Calcium in PDB 9jd0: Crystal Structure of TMPRSS2 in Complex with Nanobody

The structure of Crystal Structure of TMPRSS2 in Complex with Nanobody, PDB code: 9jd0 was solved by H.Wang, Z.Zhao, X.Liu, Y.Duan, H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.50 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	137.547, 137.547, 130.325, 90, 90, 90
R / Rfree (%)	18.8 / 22.1

The binding sites of Calcium atom in the Crystal Structure of TMPRSS2 in Complex with Nanobody (pdb code 9jd0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of TMPRSS2 in Complex with Nanobody, PDB code: 9jd0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of TMPRSS2 in Complex with Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of TMPRSS2 in Complex with Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:22.9 occ:1.00 O A:VAL136 2.2 22.0 1.0 O A:ASN131 2.2 26.2 1.0 OD2 A:ASP144 2.3 20.5 1.0 OD1 A:ASP134 2.4 25.4 1.0 OE2 A:GLU145 2.4 22.2 1.0 ND1 A:HIS138 2.5 21.4 1.0 CE1 A:HIS138 3.2 24.4 1.0 CG A:ASP134 3.4 34.7 1.0 C A:VAL136 3.4 18.5 1.0 CG A:ASP144 3.4 21.7 1.0 C A:ASN131 3.4 27.8 1.0 CD A:GLU145 3.4 26.6 1.0 CG A:HIS138 3.6 25.5 1.0 OD2 A:ASP134 3.9 29.2 1.0 CG A:GLU145 3.9 21.2 1.0 N A:HIS138 4.0 19.9 1.0 CB A:ASP144 4.0 20.1 1.0 CB A:HIS138 4.1 23.1 1.0 N A:VAL136 4.1 25.7 1.0 CB A:ASN131 4.1 27.3 1.0 CA A:ASN131 4.1 25.6 1.0 N A:ASP134 4.2 26.1 1.0 CA A:VAL136 4.2 28.8 1.0 N A:SER137 4.4 23.4 0.5 N A:SER137 4.4 23.4 0.5 NE2 A:HIS138 4.4 29.5 1.0 OD1 A:ASP144 4.4 22.0 1.0 OE1 A:GLU145 4.5 23.9 1.0 N A:TRP132 4.5 25.8 1.0 N A:CYS133 4.5 26.8 1.0 CA A:SER137 4.5 23.0 0.5 CA A:SER137 4.5 23.1 0.5 CB A:ASP134 4.5 26.9 1.0 CD2 A:HIS138 4.6 26.9 1.0 C A:SER137 4.6 25.5 0.5 C A:SER137 4.6 25.5 0.5 CD1 A:ILE127 4.6 35.0 1.0 CB A:VAL136 4.6 27.2 1.0 CA A:HIS138 4.7 22.8 1.0 CA A:TRP132 4.7 22.0 1.0 CA A:ASP134 4.8 27.2 1.0 N A:GLY135 4.8 24.9 1.0 O A:ASP144 4.8 26.0 1.0 C A:TRP132 4.9 29.5 1.0 C A:ASP134 5.0 29.7 1.0 C A:ASP144 5.0 25.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of TMPRSS2 in Complex with Nanobody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of TMPRSS2 in Complex with Nanobody within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:26.6 occ:1.00 O B:VAL136 2.2 26.2 1.0 O B:ASN131 2.3 29.6 1.0 OE2 B:GLU145 2.4 28.8 1.0 OD2 B:ASP144 2.4 28.1 1.0 OD1 B:ASP134 2.5 28.3 1.0 ND1 B:HIS138 2.5 29.8 1.0 CE1 B:HIS138 3.2 28.8 1.0 CG B:ASP134 3.4 39.5 1.0 CG B:ASP144 3.4 27.3 1.0 C B:ASN131 3.4 26.1 1.0 CD B:GLU145 3.4 31.1 1.0 C B:VAL136 3.5 24.3 1.0 CG B:HIS138 3.6 29.1 1.0 OD2 B:ASP134 3.9 35.0 1.0 N B:HIS138 4.0 23.6 1.0 CG B:GLU145 4.0 24.9 1.0 CB B:ASP144 4.0 28.2 1.0 CB B:HIS138 4.0 24.1 1.0 CA B:ASN131 4.2 32.5 1.0 CB B:ASN131 4.2 31.4 1.0 N B:VAL136 4.2 28.8 1.0 N B:ASP134 4.2 31.6 1.0 CA B:VAL136 4.3 28.9 1.0 N B:CYS133 4.4 28.6 1.0 NE2 B:HIS138 4.4 31.1 1.0 N B:SER137 4.4 30.6 1.0 OD1 B:ASP144 4.5 26.1 1.0 N B:TRP132 4.5 27.7 1.0 OE1 B:GLU145 4.5 29.1 1.0 CD1 B:ILE127 4.5 40.5 1.0 CA B:SER137 4.5 28.2 1.0 CB B:ASP134 4.6 31.8 1.0 C B:SER137 4.6 29.7 1.0 CD2 B:HIS138 4.6 29.2 1.0 CA B:TRP132 4.6 26.4 1.0 CA B:HIS138 4.7 23.0 1.0 CB B:VAL136 4.7 29.6 1.0 O B:ASP144 4.7 27.2 1.0 CA B:ASP134 4.8 29.2 1.0 C B:TRP132 4.8 29.3 1.0 N B:GLY135 4.9 31.4 1.0 C B:ASP144 4.9 28.2 1.0

Z.Zhao, Q.Yang, X.Liu, M.Li, Y.Duan, M.Du, A.Zhou, H.Liu, Y.He, W.Wang, Y.Lu, X.Zhang, H.Wang, X.Yang, H.Zhang, X.Chen, Z.Rao, H.Yang. The Crystal Structure of Coronavirus Rbd-TMPRSS2 Complex Provides Basis For the Discovery of Therapeutic Antibodies. Nat Commun V. 16 6636 2025.
ISSN: ESSN 2041-1723
PubMed: 40681508
DOI: 10.1038/S41467-025-62023-2