Calcium in PDB 9nb5: Cryo-Em Structure of the Autoinhibitory CD163 Trimer

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer (pdb code 9nb5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer, PDB code: 9nb5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


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 the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:43.8 occ:1.00 OD2 A:ASP299 2.3 38.6 1.0 O A:GLY294 2.3 43.8 1.0 O A:VAL333 2.4 48.7 1.0 OD1 A:ASP296 2.4 44.4 1.0 OD1 A:ASP299 2.9 42.5 1.0 CG A:ASP299 3.0 36.6 1.0 C A:VAL333 3.5 44.5 1.0 C A:GLY294 3.6 40.0 1.0 CG A:ASP296 3.6 44.0 1.0 CA A:SER334 3.6 43.8 1.0 N A:SER334 4.0 42.9 1.0 OD2 A:ASP296 4.1 47.0 1.0 N A:CYS335 4.2 47.1 1.0 CA A:GLY294 4.3 38.9 1.0 N A:ASP296 4.4 32.5 1.0 CB A:ASP299 4.5 30.7 1.0 C A:SER334 4.5 48.5 1.0 CB A:SER334 4.5 46.1 1.0 N A:TRP295 4.5 40.4 1.0 CA A:TRP295 4.6 35.0 1.0 CA A:VAL333 4.8 39.1 1.0 CB A:ASP296 4.8 38.4 1.0 C A:TRP295 4.9 35.8 1.0

Calcium binding site 2 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


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 the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1202 b:54.6 occ:1.00 OD2 A:ASP616 2.3 45.8 1.0 O A:HIS611 2.4 49.6 1.0 O A:PHE650 2.5 38.8 1.0 CG A:ASP616 3.2 45.6 1.0 OD1 A:ASP616 3.3 46.9 1.0 C A:HIS611 3.4 54.6 1.0 OD2 A:ASP613 3.7 68.5 1.0 C A:PHE650 3.7 31.4 1.0 CG A:ASP613 3.7 65.6 1.0 N A:ASP613 3.9 54.4 1.0 OD1 A:ASP613 4.0 65.7 1.0 CA A:HIS611 4.2 54.5 1.0 CB A:ASP613 4.3 58.7 1.0 CA A:HIS651 4.3 33.8 1.0 CB A:HIS611 4.3 52.8 1.0 N A:TRP612 4.3 57.8 1.0 N A:HIS651 4.4 30.0 1.0 CA A:TRP612 4.5 52.5 1.0 CB A:ASP616 4.6 48.0 1.0 C A:TRP612 4.7 53.4 1.0 N A:CYS652 4.7 41.9 1.0 CA A:ASP613 4.7 55.0 1.0 CA A:PHE650 4.7 29.8 1.0 N A:PHE650 4.9 27.5 1.0 CD2 A:HIS651 5.0 35.9 1.0

Calcium binding site 3 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1203 b:39.8 occ:1.00 OE1 A:GLU812 2.3 54.1 1.0 OD1 A:ASP746 2.3 58.0 1.0 OD1 A:ASP745 2.9 55.1 1.0 CG A:ASP746 3.4 61.5 1.0 CD A:GLU812 3.5 55.4 1.0 CG A:ASP745 3.6 51.7 1.0 OD2 A:ASP745 3.7 55.3 1.0 OD2 A:ASP746 4.0 66.7 1.0 CB A:GLU812 4.2 47.7 1.0 CG A:GLU812 4.3 52.4 1.0 OE2 A:GLU812 4.4 56.3 1.0 N A:ASP746 4.4 54.0 1.0 CA A:ASP746 4.6 52.5 1.0 CB A:ASP746 4.6 55.2 1.0 C A:ASP745 4.7 51.1 1.0 CE C:LYS1021 4.9 52.5 1.0 O A:ASP745 5.0 51.5 1.0 CB A:ASP745 5.0 46.7 1.0

