Calcium in PDB 8sl1: Cryo-Em Structure of Papp-A2

The structure of Cryo-Em Structure of Papp-A2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structure of Papp-A2 (pdb code 8sl1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Papp-A2, PDB code: 8sl1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Papp-A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Papp-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1803 b:24.2 occ:1.00 OD1 A:ASP798 2.4 38.5 1.0 O A:GLU679 2.4 37.4 1.0 O A:ASP798 2.4 31.2 1.0 OD1 A:ASP685 2.4 42.0 1.0 O A:GLN695 2.4 47.0 1.0 CG A:ASP685 3.4 45.0 1.0 C A:ASP798 3.5 26.2 1.0 CG A:ASP798 3.5 37.0 1.0 CB A:ASP685 3.6 39.6 1.0 C A:GLU679 3.6 43.7 1.0 C A:GLN695 3.7 48.8 1.0 N A:ASP685 3.9 43.9 1.0 CA A:ASP798 4.0 23.4 1.0 OE1 A:GLN695 4.2 46.6 1.0 CB A:ASP798 4.3 25.8 1.0 CA A:ASP685 4.3 29.4 1.0 OD2 A:ASP798 4.4 40.4 1.0 O A:PRO683 4.4 25.7 1.0 CA A:ALA696 4.5 37.3 1.0 CA A:GLU679 4.5 37.0 1.0 OD2 A:ASP685 4.5 41.9 1.0 N A:ALA696 4.5 42.7 1.0 N A:ALA680 4.5 39.3 1.0 CB A:GLN695 4.5 46.6 1.0 O A:VAL681 4.5 38.3 1.0 CA A:ALA680 4.6 21.0 1.0 N A:ALA799 4.6 19.5 1.0 CA A:GLN695 4.6 43.8 1.0 C A:PRO684 4.7 39.8 1.0 CA A:PRO684 4.8 23.9 1.0 CB A:ALA799 4.8 26.0 1.0 CD A:LYS472 4.8 30.4 1.0 CB A:GLU679 4.9 36.6 1.0 N A:VAL681 4.9 24.5 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Papp-A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Papp-A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1804 b:65.3 occ:1.00 O A:TYR880 2.3 60.9 1.0 OE2 A:GLU892 2.3 68.5 1.0 OE1 A:GLU892 2.3 70.0 1.0 OD1 A:ASP883 2.5 61.5 1.0 OD2 A:ASP895 2.6 56.8 1.0 CD A:GLU892 2.7 70.0 1.0 OD2 A:ASP883 2.9 63.1 1.0 CG A:ASP883 3.0 61.7 1.0 O A:LYS885 3.0 64.6 1.0 C A:TYR880 3.0 55.2 1.0 N A:TYR880 3.5 57.6 1.0 CG A:ASP895 3.6 55.4 1.0 N A:CYS881 3.8 45.6 1.0 CA A:TYR880 3.8 58.1 1.0 CA A:CYS881 4.0 49.9 1.0 CG A:GLU892 4.2 69.2 1.0 C A:LYS885 4.2 65.6 1.0 CB A:ASP883 4.3 60.7 1.0 CB A:PRO879 4.3 64.1 1.0 C A:PRO879 4.3 60.4 1.0 CB A:ASP895 4.4 55.0 1.0 OD1 A:ASP895 4.4 54.6 1.0 CG A:LYS885 4.5 66.8 1.0 N A:ASP883 4.6 63.0 1.0 C A:CYS881 4.6 52.4 1.0 CA A:PRO879 4.6 60.5 1.0 OG A:SER887 4.7 76.3 1.0 CB A:SER887 4.8 74.4 1.0 N A:LYS885 4.8 66.3 1.0 N A:GLY882 4.8 46.9 1.0 CA A:ASP883 4.9 64.3 1.0 CA A:LYS885 5.0 66.2 1.0 CB A:GLU892 5.0 67.0 1.0

J.Sridar, A.Mafi, R.A.Judge, J.Xu, K.A.Kong, J.C.K.Wang, V.S.Stoll, G.Koukos, R.J.Simon, D.Eaton, M.Bratkowski, Q.Hao. Cryo-Em Structure of Human Papp-A2 and Mechanism of Substrate Recognition Commun Chem V. 6 234 2023.
ISSN: ESSN 2399-3669
DOI: 10.1038/S42004-023-01032-Y