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Calcium in PDB 2hyv: Human Annexin A2 with Heparin Hexasaccharide Bound

Protein crystallography data

The structure of Human Annexin A2 with Heparin Hexasaccharide Bound, PDB code: 2hyv was solved by C.Shao, J.F.Head, B.A.Seaton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.42
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.709, 54.292, 68.571, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 22.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Annexin A2 with Heparin Hexasaccharide Bound (pdb code 2hyv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Human Annexin A2 with Heparin Hexasaccharide Bound, PDB code: 2hyv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2hyv

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Calcium binding site 1 out of 5 in the Human Annexin A2 with Heparin Hexasaccharide Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Annexin A2 with Heparin Hexasaccharide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:19.5
occ:1.00
 O A:HOH812 2.3 27.1 1.0
O A:HOH810 2.4 26.6 1.0
O A:GLY49 2.4 22.3 1.0
O A:VAL50 2.4 19.9 1.0
O A:HOH811 2.4 26.9 1.0
O A:HOH813 2.5 30.9 1.0
OE2 A:GLU52 2.5 19.3 1.0
OE1 A:GLU52 2.5 18.4 1.0
CD A:GLU52 2.8 17.2 1.0
C A:GLY49 3.4 22.5 1.0
C A:VAL50 3.5 18.9 1.0
N A:VAL50 4.1 21.8 1.0
CA A:VAL50 4.1 20.6 1.0
O A:HOH1011 4.2 38.6 1.0
CB A:VAL50 4.2 19.9 1.0
CA A:GLY49 4.3 23.5 1.0
CG A:GLU52 4.3 17.1 1.0
O A:HOH850 4.4 22.1 1.0
O A:HOH1267 4.5 46.4 1.0
O A:HOH1236 4.5 49.1 1.0
O A:HOH1105 4.5 40.4 1.0
O A:HOH927 4.6 25.9 1.0
N A:GLU52 4.6 15.4 1.0
N A:ASP51 4.6 17.8 1.0
CG1 A:VAL50 4.9 20.7 1.0
O A:HOH836 4.9 19.2 1.0
CA A:ASP51 5.0 17.3 1.0

Calcium binding site 2 out of 5 in 2hyv

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Calcium binding site 2 out of 5 in the Human Annexin A2 with Heparin Hexasaccharide Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Annexin A2 with Heparin Hexasaccharide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:21.0
occ:1.00
 O A:LYS87 2.3 20.8 1.0
O A:LEU90 2.3 18.2 1.0
O A:HOH816 2.3 25.3 1.0
O A:HOH817 2.4 26.6 1.0
OE2 A:GLU95 2.4 21.6 1.0
O A:HOH815 2.5 44.2 1.0
O A:HOH814 2.6 34.1 1.0
CD A:GLU95 3.3 20.7 1.0
C A:LEU90 3.5 16.6 1.0
C A:LYS87 3.5 20.5 1.0
OE1 A:GLU95 3.7 24.0 1.0
CA A:SER91 4.1 17.1 1.0
N A:SER91 4.2 17.6 1.0
O A:SER88 4.3 22.4 1.0
CB A:SER91 4.4 19.1 1.0
N A:SER88 4.4 20.6 1.0
CA A:SER88 4.4 21.4 1.0
C A:SER88 4.4 21.6 1.0
CA A:LYS87 4.5 19.1 1.0
N A:LEU90 4.5 16.3 1.0
CA A:LEU90 4.6 16.4 1.0
CG A:LYS87 4.6 24.1 1.0
O A:HOH1089 4.6 36.0 1.0
CG A:GLU95 4.6 17.6 1.0
O A:HOH1029 4.7 46.9 1.0

Calcium binding site 3 out of 5 in 2hyv

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Calcium binding site 3 out of 5 in the Human Annexin A2 with Heparin Hexasaccharide Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Annexin A2 with Heparin Hexasaccharide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:23.4
occ:1.00
 O A:ARG204 2.3 30.6 1.0
O A:GLY201 2.3 23.4 1.0
OE1 A:GLU246 2.3 22.5 1.0
O A:GLY206 2.4 27.8 1.0
O A:HOH819 2.4 28.7 1.0
O A:HOH818 2.5 27.5 1.0
OE2 A:GLU246 2.5 21.7 1.0
CD A:GLU246 2.8 22.1 1.0
C A:GLY201 3.2 23.5 1.0
C A:GLY206 3.5 27.8 1.0
C A:ARG204 3.5 30.8 1.0
N A:GLY206 3.7 29.8 1.0
N A:VAL202 4.0 23.1 1.0
CA A:GLY201 4.0 22.4 1.0
C A:LYS205 4.1 30.9 1.0
CA A:GLY206 4.2 28.9 1.0
OG1 A:THR207 4.2 26.7 1.0
CA A:VAL202 4.2 24.6 1.0
CG A:GLU246 4.3 21.3 1.0
CA A:LYS205 4.3 31.7 1.0
N A:LYS205 4.4 31.6 1.0
C A:VAL202 4.4 24.9 1.0
N A:ARG204 4.5 29.4 1.0
O A:VAL202 4.5 24.8 1.0
CA A:ARG204 4.5 30.3 1.0
O A:HOH935 4.5 29.9 1.0
O A:HOH924 4.6 30.4 1.0
N A:THR207 4.6 26.9 1.0
O A:HOH1125 4.6 42.7 1.0
CG A:ARG204 4.7 29.4 1.0
O A:LYS205 4.7 31.2 1.0
CA A:THR207 4.8 25.8 1.0
O A:HOH1094 4.9 33.6 1.0

