLY30 4.0 25.1 1.0 CA A:MET26 4.1 19.6 1.0 N A:GLY28 4.2 23.3 1.0 O3S A:UAP801 4.2 73.1 1.0 C A:LEU29 4.3 24.7 1.0 CG A:GLU70 4.3 17.4 1.0 OG1 A:THR31 4.3 20.4 1.0 C A:LYS27 4.4 22.1 1.0 CA A:GLY30 4.4 24.1 1.0 CA A:GLY28 4.5 24.7 1.0 O A:HOH733 4.5 38.3 1.0 N A:LYS27 4.5 21.7 1.0 N A:LEU29 4.6 26.2 1.0 CA A:LEU29 4.6 25.8 1.0 O A:HOH518 4.6 17.8 1.0 CB A:MET26 4.7 20.3 1.0 N A:THR31 4.7 23.3 1.0 O A:LYS27 4.7 21.5 1.0 O A:LEU29 4.7 23.3 1.0 CA A:LYS27 4.7 22.8 1.0 CA A:THR31 4.9 21.9 1.0

Calcium binding site 2 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:25.8 occ:1.00 O A:HOH579 2.1 28.1 1.0 O A:LEU71 2.2 20.6 1.0 O A:LYS68 2.2 22.1 1.0 OE2 A:GLU76 2.4 26.9 1.0 O A:HOH490 2.4 30.7 1.0 O A:HOH527 2.5 20.9 1.0 CD A:GLU76 3.1 25.8 1.0 OE1 A:GLU76 3.2 27.8 1.0 C A:LEU71 3.3 20.6 1.0 C A:LYS68 3.4 22.0 1.0 O2S A:SGN804 3.9 53.2 1.0 CA A:THR72 3.9 22.9 1.0 N A:THR72 4.1 22.4 1.0 CA A:LYS68 4.2 20.8 1.0 CB A:THR72 4.3 25.6 1.0 O A:SER69 4.4 18.1 1.0 CA A:LEU71 4.4 20.7 1.0 CG A:GLU76 4.4 23.0 1.0 N A:SER69 4.4 20.4 1.0 N A:LEU71 4.5 20.6 1.0 C A:SER69 4.5 18.7 1.0 CA A:SER69 4.6 20.1 1.0 O1S A:SGN804 4.7 53.5 1.0 OG1 A:THR72 4.8 30.5 1.0 CB A:LYS68 4.9 22.5 1.0 CB A:GLU76 4.9 21.9 1.0 S1 A:SGN804 4.9 52.9 1.0

Calcium binding site 3 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.1 occ:1.00 O A:HOH623 2.3 28.7 1.0 O A:THR31 2.4 22.4 1.0 OE2 A:GLU33 2.5 21.7 1.0 O A:HOH677 2.6 32.2 1.0 OE1 A:GLU33 3.0 22.3 1.0 CD A:GLU33 3.1 23.0 1.0 C A:THR31 3.6 22.4 1.0 N A:THR31 3.9 23.3 1.0 O A:HOH650 4.2 37.6 1.0 CA A:THR31 4.3 21.9 1.0 CG A:GLU33 4.6 22.7 1.0 CB A:THR31 4.6 21.0 1.0 N A:GLU33 4.7 21.0 1.0 N A:ASP32 4.7 20.8 1.0 CA A:ASP32 4.9 20.8 1.0

