Calcium in PDB 9fno: Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin

The structure of Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin (pdb code 9fno). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin, PDB code: 9fno:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin


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 Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2001 b:302.9 occ:1.00 OD2 E:ASP186 2.2 270.6 1.0 OD1 E:ASP225 2.3 275.1 1.0 OD2 E:ASP224 2.4 283.3 1.0 OD1 E:ASN247 2.4 272.4 1.0 OD1 E:ASP224 2.6 283.3 1.0 CG E:ASP224 2.8 283.3 1.0 CG E:ASP225 3.1 275.1 1.0 CG E:ASN247 3.1 272.4 1.0 OD2 E:ASP225 3.2 275.1 1.0 CG E:ASP186 3.2 270.6 1.0 ND2 E:ASN247 3.3 272.4 1.0 CB E:ASP186 3.5 270.6 1.0 SG E:CYS248 3.9 277.4 1.0 CB E:ASP224 4.3 283.3 1.0 OD1 E:ASP186 4.3 270.6 1.0 N E:ASP225 4.4 275.1 1.0 CB E:ASP225 4.5 275.1 1.0 CB E:ASN247 4.5 272.4 1.0 NZ D:LYS321 4.6 243.7 1.0 N E:ASN247 4.7 272.4 1.0 CA E:ASP225 4.9 275.1 1.0 SG E:CYS184 4.9 282.0 1.0 C E:ASP224 5.0 283.3 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin


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 Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2002 b:168.3 occ:1.00 O E:GLY294 2.2 206.8 1.0 OD2 E:ASP299 2.3 194.6 1.0 O E:VAL333 2.4 205.8 1.0 CG E:ASP299 3.3 194.6 1.0 N E:ASP296 3.3 205.2 1.0 C E:GLY294 3.4 206.8 1.0 CB E:ASP296 3.4 205.2 1.0 C E:VAL333 3.4 205.8 1.0 CA E:SER334 3.6 188.2 1.0 OD1 E:ASP299 3.6 194.6 1.0 C E:TRP295 3.9 201.9 1.0 CA E:TRP295 3.9 201.9 1.0 N E:SER334 4.0 188.2 1.0 CA E:ASP296 4.0 205.2 1.0 N E:TRP295 4.1 201.9 1.0 CB E:SER334 4.4 188.2 1.0 N E:CYS335 4.4 200.2 1.0 CA E:GLY294 4.5 206.8 1.0 CB E:ASP299 4.6 194.6 1.0 C E:SER334 4.6 188.2 1.0 OG E:SER334 4.6 188.2 1.0 CA E:VAL333 4.6 205.8 1.0 CG E:ASP296 4.7 205.2 1.0 CB E:VAL333 4.9 205.8 1.0 O E:TRP295 4.9 201.9 1.0 C E:ASP296 4.9 205.2 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin


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 Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1201 b:391.9 occ:1.00 OD2 F:ASP299 2.3 396.1 1.0 O F:GLY294 2.3 376.1 1.0 O F:VAL333 2.4 391.0 1.0 N F:ASP296 3.0 376.2 1.0 C F:GLY294 3.4 376.1 1.0 CG F:ASP299 3.4 396.1 1.0 CB F:ASP296 3.5 376.2 1.0 C F:VAL333 3.5 391.0 1.0 CA F:TRP295 3.5 377.7 1.0 C F:TRP295 3.6 377.7 1.0 OD1 F:ASP299 3.7 396.1 1.0 CA F:ASP296 3.8 376.2 1.0 CA F:SER334 3.8 385.6 1.0 N F:TRP295 3.8 377.7 1.0 N F:SER334 4.1 385.6 1.0 CB F:SER334 4.4 385.6 1.0 CA F:GLY294 4.6 376.1 1.0 O F:TRP295 4.6 377.7 1.0 CB F:ASP299 4.7 396.1 1.0 C F:ASP296 4.7 376.2 1.0 OG F:SER334 4.7 385.6 1.0 CA F:VAL333 4.7 391.0 1.0 O F:ASP296 4.8 376.2 1.0 N F:CYS335 4.9 386.4 1.0 CG F:ASP296 4.9 376.2 1.0 CB F:TRP295 4.9 377.7 1.0 C F:SER334 4.9 385.6 1.0 N F:VAL333 5.0 391.0 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin


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 Human CD163 SRCR1-9 in Complex with Haptoglobin- Hemoglobin within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca1201 b:283.7 occ:1.00 OD2 G:ASP299 2.3 275.1 1.0 O G:GLY294 2.3 299.5 1.0 O G:VAL333 2.4 293.3 1.0 CG G:ASP299 3.2 275.1 1.0 C G:VAL333 3.4 293.3 1.0 C G:GLY294 3.5 299.5 1.0 OD1 G:ASP299 3.5 275.1 1.0 N G:ASP296 3.5 270.5 1.0 CA G:SER334 3.7 274.3 1.0 CB G:ASP296 3.7 270.5 1.0 N G:SER334 4.0 274.3 1.0 CA G:TRP295 4.0 289.9 1.0 C G:TRP295 4.1 289.9 1.0 N G:TRP295 4.2 289.9 1.0 CA G:ASP296 4.2 270.5 1.0 N G:CYS335 4.4 286.3 1.0 CB G:SER334 4.5 274.3 1.0 CA G:GLY294 4.5 299.5 1.0 CB G:ASP299 4.6 275.1 1.0 CA G:VAL333 4.6 293.3 1.0 C G:SER334 4.7 274.3 1.0 OG G:SER334 4.7 274.3 1.0 CB G:VAL333 4.8 293.3 1.0

A.Etzerodt, J.H.Mikkelsen, M.Torvund-Jensen, D.Hennig, T.Boesen, J.H.Graversen, S.K.Moestrup, J.M.Kollman, C.B.F.Andersen. The Cryo-Em Structure of Human CD163 Bound to Haptoglobin-Hemoglobin Reveals Molecular Mechanisms of Hemoglobin Scavenging. Nat Commun V. 15 10871 2024.
ISSN: ESSN 2041-1723
PubMed: 39738064
DOI: 10.1038/S41467-024-55171-4