Calcium in PDB 9en2: Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5

The structure of Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5, PDB code: 9en2 was solved by P.Lagoutte, V.Gueguen-Chaignon, J.-M.Bourhis, S.Vadon-Le Goff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.83, 95.945, 110.771, 90, 90, 90
R / Rfree (%)	20.8 / 24.2

The binding sites of Calcium atom in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5 (pdb code 9en2). 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 the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5, PDB code: 9en2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5


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 the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.0 occ:1.00 OE1 A:GLU85 2.1 32.6 1.0 O A:THR137 2.1 39.5 1.0 OD1 A:ASP134 2.2 39.0 1.0 O A:HOH488 2.3 32.8 1.0 O A:GLY136 2.5 35.2 1.0 OD2 A:ASP93 2.5 31.0 1.0 OD1 A:ASP93 2.7 30.1 1.0 CG A:ASP93 2.9 31.1 1.0 C A:GLY136 3.2 37.2 1.0 C A:THR137 3.4 39.1 1.0 CG A:ASP134 3.4 37.8 1.0 CD A:GLU85 3.4 36.0 1.0 N A:THR137 3.9 37.4 1.0 OD2 A:ASP134 3.9 37.7 1.0 CA A:THR137 4.0 37.4 1.0 N A:GLY136 4.0 38.0 1.0 CA A:GLY136 4.1 37.6 1.0 N A:ASP134 4.1 35.9 1.0 OE2 A:GLU85 4.2 37.7 1.0 CB A:GLU85 4.2 36.7 1.0 CB A:THR137 4.3 38.2 1.0 O A:ASP134 4.3 36.1 1.0 CB A:ASP93 4.4 31.6 1.0 CG A:GLU85 4.4 36.0 1.0 C A:ASP134 4.4 36.4 1.0 O A:HOH544 4.4 28.8 1.0 N A:GLY138 4.5 39.4 1.0 CB A:ASP134 4.5 36.3 1.0 CA A:ASP134 4.6 36.2 1.0 CE1 A:TYR57 4.7 32.3 1.0 OH A:TYR57 4.7 30.6 1.0 CA A:GLY138 4.8 40.4 1.0 CB A:TYR92 5.0 43.8 1.0 N A:GLU135 5.0 36.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5


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 the Metalloproteinase Enhancer Pcpe-1 Complexed with Nanobodies Vhh-H4 and Vhh-I5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:30.4 occ:1.00 O A:SER260 2.2 35.6 1.0 O A:VAL261 2.2 34.6 1.0 OE1 A:GLU208 2.2 29.7 1.0 O A:HOH409 2.3 28.4 1.0 OD1 A:ASP216 2.3 31.6 1.0 OD1 A:ASP258 2.4 34.8 1.0 OD2 A:ASP216 2.5 32.3 1.0 CG A:ASP216 2.7 32.0 1.0 C A:SER260 3.3 35.9 1.0 C A:VAL261 3.3 36.4 1.0 CD A:GLU208 3.4 31.3 1.0 CG A:ASP258 3.4 36.4 1.0 NZ B:LYS79 3.9 36.6 1.0 N A:VAL261 4.0 36.9 1.0 CA A:VAL261 4.0 37.4 1.0 OD2 A:ASP258 4.0 36.5 1.0 N A:ASP258 4.0 38.0 1.0 OE2 A:GLU208 4.1 33.0 1.0 CB A:ASP216 4.2 31.3 1.0 CB A:GLU208 4.2 31.1 1.0 CB A:VAL261 4.2 39.8 1.0 O A:ASP258 4.3 41.3 1.0 CG A:GLU208 4.3 31.3 1.0 N A:SER260 4.3 38.5 1.0 N A:THR262 4.4 35.7 1.0 C A:ASP258 4.4 41.8 1.0 CA A:SER260 4.4 36.8 1.0 CB A:ASP258 4.5 36.2 1.0 OG A:SER257 4.5 33.2 1.0 CA A:ASP258 4.5 38.5 1.0 N A:ASP216 4.7 34.9 1.0 CA A:THR262 4.7 34.4 1.0 CE1 A:TYR180 4.9 31.7 1.0 CA A:ASP216 4.9 32.7 1.0 CB A:TYR215 4.9 36.1 1.0 C A:SER257 5.0 36.2 1.0

P.Lagoutte, J.M.Bourhis, N.Mariano, V.Gueguen-Chaignon, D.Vandroux, C.Moali, S.Vadon-Le Goff. Mono- and Bi-Specific Nanobodies Targeting the Cub Domains of Pcpe-1 Reduce the Proteolytic Processing of Fibrillar Procollagens. J.Mol.Biol. 68667 2024.
ISSN: ESSN 1089-8638
PubMed: 38901640
DOI: 10.1016/J.JMB.2024.168667