Calcium binding site 4 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:42.5 occ:1.00 OD1 A:ASP142 2.3 32.3 1.0 O A:GLY100 2.4 35.0 1.0 O A:GLY102 2.5 31.4 1.0 O A:HOH730 2.5 39.5 1.0 O A:LEU98 2.6 31.7 1.0 CG A:ASP142 3.0 26.9 1.0 OD2 A:ASP142 3.3 28.1 1.0 C A:LEU98 3.3 29.8 1.0 C A:GLY100 3.5 36.6 1.0 OG1 A:THR103 3.6 29.1 1.0 O A:ALA101 3.7 38.2 1.0 C A:GLY102 3.7 31.2 1.0 C A:ALA101 3.9 36.6 1.0 O A:LYS99 3.9 35.6 1.0 C A:LYS99 4.0 35.0 1.0 CA A:LEU98 4.0 27.9 1.0 N A:GLY100 4.2 36.1 1.0 N A:LYS99 4.2 32.1 1.0 N A:GLY102 4.3 35.4 1.0 CB A:ASP142 4.3 23.3 1.0 N A:ALA101 4.4 37.1 1.0 CA A:ALA101 4.4 37.5 1.0 CA A:GLY100 4.4 35.8 1.0 CA A:LYS99 4.5 35.7 1.0 CA A:THR103 4.5 27.0 1.0 N A:THR103 4.5 28.4 1.0 CA A:GLY102 4.6 32.9 1.0 CB A:THR103 4.7 27.5 1.0 CB A:LEU98 4.7 26.5 1.0 O A:ALA97 4.9 25.1 1.0

Calcium binding site 5 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:26.3 occ:1.00 O A:HOH645 2.2 43.0 1.0 O A:THR103 2.3 22.1 1.0 O A:HOH569 2.4 26.2 1.0 OE1 A:GLU105 2.4 16.7 1.0 O A:HOH485 2.5 33.0 1.0 O A:HOH732 2.6 37.2 1.0 CD A:GLU105 3.3 19.4 1.0 OE2 A:GLU105 3.5 16.5 1.0 C A:THR103 3.5 24.4 1.0 N A:THR103 4.1 28.4 1.0 CA A:THR103 4.3 27.0 1.0 N A:GLU105 4.4 20.1 1.0 O A:HOH735 4.4 38.7 1.0 N A:ASP104 4.5 23.6 1.0 CA A:ASP104 4.6 22.8 1.0 CB A:THR103 4.7 27.5 1.0 CG A:GLU105 4.7 17.9 1.0

Calcium binding site 6 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:14.6 occ:1.00 O A:LYS184 2.3 9.6 1.0 O A:GLY181 2.3 10.7 1.0 O A:GLY186 2.4 12.5 1.0 OE1 A:GLU226 2.4 11.5 1.0 OE2 A:GLU226 2.6 14.9 1.0 O A:HOH671 2.8 35.2 1.0 CD A:GLU226 2.8 13.0 1.0 C A:GLY181 3.4 11.4 1.0 C A:LYS184 3.5 12.4 1.0 C A:GLY186 3.5 12.9 1.0 N A:GLY186 3.7 12.6 1.0 N A:LYS184 4.2 13.4 1.0 CA A:GLY181 4.2 11.8 1.0 CA A:LYS184 4.2 13.3 1.0 CA A:GLY186 4.2 13.6 1.0 N A:GLU182 4.3 10.2 1.0 OG1 A:THR187 4.3 13.0 1.0 O A:HOH580 4.3 29.1 1.0 CG A:GLU226 4.3 11.8 1.0 CA A:GLU182 4.4 10.7 1.0 O A:HOH550 4.4 16.4 1.0 CB A:LYS184 4.4 14.5 1.0 O A:GLU182 4.5 11.6 1.0 C A:GLU182 4.5 12.4 1.0 N A:TRP185 4.5 12.9 1.0 C A:TRP185 4.5 14.1 1.0 N A:THR187 4.6 14.1 1.0 CA A:TRP185 4.7 13.7 1.0 CA A:THR187 4.8 12.8 1.0

