Calcium in PDB 9nb8: Cryo-Em Structure of the CD163/Hpsphb Complex

The structure of Cryo-Em Structure of the CD163/Hpsphb Complex also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the CD163/Hpsphb Complex (pdb code 9nb8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 21 binding sites of Calcium where determined in the Cryo-Em Structure of the CD163/Hpsphb Complex, PDB code: 9nb8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1201 b:212.2 occ:1.00 OD1 A:ASN247 2.3 196.8 1.0 OD1 A:ASP224 2.3 212.1 1.0 OD1 A:ASP225 2.3 216.3 1.0 OD2 A:ASP186 2.4 204.9 1.0 CB A:ASP186 2.7 204.9 1.0 CG A:ASP186 2.8 204.9 1.0 CG A:ASP224 3.1 212.1 1.0 CG A:ASP225 3.1 216.3 1.0 CG A:ASN247 3.2 196.8 1.0 OD2 A:ASP224 3.2 212.1 1.0 OD2 A:ASP225 3.4 216.3 1.0 ND2 A:ASN247 3.5 196.8 1.0 OD1 A:ASP186 4.0 204.9 1.0 N A:ASP225 4.1 216.3 1.0 CA A:ASP186 4.2 204.9 1.0 CB A:ASP225 4.4 216.3 1.0 CB A:ASN247 4.5 196.8 1.0 CB A:ASP224 4.5 212.1 1.0 CA A:ASP225 4.6 216.3 1.0 C A:ASP224 4.8 212.1 1.0 N A:CYS248 4.8 193.8 1.0 C A:ASP186 4.8 204.9 1.0 SG A:CYS184 4.9 200.3 1.0 CA A:ASP224 4.9 212.1 1.0 N A:ASN247 4.9 196.8 1.0 NZ F:LYS262 5.0 93.3 1.0 O A:ASP186 5.0 204.9 1.0

Calcium binding site 2 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1202 b:191.7 occ:1.00 OD1 A:ASP185 2.3 200.4 1.0 OD1 A:ASP186 2.3 204.9 1.0 OE2 A:GLU252 2.4 194.2 1.0 CG A:ASP185 3.0 200.4 1.0 CD A:GLU252 3.1 194.2 1.0 OD2 A:ASP185 3.2 200.4 1.0 CG A:GLU252 3.2 194.2 1.0 CG A:ASP186 3.5 204.9 1.0 N A:ASP186 4.0 204.9 1.0 CA A:ASP186 4.0 204.9 1.0 C A:ASP185 4.2 200.4 1.0 OE1 A:GLU252 4.3 194.2 1.0 CB A:ASP185 4.4 200.4 1.0 OD2 A:ASP186 4.4 204.9 1.0 CB A:ASP186 4.4 204.9 1.0 O A:ASP185 4.4 200.4 1.0 CB A:GLU252 4.6 194.2 1.0 NZ F:LYS262 4.7 93.3 1.0 O A:GLU252 4.7 194.2 1.0 CA A:ASP185 4.8 200.4 1.0

Calcium binding site 3 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1203 b:88.9 occ:1.00 OE2 A:GLU359 2.3 75.1 1.0 OD1 A:ASP293 2.3 78.1 1.0 OD2 A:ASP293 2.4 78.1 1.0 CG A:ASP293 2.6 78.1 1.0 CD A:GLU359 2.8 75.1 1.0 OE1 A:GLU359 2.8 75.1 1.0 CG A:GLU359 4.1 75.1 1.0 CB A:ASP293 4.1 78.1 1.0 N A:ASP293 4.6 78.1 1.0 CA A:ASP293 4.8 78.1 1.0 SG A:CYS291 4.9 77.2 1.0 CD D:LYS12 4.9 53.2 1.0

