Calcium in PDB 4ag4: Crystal Structure of A DDR1-Fab Complex

All present enzymatic activity of Crystal Structure of A DDR1-Fab Complex:
2.7.10.1;

The structure of Crystal Structure of A DDR1-Fab Complex, PDB code: 4ag4 was solved by F.Carafoli, M.C.Mayer, K.Shiraishi, M.A.Pecheva, L.Y.Chan, R.Nan, B.Leitinger, E.Hohenester, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.510, 251.480, 75.370, 90.00, 90.00, 90.00
R / Rfree (%)	21.56 / 28.55

The binding sites of Calcium atom in the Crystal Structure of A DDR1-Fab Complex (pdb code 4ag4). 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 A DDR1-Fab Complex, PDB code: 4ag4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A DDR1-Fab Complex


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 A DDR1-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5001 b:39.9 occ:1.00 O A:VAL235 2.2 35.4 1.0 O A:GLN230 2.2 34.7 1.0 O A:SER360 2.3 38.2 1.0 OD1 A:ASP233 2.3 34.8 1.0 OE1 A:GLU361 2.6 45.0 1.0 CG A:ASP233 3.3 37.6 1.0 C A:VAL235 3.3 35.5 1.0 C A:GLN230 3.4 35.6 1.0 C A:SER360 3.5 35.5 1.0 N A:VAL235 3.6 36.9 1.0 OD2 A:ASP233 3.7 41.0 1.0 CD A:GLU361 3.8 42.2 1.0 CA A:VAL235 3.8 35.8 1.0 CB A:VAL235 3.8 35.3 1.0 CB A:GLU361 4.0 37.9 1.0 N A:ASP233 4.2 37.6 1.0 CA A:GLU361 4.2 37.5 1.0 CA A:GLN230 4.2 36.9 1.0 N A:GLU361 4.3 35.1 1.0 N A:LEU231 4.4 36.7 1.0 N A:GLY234 4.5 37.4 1.0 N A:VAL236 4.5 37.0 1.0 CA A:LEU231 4.5 37.5 1.0 CB A:ASP233 4.5 37.0 1.0 CG A:GLU361 4.5 39.9 1.0 CA A:SER360 4.5 34.9 1.0 C A:LEU231 4.6 38.8 1.0 CB A:GLN230 4.6 36.7 1.0 CG1 A:VAL235 4.6 35.9 1.0 OE2 A:GLU361 4.7 42.1 1.0 CA A:ASP233 4.7 38.2 1.0 C A:GLY234 4.7 37.8 1.0 C A:ASP233 4.7 38.5 1.0 N A:ALA232 4.8 38.3 1.0 CB A:SER360 4.8 34.5 1.0 O A:ASP254 4.9 42.0 1.0 CA A:VAL236 4.9 37.6 1.0 OG A:SER360 4.9 34.3 1.0 O A:LEU231 5.0 39.3 1.0 CG2 A:VAL235 5.0 33.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A DDR1-Fab Complex


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 A DDR1-Fab Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5002 b:69.7 occ:1.00 O A:ASN211 2.2 49.4 1.0 O A:TYR255 2.5 36.8 1.0 O A:TYR253 2.6 37.2 1.0 OE1 A:GLN230 2.6 43.3 1.0 C A:ASN211 3.4 46.7 1.0 C A:TYR253 3.5 37.9 1.0 CD A:GLN230 3.5 43.0 1.0 C A:TYR255 3.6 36.8 1.0 N A:ASN211 3.7 45.5 1.0 NE2 A:GLN230 3.7 43.1 1.0 O A:GLY252 3.7 43.5 1.0 OD1 A:ASN211 3.7 52.5 1.0 CA A:TYR253 3.9 38.7 1.0 O A:TYR209 3.9 49.8 1.0 N A:SER213 4.0 44.3 1.0 C A:LEU210 4.1 47.4 1.0 N A:TYR255 4.2 38.5 1.0 CA A:ASN211 4.2 46.6 1.0 N A:ASP212 4.3 44.9 1.0 CA A:LEU210 4.4 48.3 1.0 CB A:SER213 4.4 46.1 1.0 CA A:ASP212 4.4 45.3 1.0 CA A:TYR255 4.5 36.7 1.0 C A:GLY252 4.5 42.0 1.0 CG2 A:VAL256 4.6 36.4 1.0 N A:VAL256 4.6 37.5 1.0 N A:ASP254 4.6 37.7 1.0 CG A:ASN211 4.6 50.7 1.0 C A:ASP254 4.6 38.7 1.0 N A:TYR253 4.7 39.7 1.0 C A:ASP212 4.7 44.9 1.0 CA A:VAL256 4.8 38.6 1.0 O A:LEU210 4.8 49.0 1.0 NE1 A:TRP250 4.8 37.6 1.0 CA A:SER213 4.8 44.2 1.0 C A:TYR209 4.9 50.7 1.0 CG A:GLN230 4.9 40.2 1.0

F.Carafoli, M.C.Mayer, K.Shiraishi, M.A.Pecheva, L.Y.Chan, R.Nan, B.Leitinger, E.Hohenester. Structure of the Discoidin Domain Receptor 1 Extracellular Region Bound to An Inhibitory Fab Fragment Reveals Features Important For Signaling. Structure V. 20 688 2012.
ISSN: ISSN 0969-2126
PubMed: 22483115
DOI: 10.1016/J.STR.2012.02.011