Calcium binding site 7 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:17.9 occ:1.00 O A:ASP224 2.2 16.4 1.0 O A:THR227 2.3 12.9 1.0 OE2 A:GLU232 2.3 22.2 1.0 O A:HOH444 2.4 22.3 1.0 O A:HOH573 2.4 19.1 1.0 O A:HOH525 2.4 18.6 1.0 OD2 A:ASP224 2.6 23.5 1.0 C A:ASP224 3.2 17.7 1.0 CD A:GLU232 3.3 20.8 1.0 C A:THR227 3.5 13.8 1.0 CA A:ASP224 3.7 17.8 1.0 CG A:ASP224 3.7 24.4 1.0 OE1 A:GLU232 3.9 26.3 1.0 CA A:SER228 4.2 13.3 1.0 N A:SER228 4.3 13.9 1.0 CB A:ASP224 4.3 21.0 1.0 CB A:SER228 4.3 12.4 1.0 N A:ARG225 4.4 15.1 1.0 CG A:GLU232 4.5 19.1 1.0 N A:THR227 4.5 13.5 1.0 O A:ILE223 4.5 15.8 1.0 CA A:THR227 4.6 13.2 1.0 O A:HOH629 4.6 23.8 1.0 OD1 A:ASP224 4.7 26.6 1.0 N A:ASP224 4.9 16.1 1.0 CA A:ARG225 4.9 15.8 1.0 CB A:GLU232 5.0 14.5 1.0 C A:ARG225 5.0 17.1 1.0

Calcium binding site 8 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:45.8 occ:1.00 O A:HOH455 2.4 33.0 1.0 OE1 A:GLU189 2.4 17.6 1.0 O A:THR187 2.4 12.9 1.0 CD A:GLU189 3.1 19.7 1.0 OE2 A:GLU189 3.1 22.1 1.0 C A:THR187 3.6 13.5 1.0 N A:THR187 4.1 14.1 1.0 CA A:THR187 4.3 12.8 1.0 CG A:GLU189 4.5 17.7 1.0 CB A:THR187 4.6 12.9 1.0 N A:GLU189 4.6 13.3 1.0 O A:HOH465 4.6 30.0 1.0 N A:ASP188 4.7 14.0 1.0 O A:HOH609 4.7 17.3 1.0 CA A:ASP188 4.8 15.5 1.0 CE1 A:TYR146 4.8 21.5 1.0 OH A:TYR146 4.9 25.6 1.0

Calcium binding site 9 out of 9 in the Annexin V Complex with Heparin Oligosaccharides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Annexin V Complex with Heparin Oligosaccharides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca410 b:44.5 occ:1.00 OD1 A:ASP301 2.4 31.2 1.0 O A:GLY261 2.4 48.7 1.0 OD2 A:ASP301 2.6 37.1 1.0 O A:GLY259 2.7 61.5 1.0 CG A:ASP301 2.8 33.5 1.0 O A:MET257 3.0 44.7 1.0 O A:HOH657 3.1 54.9 1.0 C A:GLY261 3.5 49.1 1.0 C A:MET257 3.6 44.4 1.0 C A:GLY259 3.8 60.8 1.0 CA A:MET257 4.0 40.2 1.0 N A:GLY261 4.0 55.3 1.0 N A:GLY259 4.3 59.0 1.0 CA A:GLY261 4.3 51.9 1.0 CB A:ASP301 4.3 32.7 1.0 N A:THR262 4.4 46.5 1.0 N A:LYS258 4.4 50.3 1.0 CB A:THR262 4.4 44.3 1.0 CA A:THR262 4.5 43.5 1.0 CB A:MET257 4.6 37.1 1.0 C A:LYS258 4.6 57.1 1.0 CA A:GLY259 4.6 60.5 1.0 CG2 A:THR262 4.6 42.8 1.0 O A:HOH658 4.7 60.8 1.0 C A:ALA260 4.7 58.2 1.0 N A:ALA260 4.9 60.8 1.0 CA A:ASP301 4.9 31.0 1.0 CA A:LYS258 4.9 55.7 1.0

I.Capila, M.J.Hernaiz, Y.D.Mo, T.R.Mealy, B.Campos, J.R.Dedman, R.J.Linhardt, B.A.Seaton. Annexin V--Heparin Oligosaccharide Complex Suggests Heparan Sulfate--Mediated Assembly on Cell Surfaces. Structure V. 9 57 2001.
ISSN: ISSN 0969-2126
PubMed: 11342135
DOI: 10.1016/S0969-2126(00)00549-9