Magnesium in PDB 5xp7: C-Src in Complex with Atp-Chcl

All present enzymatic activity of C-Src in Complex with Atp-Chcl:
2.7.10.2;

The structure of C-Src in Complex with Atp-Chcl, PDB code: 5xp7 was solved by M.Guo, S.Dai, Y.Duan, L.Chen, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.55 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.276, 63.978, 74.003, 101.03, 89.83, 90.60
R / Rfree (%)	16.8 / 19.8

The structure of C-Src in Complex with Atp-Chcl also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the C-Src in Complex with Atp-Chcl (pdb code 5xp7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the C-Src in Complex with Atp-Chcl, PDB code: 5xp7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the C-Src in Complex with Atp-Chcl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C-Src in Complex with Atp-Chcl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:74.4 occ:1.00 O1A A:8C6600 2.1 0.0 1.0 O A:HOH835 2.5 54.2 1.0 OD2 A:ASP404 2.6 78.9 1.0 O1B A:8C6600 2.7 0.2 1.0 OD1 A:ASN391 3.1 38.0 1.0 O A:ALA390 3.2 29.7 1.0 PA A:8C6600 3.5 0.8 1.0 O A:HOH755 3.8 58.5 1.0 PB A:8C6600 3.8 0.6 1.0 CG A:ASP404 3.8 72.6 1.0 O A:HOH736 4.1 43.5 1.0 O2A A:8C6600 4.1 0.7 1.0 C3A A:8C6600 4.1 0.1 1.0 C A:ALA390 4.1 29.8 1.0 CG A:ASN391 4.3 33.8 1.0 OD1 A:ASP404 4.5 81.4 1.0 O3B A:8C6600 4.5 0.1 1.0 CA A:ASN391 4.6 26.4 1.0 O5' A:8C6600 4.6 78.2 1.0 N A:ASN391 4.8 29.0 1.0 CB A:ALA390 4.9 26.9 1.0 O2B A:8C6600 4.9 0.9 1.0 C5' A:8C6600 4.9 81.9 1.0 CB A:ASP404 5.0 51.3 1.0

Magnesium binding site 2 out of 2 in the C-Src in Complex with Atp-Chcl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C-Src in Complex with Atp-Chcl within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:49.0 occ:1.00 OD1 B:ASP404 2.2 61.3 1.0 O2B B:8C6601 2.3 67.4 1.0 O B:HOH775 2.3 57.5 1.0 O B:HOH856 2.3 35.0 1.0 O2A B:8C6601 2.4 56.8 1.0 OD1 B:ASN391 2.6 34.9 1.0 O B:HOH705 3.3 48.4 1.0 CG B:ASP404 3.3 68.5 1.0 PB B:8C6601 3.3 67.0 1.0 CG B:ASN391 3.5 32.9 1.0 O1B B:8C6601 3.5 63.1 1.0 PA B:8C6601 3.5 61.2 1.0 ND2 B:ASN391 3.7 27.4 1.0 CB B:ASP404 3.9 39.6 1.0 C3A B:8C6601 3.9 98.4 1.0 O B:HOH726 3.9 50.7 1.0 O1A B:8C6601 4.0 62.5 1.0 OD2 B:ASP404 4.3 66.1 1.0 OD2 B:ASP386 4.4 45.5 1.0 O B:HOH848 4.5 67.4 1.0 O3B B:8C6601 4.6 64.6 1.0 O B:HOH854 4.6 40.2 1.0 O5' B:8C6601 4.8 41.8 1.0 CB B:ASN391 4.9 22.4 1.0 O B:HOH807 4.9 54.7 1.0 O B:HOH808 5.0 46.5 1.0

F.Ni, A.Kung, Y.Duan, V.Shah, C.D.Amador, M.Guo, X.Fan, L.Chen, Y.Chen, C.E.Mckenna, C.Zhang. Remarkably Stereospecific Utilization of Atp Alpha , Beta-Halomethylene Analogues By Protein Kinases. J. Am. Chem. Soc. V. 139 7701 2017.
ISSN: ESSN 1520-5126
PubMed: 28535041
DOI: 10.1021/JACS.7B03266