Magnesium in PDB 5xp5: C-Src in Complex with Atp-Chf

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

The structure of C-Src in Complex with Atp-Chf, PDB code: 5xp5 was solved by Y.Duan, M.Guo, S.Dai, L.Chen, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.45 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	42.288, 63.687, 73.815, 79.07, 89.23, 89.24
R / Rfree (%)	21.8 / 24.6

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

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the C-Src in Complex with Atp-Chf (pdb code 5xp5). 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-Chf, PDB code: 5xp5:
Jump to Magnesium binding site number: 1; 2;

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


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-Chf within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:30.0 occ:1.00 OD2 A:ASP404 1.9 78.1 1.0 O1B A:8BU601 2.2 0.4 1.0 O2A A:8BU601 2.4 0.5 1.0 PB A:8BU601 2.9 0.1 1.0 CG A:ASP404 3.0 78.6 1.0 OD1 A:ASN391 3.2 43.2 1.0 O2B A:8BU601 3.2 0.2 1.0 C01 A:8BU601 3.3 0.4 1.0 PA A:8BU601 3.3 0.0 1.0 OD1 A:ASP404 3.6 89.0 1.0 O A:ALA390 3.7 32.7 1.0 O1A A:8BU601 4.1 0.7 1.0 CB A:ASP404 4.2 59.8 1.0 F01 A:8BU601 4.2 0.9 1.0 CG A:ASN391 4.3 36.6 1.0 O3B A:8BU601 4.4 0.4 1.0 CA A:ASN391 4.6 34.8 1.0 C A:ALA390 4.6 31.6 1.0 O5' A:8BU601 4.7 0.1 1.0 O3G A:8BU601 4.9 1.0 1.0 CB A:ASN391 5.0 33.6 1.0

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


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-Chf within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:30.0 occ:1.00 OD2 B:ASP404 2.3 68.9 1.0 O1A B:8BU601 2.4 0.1 1.0 OD1 B:ASP404 2.9 90.5 1.0 CG B:ASP404 2.9 71.0 1.0 PA B:8BU601 3.5 0.1 1.0 O2A B:8BU601 3.8 1.0 1.0 O B:ALA390 3.9 44.7 1.0 O5' B:8BU601 4.2 87.6 1.0 C8 B:8BU601 4.2 53.7 1.0 CD2 B:LEU393 4.2 44.6 1.0 CB B:ALA403 4.4 42.1 1.0 CG B:LEU393 4.4 44.9 1.0 OD1 B:ASN391 4.4 55.0 1.0 CB B:ASP404 4.4 44.2 1.0 CD1 B:LEU393 4.5 35.2 1.0 O1B B:8BU601 4.5 0.7 1.0 CA B:ASN391 4.5 35.9 1.0 O1G B:8BU601 4.6 0.3 1.0 C5' B:8BU601 4.7 89.2 1.0 N7 B:8BU601 4.7 52.7 1.0 C01 B:8BU601 4.8 0.0 1.0 C2' B:8BU601 4.9 71.5 1.0 N B:ASP404 4.9 53.9 1.0 C B:ASN391 5.0 35.8 1.0 C B:ALA390 5.0 40.5 1.0 N9 B:8BU601 5.0 56.1 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