Calcium in PDB 4ra0: An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis

All present enzymatic activity of An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis:
2.7.10.1;

The structure of An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis, PDB code: 4ra0 was solved by M.S.Kariolis, S.Kapur, I.I.Mathews, J.R.Cochran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.01 / 3.07
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.370, 112.370, 361.260, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.3

The structure of An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis (pdb code 4ra0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis, PDB code: 4ra0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:71.8 occ:1.00 OD2 A:ASP329 2.3 75.2 1.0 OD1 A:ASP329 2.3 65.4 1.0 O A:GLU331 2.3 82.8 1.0 OD2 A:ASP656 2.3 77.0 1.0 O A:ARG440 2.3 78.7 1.0 CG A:ASP329 2.4 67.7 1.0 CG A:ASP656 3.4 78.9 1.0 C A:GLU331 3.5 79.3 1.0 C A:ARG440 3.6 79.9 1.0 CB A:ASP329 3.9 65.4 1.0 CE1 A:HIS668 4.0 84.8 1.0 CB A:ASP656 4.1 77.3 1.0 CA A:LEU441 4.2 75.6 1.0 CA A:GLU331 4.2 75.6 1.0 N A:GLU331 4.3 72.6 1.0 N A:LEU441 4.3 75.3 1.0 OD1 A:ASP656 4.3 79.3 1.0 CB A:GLU331 4.4 80.3 1.0 ND1 A:HIS668 4.4 89.0 1.0 N A:GLY332 4.5 81.4 1.0 O A:ASN438 4.5 90.0 1.0 N A:ASP442 4.7 78.5 1.0 CA A:GLY332 4.7 79.1 1.0 CA A:ARG440 4.7 81.9 1.0 CG A:GLU331 4.7 80.8 1.0 CB A:ARG440 4.8 83.2 1.0 NE2 A:HIS668 4.8 87.3 1.0 CA A:ASP329 4.9 66.8 1.0 OD1 A:ASP654 4.9 75.9 1.0 OD2 A:ASP654 5.0 78.0 1.0 C A:LEU441 5.0 75.6 1.0

Calcium binding site 2 out of 2 in the An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:70.5 occ:1.00 OD2 B:ASP329 2.3 74.3 1.0 OD1 B:ASP329 2.3 73.2 1.0 O B:GLU331 2.3 67.7 1.0 OD2 B:ASP656 2.3 80.9 1.0 O B:ARG440 2.3 70.9 1.0 CG B:ASP329 2.4 68.0 1.0 CG B:ASP656 3.4 77.8 1.0 C B:GLU331 3.4 67.0 1.0 C B:ARG440 3.6 67.0 1.0 CB B:ASP656 4.0 74.8 1.0 CE1 B:HIS668 4.0 71.6 1.0 CB B:ASP329 4.0 65.7 1.0 CA B:GLU331 4.1 70.3 1.0 CB B:GLU331 4.1 73.7 1.0 N B:GLU331 4.1 69.0 1.0 CA B:LEU441 4.3 68.2 1.0 OD1 B:ASP656 4.4 73.2 1.0 N B:LEU441 4.4 66.7 1.0 O B:ASN438 4.4 69.8 1.0 ND1 B:HIS668 4.4 70.3 1.0 N B:GLY332 4.5 65.6 1.0 OD2 B:ASP654 4.6 85.6 1.0 CA B:GLY332 4.7 66.0 1.0 CA B:ARG440 4.7 65.4 1.0 OD1 B:ASP654 4.8 77.5 1.0 CB B:ARG440 4.8 68.7 1.0 NE2 B:HIS668 4.9 73.0 1.0 N B:ASP442 4.9 70.7 1.0 CA B:ASP329 4.9 68.0 1.0 CG B:GLU331 4.9 77.3 1.0

M.S.Kariolis, Y.R.Miao, D.S.Jones, S.Kapur, I.I.Mathews, A.J.Giaccia, J.R.Cochran. An Engineered Axl 'Decoy Receptor' Effectively Silences the GAS6-Axl Signaling Axis. Nat.Chem.Biol. V. 10 977 2014.
ISSN: ISSN 1552-4450
PubMed: 25242553
DOI: 10.1038/NCHEMBIO.1636