Calcium binding site 4 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1204 b:69.7 occ:1.00 OD1 A:ASP296 2.3 77.4 1.0 O A:VAL333 2.3 77.0 1.0 OD2 A:ASP299 2.6 81.7 1.0 CG A:ASP296 2.8 77.4 1.0 OD2 A:ASP296 3.0 77.4 1.0 O A:GLY294 3.2 73.8 1.0 CG A:ASP299 3.3 81.7 1.0 OD1 A:ASP299 3.4 81.7 1.0 C A:VAL333 3.5 77.0 1.0 N A:ASP296 3.7 77.4 1.0 C A:GLY294 3.7 73.8 1.0 CA A:SER334 3.8 81.0 1.0 CB A:ASP296 4.0 77.4 1.0 N A:SER334 4.1 81.0 1.0 N A:TRP295 4.1 67.3 1.0 CA A:TRP295 4.1 67.3 1.0 C A:TRP295 4.3 67.3 1.0 CA A:ASP296 4.4 77.4 1.0 CA A:GLY294 4.5 73.8 1.0 N A:CYS335 4.6 89.4 1.0 C A:SER334 4.6 81.0 1.0 CB A:ASP299 4.7 81.7 1.0 CA A:VAL333 4.7 77.0 1.0 CB A:SER334 4.7 81.0 1.0 N A:VAL333 5.0 77.0 1.0

Calcium binding site 5 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1205 b:113.8 occ:1.00 OD1 A:ASP746 2.3 118.2 1.0 OE2 C:GLU981 2.3 107.6 1.0 OE1 A:GLU812 2.4 117.2 1.0 CD C:GLU981 2.9 107.6 1.0 OE1 C:GLU981 2.9 107.6 1.0 CG A:ASP746 3.3 118.2 1.0 OD1 A:ASP745 3.5 120.3 1.0 OD2 A:ASP745 3.5 120.3 1.0 CD A:GLU812 3.6 117.2 1.0 OD2 A:ASP746 3.7 118.2 1.0 CG A:ASP745 3.8 120.3 1.0 CA C:CA1204 4.2 87.2 1.0 CG C:GLU981 4.3 107.6 1.0 CB A:GLU812 4.3 117.2 1.0 OE2 A:GLU812 4.4 117.2 1.0 CG A:GLU812 4.6 117.2 1.0 CB A:ASP746 4.6 118.2 1.0 CA A:ASP746 4.8 118.2 1.0 N A:ASP746 4.8 118.2 1.0

Calcium binding site 6 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1206 b:124.8 occ:1.00 OD2 A:ASP752 2.3 118.2 1.0 O A:MET786 2.3 131.2 1.0 O A:SER747 2.5 120.5 1.0 CA A:LYS787 2.9 133.4 1.0 CG A:ASP752 3.1 118.2 1.0 OD1 A:ASP752 3.2 118.2 1.0 C A:MET786 3.2 131.2 1.0 N A:LYS787 3.5 133.4 1.0 CD A:LYS787 3.6 133.4 1.0 CB A:LYS787 3.6 133.4 1.0 C A:SER747 3.6 120.5 1.0 N A:CYS788 3.8 137.4 1.0 C A:LYS787 3.9 133.4 1.0 CB A:SER747 4.0 120.5 1.0 OG A:SER747 4.1 120.5 1.0 CG A:LYS787 4.2 133.4 1.0 OD1 A:ASP749 4.2 119.3 1.0 CA A:SER747 4.4 120.5 1.0 CB A:ASP752 4.5 118.2 1.0 N A:TRP748 4.6 117.2 1.0 CA A:MET786 4.7 131.2 1.0 CA A:TRP748 4.9 117.2 1.0 CE A:LYS787 4.9 133.4 1.0

