Calcium in PDB 6fgo: Fc in Complex with Engineered Calcium Binding Domain Z

The structure of Fc in Complex with Engineered Calcium Binding Domain Z, PDB code: 6fgo was solved by R.Venskutonyte, S.Kanje, S.Hober, K.Lindkvist-Petersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.53 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.229, 120.296, 126.330, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.2

The structure of Fc in Complex with Engineered Calcium Binding Domain Z also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Calcium atom in the Fc in Complex with Engineered Calcium Binding Domain Z (pdb code 6fgo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Fc in Complex with Engineered Calcium Binding Domain Z, PDB code: 6fgo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Fc in Complex with Engineered Calcium Binding Domain Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fc in Complex with Engineered Calcium Binding Domain Z within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca101 b:45.5 occ:1.00 OD1 E:ASP40 2.3 53.0 1.0 OD1 E:ASN42 2.3 46.2 1.0 OD1 E:ASN44 2.3 42.8 1.0 O E:TYR46 2.3 47.8 1.0 OE1 E:GLU51 2.4 64.8 1.0 OE2 E:GLU51 2.5 61.9 1.0 OD2 E:ASP48 2.6 66.0 1.0 CD E:GLU51 2.8 61.5 1.0 CG E:ASN44 3.1 42.9 1.0 CG E:ASN42 3.2 47.0 1.0 CG E:ASP40 3.4 53.7 1.0 ND2 E:ASN42 3.4 45.0 1.0 CG E:ASP48 3.4 64.5 1.0 ND2 E:ASN44 3.5 44.4 1.0 C E:TYR46 3.6 47.5 1.0 N E:ASP48 4.0 54.4 1.0 OD1 E:ASP48 4.1 65.7 1.0 OD2 E:ASP40 4.1 54.7 1.0 N E:ASN44 4.2 43.0 1.0 CB E:ASP48 4.3 60.8 1.0 CG E:GLU51 4.3 58.8 1.0 CB E:ASN44 4.3 42.6 1.0 N E:TYR46 4.3 47.9 1.0 CB E:ASP40 4.4 50.5 1.0 CA E:ASP40 4.4 50.8 1.0 N E:LEU47 4.5 51.3 1.0 CA E:LEU47 4.5 52.0 1.0 CA E:TYR46 4.5 48.1 1.0 N E:ASN42 4.5 49.0 1.0 CB E:ASN42 4.5 48.2 1.0 N E:GLY43 4.7 45.5 1.0 C E:ASP40 4.7 50.5 1.0 C E:LEU47 4.7 55.9 1.0 CA E:ASN44 4.7 44.4 1.0 CA E:ASP48 4.8 54.1 1.0 N E:THR41 4.8 53.7 1.0 CA E:ASN42 4.9 49.2 1.0 C E:ASN42 4.9 47.5 1.0 N E:GLY45 5.0 44.7 1.0 CB E:TYR46 5.0 50.0 1.0

Calcium binding site 2 out of 4 in the Fc in Complex with Engineered Calcium Binding Domain Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fc in Complex with Engineered Calcium Binding Domain Z within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca101 b:40.3 occ:1.00 O F:TYR46 2.2 41.9 1.0 OD1 F:ASN44 2.3 35.2 1.0 OE2 F:GLU51 2.3 49.6 1.0 OD1 F:ASN42 2.4 42.8 1.0 OD1 F:ASP40 2.5 45.2 1.0 OE1 F:GLU51 2.5 47.4 1.0 OD2 F:ASP48 2.6 44.0 1.0 CD F:GLU51 2.7 47.9 1.0 CG F:ASN44 3.1 36.5 1.0 CG F:ASN42 3.1 41.8 1.0 ND2 F:ASN42 3.3 39.6 1.0 C F:TYR46 3.5 39.2 1.0 ND2 F:ASN44 3.5 36.0 1.0 CG F:ASP48 3.5 42.9 1.0 CG F:ASP40 3.6 45.1 1.0 N F:ASP48 3.9 40.1 1.0 OD1 F:ASP48 4.2 43.7 1.0 N F:TYR46 4.2 37.8 1.0 CG F:GLU51 4.2 46.5 1.0 CA F:ASP40 4.3 43.2 1.0 CB F:ASP48 4.3 41.7 1.0 N F:ASN44 4.3 36.0 1.0 CB F:ASP40 4.4 44.9 1.0 CB F:ASN44 4.4 33.4 1.0 CA F:TYR46 4.4 37.8 1.0 OD2 F:ASP40 4.4 44.7 1.0 N F:LEU47 4.4 39.0 1.0 CA F:LEU47 4.4 42.6 1.0 CB F:ASN42 4.5 41.7 1.0 N F:ASN42 4.6 42.5 1.0 C F:ASP40 4.6 42.8 1.0 C F:LEU47 4.6 41.1 1.0 CA F:ASP48 4.7 41.0 1.0 N F:GLY43 4.8 41.5 1.0 N F:THR41 4.8 38.7 1.0 CA F:ASN44 4.8 35.8 1.0 N F:GLY45 4.8 38.2 1.0 CB F:TYR46 4.9 37.2 1.0 CA F:ASN42 4.9 43.2 1.0 C F:ASN44 5.0 37.4 1.0