Calcium binding site 4 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1204 b:45.7 occ:1.00 OD1 A:ASP752 2.4 52.0 1.0 O A:MET786 2.6 66.6 1.0 O A:SER747 2.8 56.1 1.0 OD2 A:ASP752 2.9 62.4 1.0 CG A:ASP752 3.0 52.6 1.0 C A:MET786 3.6 67.0 1.0 CA A:LYS787 3.6 70.5 1.0 N A:CYS788 3.9 68.9 1.0 C A:SER747 4.0 53.2 1.0 N A:LYS787 4.1 69.9 1.0 C A:LYS787 4.3 73.5 1.0 N A:ASP749 4.4 47.5 1.0 CB A:ASP752 4.5 46.2 1.0 CB A:ASP749 4.5 48.6 1.0 CB A:SER747 4.6 58.4 1.0 CB A:LYS787 4.6 71.4 1.0 CA A:TRP748 4.8 44.4 1.0 N A:ASP752 4.8 43.0 1.0 N A:TRP748 4.8 51.5 1.0 CA A:MET786 4.9 65.3 1.0 O A:CYS788 4.9 66.1 1.0 CA A:SER747 4.9 52.1 1.0

Calcium binding site 5 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1205 b:66.7 occ:1.00 OD1 A:ASN807 2.6 67.6 1.0 OE1 A:GLU785 2.9 70.7 1.0 OD2 A:ASP784 3.1 69.1 1.0 CG A:ASN807 3.3 66.8 1.0 ND2 A:ASN807 3.3 67.4 1.0 OD2 A:ASP746 3.5 66.7 1.0 OD1 A:ASP784 3.7 66.9 1.0 CG A:ASP784 3.8 66.6 1.0 CD A:GLU785 4.1 72.1 1.0 CG A:ASP746 4.3 61.5 1.0 CB A:ASP746 4.3 55.2 1.0 CB A:ASN807 4.7 64.3 1.0 SG A:CYS808 4.8 69.8 1.0 CB A:GLU785 4.9 67.6 1.0 OE2 A:GLU785 4.9 71.1 1.0 CG A:GLU785 4.9 70.9 1.0 CE C:LYS1021 5.0 52.5 1.0 CD C:LYS1021 5.0 55.8 1.0

Calcium binding site 6 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1206 b:53.3 occ:1.00 OD1 A:ASP955 2.4 54.9 1.0 OD1 A:ASP956 2.5 52.7 1.0 OE1 A:GLU1022 2.8 55.2 1.0 CG A:ASP955 3.0 50.9 1.0 OD2 A:ASP955 3.1 53.1 1.0 CG A:ASP956 3.7 53.6 1.0 CD A:GLU1022 4.0 54.4 1.0 OE2 A:GLU981 4.1 58.4 1.0 N A:ASP956 4.1 51.9 1.0 CB A:GLU1022 4.3 49.1 1.0 CB A:ASP955 4.3 45.2 1.0 OD2 A:ASP956 4.4 50.0 1.0 C A:ASP955 4.4 52.2 1.0 CA A:ASP956 4.5 51.1 1.0 NZ B:LYS811 4.6 51.3 1.0 CG A:GLU1022 4.6 51.2 1.0 CB A:ASP956 4.7 52.2 1.0 SG A:CYS954 4.8 62.0 1.0 CA A:ASP955 4.8 48.9 1.0 O A:ASP955 4.9 55.2 1.0 N A:ASP955 4.9 51.1 1.0 OE2 A:GLU1022 5.0 57.2 1.0 SG A:CYS1018 5.0 71.2 1.0

Calcium binding site 7 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1207 b:68.7 occ:1.00 OD1 A:ASP959 2.3 61.1 1.0 O A:SER957 2.3 57.3 1.0 O A:VAL996 2.5 66.4 1.0 OD2 A:ASP962 2.5 66.8 1.0 CG A:ASP962 3.2 65.8 1.0 OD1 A:ASP962 3.2 68.7 1.0 CG A:ASP959 3.3 64.2 1.0 C A:SER957 3.5 54.5 1.0 C A:VAL996 3.6 65.7 1.0 OD2 A:ASP959 3.6 68.6 1.0 CA A:LYS997 3.7 69.0 1.0 N A:LYS997 4.1 68.0 1.0 CB A:SER957 4.2 56.3 1.0 N A:CYS998 4.3 75.5 1.0 N A:ASP959 4.4 64.0 1.0 C A:LYS997 4.4 74.2 1.0 CA A:SER957 4.4 55.8 1.0 N A:TRP958 4.4 51.4 1.0 CA A:TRP958 4.5 53.3 1.0 CB A:ASP962 4.6 61.2 1.0 CB A:ASP959 4.7 64.5 1.0 C A:TRP958 4.7 61.6 1.0 O A:CYS998 4.7 80.0 1.0 CB A:LYS997 4.8 70.7 1.0 CA A:VAL996 4.8 62.6 1.0 CG A:LYS997 5.0 69.7 1.0