Calcium binding site 7 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1207 b:96.1 occ:1.00 OE2 A:GLU785 2.2 129.7 1.0 NZ C:LYS1021 2.9 108.3 1.0 OD2 A:ASP784 3.2 133.2 1.0 CD A:GLU785 3.2 129.7 1.0 CB A:ASN807 3.7 128.0 1.0 SG A:CYS808 3.7 129.0 1.0 CG A:GLU785 3.8 129.7 1.0 OD1 A:ASP784 3.9 133.2 1.0 CG A:ASP784 3.9 133.2 1.0 CD C:LYS1021 3.9 108.3 1.0 CE C:LYS1021 4.0 108.3 1.0 OE1 A:GLU785 4.1 129.7 1.0 OD2 A:ASP746 4.1 118.2 1.0 C A:ASN807 4.3 128.0 1.0 O A:ASN807 4.4 128.0 1.0 N A:CYS808 4.6 129.0 1.0 CA A:ASN807 4.6 128.0 1.0 CG A:ASN807 4.8 128.0 1.0 OD1 A:ASN807 5.0 128.0 1.0

Calcium binding site 8 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1208 b:105.0 occ:1.00 OE2 A:GLU1022 2.2 107.2 1.0 OD2 A:ASP955 3.2 104.3 1.0 OD1 A:ASP955 3.3 104.3 1.0 CD A:GLU1022 3.4 107.2 1.0 CG A:ASP955 3.6 104.3 1.0 OD1 A:ASP956 3.7 106.7 1.0 CG A:GLU1022 4.1 107.2 1.0 OE1 A:GLU1022 4.4 107.2 1.0 CG A:ASP956 4.9 106.7 1.0

Calcium binding site 9 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1209 b:129.4 occ:1.00 OD2 A:ASP962 2.2 130.2 1.0 OD2 A:ASP959 2.3 127.6 1.0 O A:VAL996 2.6 128.4 1.0 O A:SER957 2.6 112.8 1.0 CA A:LYS997 2.7 130.0 1.0 CG A:ASP962 3.0 130.2 1.0 OD1 A:ASP962 3.0 130.2 1.0 CG A:ASP959 3.1 127.6 1.0 C A:VAL996 3.4 128.4 1.0 N A:CYS998 3.4 138.2 1.0 N A:LYS997 3.5 130.0 1.0 CB A:LYS997 3.5 130.0 1.0 OD1 A:ASP959 3.5 127.6 1.0 C A:LYS997 3.6 130.0 1.0 C A:SER957 3.8 112.8 1.0 OG A:SER957 4.3 112.8 1.0 CB A:ASP959 4.3 127.6 1.0 N A:ASP959 4.4 127.6 1.0 CB A:SER957 4.4 112.8 1.0 CB A:ASP962 4.4 130.2 1.0 CA A:TRP958 4.7 118.1 1.0 N A:TRP958 4.7 118.1 1.0 CA A:SER957 4.7 112.8 1.0 O A:CYS998 4.7 138.2 1.0 CA A:CYS998 4.7 138.2 1.0 C A:TRP958 4.7 118.1 1.0 O A:LYS997 4.8 130.0 1.0 CA A:VAL996 4.8 128.4 1.0 CG A:LYS997 4.9 130.0 1.0 CA A:ASP959 5.0 127.6 1.0

Calcium binding site 10 out of 21 in the Cryo-Em Structure of the CD163/Hpsphb Complex


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 CD163/Hpsphb Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1201 b:213.4 occ:1.00 OE1 B:GLU359 2.3 196.7 1.0 OD1 B:ASP293 2.3 201.8 1.0 OD2 B:ASP292 2.4 205.5 1.0 CD B:GLU359 2.7 196.7 1.0 OE2 B:GLU359 3.1 196.7 1.0 CG B:ASP293 3.2 201.8 1.0 CG B:ASP292 3.4 205.5 1.0 CG B:GLU359 3.7 196.7 1.0 OD2 B:ASP293 3.8 201.8 1.0 CB B:ASP292 3.8 205.5 1.0 CB B:GLU359 3.9 196.7 1.0 N B:ASP293 4.0 201.8 1.0 CB B:ASP293 4.2 201.8 1.0 CA B:ASP293 4.4 201.8 1.0 C B:ASP292 4.5 205.5 1.0 OD1 B:ASP292 4.5 205.5 1.0 CA B:ASP292 4.7 205.5 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.