Calcium binding site 3 out of 4 in the Fc in Complex with Engineered Calcium Binding Domain Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fc in Complex with Engineered Calcium Binding Domain Z within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca101 b:80.4 occ:1.00 O G:TYR46 2.3 88.7 1.0 OE1 G:GLU51 2.3 1.0 1.0 OD1 G:ASN44 2.4 81.9 1.0 OD1 G:ASN42 2.5 94.4 1.0 OE2 G:GLU51 2.5 0.2 1.0 OD2 G:ASP48 2.6 85.9 1.0 OD1 G:ASP40 2.7 91.1 1.0 CD G:GLU51 2.7 0.7 1.0 CG G:ASN44 3.1 85.3 1.0 ND2 G:ASN44 3.3 85.2 1.0 CG G:ASP48 3.3 83.3 1.0 CG G:ASN42 3.4 97.7 1.0 C G:TYR46 3.5 81.8 1.0 N G:ASP48 3.6 73.6 1.0 CG G:ASP40 3.8 89.3 1.0 ND2 G:ASN42 3.8 98.2 1.0 OD1 G:ASP48 4.1 83.1 1.0 CB G:ASP48 4.1 81.9 1.0 CA G:LEU47 4.1 69.5 1.0 CG G:GLU51 4.2 0.2 1.0 N G:LEU47 4.3 73.4 1.0 C G:LEU47 4.4 69.7 1.0 CA G:ASP40 4.4 82.5 1.0 N G:TYR46 4.4 80.2 1.0 CB G:ASN44 4.5 91.0 1.0 CA G:ASP48 4.5 77.0 1.0 CB G:ASP40 4.5 85.1 1.0 CA G:TYR46 4.5 82.7 1.0 OD2 G:ASP40 4.6 90.7 1.0 N G:ASN44 4.7 98.6 1.0 N G:ASN42 4.7 94.1 1.0 CB G:ASN42 4.8 0.6 1.0 C G:ASP40 4.8 85.5 1.0 O G:ASN42 4.8 0.2 1.0 N G:THR41 4.9 83.7 1.0 C G:ASN42 4.9 0.6 1.0 CB G:GLU51 5.0 96.8 1.0

Calcium binding site 4 out of 4 in the Fc in Complex with Engineered Calcium Binding Domain Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fc in Complex with Engineered Calcium Binding Domain Z within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca101 b:0.8 occ:1.00 O H:TYR46 2.3 0.5 1.0 OE2 H:GLU51 2.3 0.4 1.0 OD2 H:ASP48 2.4 0.3 1.0 OD1 H:ASN42 2.4 0.2 1.0 OD1 H:ASN44 2.5 0.8 1.0 ND2 H:ASN44 2.6 0.2 1.0 CG H:ASN44 2.9 0.6 1.0 OE1 H:GLU51 3.0 0.3 1.0 CD H:GLU51 3.0 0.4 1.0 ND2 H:ASN42 3.1 1.0 1.0 CG H:ASN42 3.1 0.9 1.0 OD1 H:ASP40 3.2 0.5 1.0 CG H:ASP48 3.2 0.7 1.0 C H:TYR46 3.5 0.8 1.0 N H:ASP48 3.7 0.3 1.0 OD1 H:ASP48 3.9 0.2 1.0 CB H:ASP48 4.0 0.1 1.0 CG H:ASP40 4.2 0.4 1.0 CB H:ASN44 4.3 0.1 1.0 CA H:LEU47 4.4 0.2 1.0 N H:LEU47 4.4 0.8 1.0 N H:TYR46 4.4 0.0 1.0 O H:ASN42 4.5 0.9 1.0 CG H:GLU51 4.5 0.9 1.0 CA H:TYR46 4.5 0.2 1.0 CA H:ASP48 4.5 0.6 1.0 C H:LEU47 4.5 0.9 1.0 CB H:ASN42 4.6 0.3 1.0 OD2 H:ASP40 4.8 0.6 1.0 CB H:TYR46 4.9 0.3 1.0

S.Kanje, R.Venskutonyte, J.Scheffel, J.Nilvebrant, K.Lindkvist-Petersson, S.Hober. Protein Engineering Allows For Mild Affinity-Based Elution of Therapeutic Antibodies. J. Mol. Biol. V. 430 3427 2018.
ISSN: ESSN 1089-8638
PubMed: 29886013
DOI: 10.1016/J.JMB.2018.06.004