Magnesium in PDB 3dqw: C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs

All present enzymatic activity of C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs:
2.7.10.2;

The structure of C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs, PDB code: 3dqw was solved by M.Azam, M.A.Seeliger, N.Gray, J.Kuriyan, G.Q.Daley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.69 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.420, 103.650, 83.690, 90.00, 103.94, 90.00
R / Rfree (%)	20.5 / 24.5

The binding sites of Magnesium atom in the C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs (pdb code 3dqw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs, PDB code: 3dqw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:57.2 occ:1.00 ND2 A:ASN391 2.5 24.0 1.0 O2B A:AGS534 2.5 58.1 1.0 O2A A:AGS534 2.6 51.3 1.0 OD2 A:ASP404 2.7 43.1 1.0 O A:HOH717 3.1 54.7 1.0 CG A:ASN391 3.4 27.4 1.0 O A:HOH735 3.5 47.0 1.0 OD1 A:ASN391 3.6 26.9 1.0 PB A:AGS534 3.7 69.4 1.0 O3B A:AGS534 3.8 66.1 1.0 CG A:ASP404 3.8 43.0 1.0 O3G A:AGS534 3.9 52.6 1.0 PA A:AGS534 4.0 46.9 1.0 O3A A:AGS534 4.1 58.4 1.0 PG A:AGS534 4.4 74.2 1.0 CB A:ASP404 4.4 30.0 1.0 OD2 A:ASP386 4.6 27.5 1.0 O A:HOH640 4.7 33.5 1.0 O A:ALA390 4.7 23.8 1.0 O A:HOH661 4.8 42.9 1.0 CB A:ASN391 4.8 18.9 1.0 O A:HOH535 4.8 56.8 1.0 OD1 A:ASP404 4.8 44.4 1.0 O1A A:AGS534 4.9 48.2 1.0 O5' A:AGS534 5.0 46.9 1.0 O1B A:AGS534 5.0 77.7 1.0

Magnesium binding site 2 out of 4 in the C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:53.6 occ:1.00 OD1 B:ASN391 2.7 31.7 1.0 O1A B:AGS534 2.9 45.9 1.0 O1B B:AGS534 3.0 48.1 1.0 O B:HOH698 3.6 42.0 1.0 O B:ALA390 3.7 28.1 1.0 CG B:ASN391 3.8 28.8 1.0 OD2 B:ASP404 4.0 44.9 1.0 PA B:AGS534 4.2 49.6 1.0 C B:ALA390 4.3 26.7 1.0 PB B:AGS534 4.4 66.6 1.0 O3A B:AGS534 4.4 57.5 1.0 ND2 B:ASN391 4.4 25.8 1.0 CB B:ALA390 4.5 26.6 1.0 O5' B:AGS534 4.6 49.3 1.0 C5' B:AGS534 4.6 45.2 1.0 O3' B:AGS534 4.9 41.0 1.0 N B:ASN391 4.9 20.6 1.0 CA B:ASN391 4.9 19.6 1.0 CB B:ASN391 5.0 20.1 1.0

Magnesium binding site 3 out of 4 in the C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3 b:63.7 occ:1.00 O1B C:AGS534 2.6 70.8 1.0 OD1 C:ASN391 2.8 31.1 1.0 O3G C:AGS534 3.1 76.7 1.0 O C:HOH599 3.5 51.4 1.0 ND2 C:ASN391 3.5 30.4 1.0 CG C:ASN391 3.5 31.5 1.0 O1A C:AGS534 4.0 46.1 1.0 OD1 C:ASP404 4.1 44.0 1.0 PB C:AGS534 4.1 81.5 1.0 OD2 C:ASP386 4.1 35.5 1.0 O3B C:AGS534 4.2 74.0 1.0 PG C:AGS534 4.2 88.3 1.0 CG C:ASP404 4.5 40.9 1.0 CB C:ASP404 4.8 32.1 1.0 O2B C:AGS534 4.8 72.0 1.0 O3A C:AGS534 4.9 48.7 1.0 CB C:ASN391 5.0 24.4 1.0 CG C:ASP386 5.0 40.6 1.0

Magnesium binding site 4 out of 4 in the C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of C-Src Kinase Domain THR338ILE Mutant in Complex with Atpgs within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4 b:66.1 occ:1.00 O2B D:AGS534 2.5 72.3 1.0 OD1 D:ASN391 2.8 41.0 1.0 O2A D:AGS534 3.1 51.2 1.0 CG D:ASN391 3.8 42.3 1.0 O3G D:AGS534 3.8 75.8 1.0 O D:HOH550 4.0 54.9 1.0 PB D:AGS534 4.0 84.4 1.0 ND2 D:ASN391 4.0 38.4 1.0 PA D:AGS534 4.5 50.1 1.0 O D:ALA390 4.5 37.2 1.0 OD2 D:ASP404 4.5 49.1 1.0 O3A D:AGS534 4.5 56.5 1.0 OD1 D:ASP404 4.6 49.0 1.0 CG D:ASP404 4.6 47.1 1.0 O1B D:AGS534 4.6 72.4 1.0 CB D:ALA390 4.7 40.7 1.0 O3B D:AGS534 4.8 80.8 1.0 PG D:AGS534 4.9 90.4 1.0 C D:ALA390 4.9 41.0 1.0

M.Azam, M.A.Seeliger, N.S.Gray, J.Kuriyan, G.Q.Daley. Activation of Tyrosine Kinases By Mutation of the Gatekeeper Threonine. Nat.Struct.Mol.Biol. V. 15 1109 2008.
ISSN: ISSN 1545-9993
PubMed: 18794843
DOI: 10.1038/NSMB.1486