Calcium binding site 8 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1201 b:74.9 occ:1.00 OE1 B:GLU359 2.4 73.1 1.0 OD1 B:ASP293 2.4 78.4 1.0 OD1 B:ASP292 3.0 63.7 1.0 OD2 B:ASP292 3.5 61.7 1.0 CD B:GLU359 3.6 71.1 1.0 CG B:ASP293 3.6 73.1 1.0 CG B:ASP292 3.6 57.0 1.0 NZ A:LYS352 3.8 46.4 1.0 CD A:LYS352 4.2 42.8 1.0 OD2 B:ASP293 4.2 71.6 1.0 OE2 B:GLU359 4.3 74.1 1.0 CB B:GLU359 4.4 51.8 1.0 CE A:LYS352 4.6 44.5 1.0 CG B:GLU359 4.6 61.6 1.0 N B:ASP293 4.6 53.8 1.0 CB B:ASP293 4.7 57.2 1.0 CA B:ASP293 4.8 51.5 1.0

Calcium binding site 9 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1202 b:44.6 occ:1.00 O B:GLY294 2.2 48.5 1.0 O B:VAL333 2.4 67.3 1.0 OD1 B:ASP296 2.6 55.8 1.0 OD2 B:ASP299 2.7 58.5 1.0 OD1 B:ASP299 3.0 50.2 1.0 CG B:ASP299 3.2 50.3 1.0 C B:GLY294 3.4 47.0 1.0 C B:VAL333 3.5 63.2 1.0 CA B:SER334 3.6 65.9 1.0 CG B:ASP296 3.7 54.3 1.0 N B:SER334 4.0 64.0 1.0 OD2 B:ASP296 4.0 60.5 1.0 CA B:GLY294 4.2 47.3 1.0 N B:CYS335 4.2 64.9 1.0 N B:TRP295 4.5 41.0 1.0 CB B:SER334 4.5 65.2 1.0 N B:ASP296 4.5 42.5 1.0 C B:SER334 4.5 69.2 1.0 CA B:TRP295 4.6 38.1 1.0 CB B:ASP299 4.7 42.5 1.0 CA B:VAL333 4.8 60.4 1.0 C B:TRP295 4.9 43.5 1.0 CB B:ASP296 5.0 45.0 1.0

Calcium binding site 10 out of 20 in the Cryo-Em Structure of the Autoinhibitory CD163 Trimer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of the Autoinhibitory CD163 Trimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1203 b:40.3 occ:1.00 OD2 B:ASP616 2.3 36.9 1.0 OD1 B:ASP616 2.4 36.8 1.0 CG B:ASP616 2.6 33.0 1.0 O B:PHE650 2.7 37.4 1.0 O B:HIS611 3.3 40.6 1.0 OD2 B:ASP613 3.6 59.2 1.0 C B:PHE650 3.8 25.8 1.0 CB B:ASP613 3.9 45.1 1.0 CG B:ASP613 3.9 57.1 1.0 N B:ASP613 4.1 38.7 1.0 CB B:ASP616 4.1 26.9 1.0 CA B:HIS651 4.1 22.5 1.0 N B:CYS652 4.1 31.1 1.0 C B:HIS611 4.4 44.1 1.0 N B:HIS651 4.4 23.8 1.0 CA B:ASP613 4.6 38.0 1.0 N B:ASP616 4.6 34.7 1.0 C B:HIS651 4.7 29.9 1.0 OD1 B:ASP613 4.8 55.9 1.0 C B:TRP612 4.9 39.1 1.0 CA B:TRP612 4.9 36.9 1.0 CA B:ASP616 4.9 30.1 1.0 O B:CYS652 5.0 40.9 1.0

C.-S.Huang, H.Wang, J.B.R.White, O.Degtjarik, C.Huynh, K.Brannstrom, M.T.Horn, S.P.Muench, W.S.Somers, J.Chaparro-Riggers, L.Lin, L.Mosyak. Structural Elucidation of the Haptoglobin-Hemoglobin Clearance Mechanism By Macrophage Scavenger Receptor CD163 To Be Published.