Calcium binding site 4 out of 5 in 2hyv

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Calcium binding site 4 out of 5 in the Human Annexin A2 with Heparin Hexasaccharide Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Annexin A2 with Heparin Hexasaccharide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:15.6
occ:1.00
 O A:MET277 2.3 14.5 1.0
O A:HOH807 2.3 18.5 1.0
O A:GLY279 2.4 15.8 1.0
OD1 A:ASP321 2.5 16.4 1.0
O A:GLY281 2.5 15.7 1.0
O A:HOH806 2.5 23.8 1.0
OD2 A:ASP321 2.6 15.0 1.0
CG A:ASP321 2.9 16.6 1.0
C A:MET277 3.4 14.7 1.0
C A:GLY279 3.6 16.0 1.0
C A:GLY281 3.6 15.4 1.0
N A:GLY281 4.0 15.8 1.0
O A:HOH1258 4.1 40.6 1.0
C A:LYS280 4.1 16.0 1.0
CA A:MET277 4.1 13.5 1.0
C A:LYS278 4.2 16.2 1.0
N A:GLY279 4.2 16.0 1.0
O A:LYS278 4.3 16.1 1.0
CA A:GLY281 4.3 15.6 1.0
CB A:ASP321 4.4 15.1 1.0
OG1 A:THR282 4.4 14.2 1.0
O61 A:UAP801 4.4 51.6 1.0
O A:LYS280 4.4 15.6 1.0
N A:LYS278 4.5 15.1 1.0
CA A:GLY279 4.5 16.4 1.0
N A:LYS280 4.5 16.6 1.0
O A:HOH1034 4.5 40.1 1.0
CA A:LYS280 4.6 16.6 1.0
CB A:MET277 4.6 13.7 1.0
O A:HOH808 4.7 18.6 1.0
N A:THR282 4.7 14.6 1.0
CA A:LYS278 4.7 16.7 1.0
O A:HOH1150 4.7 40.0 1.0
CA A:THR282 4.9 14.9 1.0
O A:HOH898 4.9 25.0 1.0

Calcium binding site 5 out of 5 in 2hyv

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Calcium binding site 5 out of 5 in the Human Annexin A2 with Heparin Hexasaccharide Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Annexin A2 with Heparin Hexasaccharide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca608

b:22.3
occ:1.00
 O A:ASP321 2.3 15.1 1.0
OG1 A:THR282 2.3 14.2 1.0
O A:HOH809 2.4 16.0 1.0
O1S A:SGN802 2.5 16.6 1.0
O1S A:IDS803 2.5 15.4 1.0
O A:HOH808 2.5 18.6 1.0
CB A:THR282 3.4 12.8 1.0
C A:ASP321 3.6 14.9 1.0
S1 A:SGN802 3.6 15.5 1.0
S A:IDS803 3.7 15.6 1.0
N A:SGN802 3.8 16.2 1.0
O2S A:IDS803 3.9 15.1 1.0
O A:HOH865 4.0 20.0 1.0
O2S A:SGN802 4.2 17.2 1.0
CG2 A:THR282 4.2 13.6 1.0
O A:HOH1192 4.3 17.1 1.0
OD2 A:ASP321 4.3 15.0 1.0
CA A:THR322 4.3 14.8 1.0
CG2 A:THR322 4.3 14.9 1.0
N A:THR322 4.4 15.1 1.0
N A:THR282 4.4 14.6 1.0
CA A:THR282 4.5 14.9 1.0
CA A:ASP321 4.5 15.8 1.0
O2 A:IDS803 4.6 15.8 1.0
C A:GLY281 4.6 15.4 1.0
CB A:ASP321 4.7 15.1 1.0
CG A:ASP321 4.8 16.6 1.0
O3S A:SGN802 4.8 16.2 1.0
O A:HOH807 4.8 18.5 1.0
O3S A:IDS803 4.8 17.5 1.0
OD1 A:ASP284 4.8 14.0 1.0
CB A:THR322 4.9 14.0 1.0
O A:GLY281 4.9 15.7 1.0

Reference:

C.Shao, F.Zhang, M.M.Kemp, R.J.Linhardt, D.M.Waisman, J.F.Head, B.A.Seaton. Crystallographic Analysis of Calcium-Dependent Heparin Binding to Annexin A2. J.Biol.Chem. V. 281 31689 2006.
ISSN: ISSN 0021-9258
PubMed: 16882661
DOI: 10.1074/JBC.M604502200
Page generated: Tue Jul 8 06:05:09 2025

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