Calcium in PDB 6vvu: Anti-Tryptase Fab E104.V1 Bound to Tryptase

All present enzymatic activity of Anti-Tryptase Fab E104.V1 Bound to Tryptase:
3.4.21.59;

The structure of Anti-Tryptase Fab E104.V1 Bound to Tryptase, PDB code: 6vvu was solved by M.Ultsch, J.T.Koerber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.83 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.573, 168.811, 114.652, 90, 109.97, 90
R / Rfree (%)	18.7 / 23.2

The binding sites of Calcium atom in the Anti-Tryptase Fab E104.V1 Bound to Tryptase (pdb code 6vvu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Anti-Tryptase Fab E104.V1 Bound to Tryptase, PDB code: 6vvu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Anti-Tryptase Fab E104.V1 Bound to Tryptase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Anti-Tryptase Fab E104.V1 Bound to Tryptase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:98.5 occ:1.00 OE1 A:0GJ302 3.2 64.4 1.0 OE2 A:0GJ302 3.2 61.9 1.0 OD2 A:ASP147 3.5 90.6 1.0 OD1 A:ASN146 3.5 84.5 1.0 CD A:0GJ302 3.6 60.9 1.0 OD1 A:ASP147 4.2 83.8 1.0 CG A:ASP147 4.2 79.2 1.0 CG A:ASN146 4.5 77.1 1.0 NE2 A:GLN192 4.5 52.9 1.0 CA A:GLY219 4.8 46.0 1.0 CB A:ASN146 4.9 46.8 1.0

Calcium binding site 2 out of 3 in the Anti-Tryptase Fab E104.V1 Bound to Tryptase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Anti-Tryptase Fab E104.V1 Bound to Tryptase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:76.2 occ:1.00 OE1 B:0GJ302 3.0 72.0 1.0 OE2 B:0GJ302 3.1 70.5 1.0 OD2 B:ASP147 3.5 82.3 1.0 CD B:0GJ302 3.5 68.3 1.0 OD1 B:ASN146 3.8 62.3 1.0 OD1 B:ASP147 4.1 77.2 1.0 CG B:ASP147 4.1 74.3 1.0 NE2 B:GLN192 4.5 63.9 1.0 CG B:ASN146 4.7 67.2 1.0 CG B:0GJ302 5.0 58.1 1.0 CA B:GLY219 5.0 41.0 1.0

Calcium binding site 3 out of 3 in the Anti-Tryptase Fab E104.V1 Bound to Tryptase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Anti-Tryptase Fab E104.V1 Bound to Tryptase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:81.0 occ:1.00 OE1 D:0GJ302 3.0 73.3 1.0 OD2 D:ASP147 3.5 82.1 1.0 OD1 D:ASN146 3.7 62.0 1.0 OE2 D:0GJ302 3.7 72.4 1.0 CD D:0GJ302 3.8 70.8 1.0 OD1 D:ASP147 4.0 75.7 1.0 CG D:ASP147 4.1 72.7 1.0 NE2 D:GLN192 4.2 58.0 1.0 CG D:ASN146 4.7 56.5 1.0 N D:ASP147 4.9 44.5 1.0 CB D:ASN146 5.0 39.6 1.0 CD D:GLN192 5.0 66.7 1.0

H.R.Maun, R.Vij, B.T.Walters, A.Morando, J.K.Jackman, P.Wu, A.Estevez, X.Chen, Y.Franke, M.T.Lipari, M.S.Dennis, D.Kirchhofer, C.Ciferri, K.M.Loyet, T.Yi, C.Eigenbrot, R.A.Lazarus, J.T.Koerber. Bivalent Antibody Pliers Inhibit Beta-Tryptase By An Allosteric Mechanism Dependent on the Igg Hinge. Nat Commun V. 11 6435 2020.
ISSN: ESSN 2041-1723
PubMed: 33353951
DOI: 10.1038/S41467-020-20143-X