Calcium in PDB 5xcv: Crystal Structure of Nz-1 Fv-Clasp Fragment with Its Antigen Peptide

The structure of Crystal Structure of Nz-1 Fv-Clasp Fragment with Its Antigen Peptide, PDB code: 5xcv was solved by T.Arimori, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.76 / 2.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.617, 50.122, 121.868, 90.00, 110.46, 90.00
R / Rfree (%)	22.8 / 27.7

The binding sites of Calcium atom in the Crystal Structure of Nz-1 Fv-Clasp Fragment with Its Antigen Peptide (pdb code 5xcv). 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 Nz-1 Fv-Clasp Fragment with Its Antigen Peptide, PDB code: 5xcv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Nz-1 Fv-Clasp Fragment with Its Antigen Peptide


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 Nz-1 Fv-Clasp Fragment with Its Antigen Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:38.3 occ:1.00 O A:HOH336 2.3 49.4 1.0 OE2 A:GLU145 2.4 34.7 1.0 O D:HOH334 2.4 41.8 1.0 OE1 A:GLN148 2.6 38.9 1.0 OE1 A:GLU145 2.6 33.6 1.0 OD2 D:ASP127 2.6 36.8 1.0 CD A:GLU145 2.8 33.4 1.0 CG D:ASP127 3.4 36.5 1.0 CD A:GLN148 3.4 38.5 1.0 OD1 D:ASP127 3.5 37.7 1.0 NE2 A:GLN148 3.7 39.3 1.0 CG2 D:THR124 4.1 36.2 1.0 O A:HOH346 4.3 33.3 1.0 CG A:GLU145 4.4 31.7 1.0 N D:THR124 4.7 37.0 1.0 CB D:ASP127 4.7 34.7 1.0 CG A:GLN148 4.8 37.1 1.0 O D:SER122 4.9 38.1 1.0 O D:HOH333 4.9 41.2 1.0 OG1 D:THR124 4.9 39.8 1.0 CB A:GLN148 5.0 35.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Nz-1 Fv-Clasp Fragment with Its Antigen Peptide


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 Nz-1 Fv-Clasp Fragment with Its Antigen Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:33.2 occ:1.00 O D:HOH341 2.1 32.6 1.0 O D:HOH314 2.2 35.2 1.0 OE1 D:GLN148 2.3 36.6 1.0 O D:HOH356 2.4 49.8 1.0 OD1 A:ASP127 2.4 40.3 1.0 OE2 D:GLU145 2.4 35.3 1.0 OE1 D:GLU145 2.6 36.0 1.0 CD D:GLU145 2.8 34.4 1.0 CD D:GLN148 3.2 36.5 1.0 CG A:ASP127 3.3 41.4 1.0 NE2 D:GLN148 3.4 37.6 1.0 OD2 A:ASP127 3.6 40.8 1.0 CG D:GLU145 4.4 31.8 1.0 CG2 A:THR124 4.4 43.7 1.0 O A:HOH306 4.5 29.6 1.0 CB A:ASP127 4.5 39.8 1.0 N A:THR124 4.6 44.5 1.0 CG D:GLN148 4.6 35.3 1.0 O A:SER122 4.7 45.2 1.0 OG1 A:THR124 4.8 43.3 1.0 CA A:TRP123 4.8 43.1 1.0 CB D:GLN148 4.9 34.1 1.0

T.Arimori, Y.Kitago, M.Umitsu, Y.Fujii, R.Asaki, K.Tamura-Kawakami, J.Takagi. Fv-Clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability Structure V. 25 1611 2017.
ISSN: ISSN 1878-4186
PubMed: 28919443
DOI: 10.1016/J.STR.2017.08.011