Magnesium in PDB 4pzy: Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands

All present enzymatic activity of Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands:
3.6.5.2;

The structure of Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands, PDB code: 4pzy was solved by Q.Sun, J.Phan, A.Friberg, D.V.Camper, E.T.Olejniczak, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.30 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.101, 55.964, 120.761, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.8

The binding sites of Magnesium atom in the Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands (pdb code 4pzy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands, PDB code: 4pzy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:18.9 occ:1.00 O A:HOH301 2.1 10.3 1.0 O A:HOH304 2.2 14.9 1.0 O A:HOH302 2.2 9.5 1.0 O A:HOH357 2.3 13.5 1.0 O2B A:GDP201 2.4 10.3 1.0 OG A:SER17 2.5 11.1 1.0 PB A:GDP201 3.4 11.0 1.0 CB A:SER17 3.4 13.5 1.0 O3B A:GDP201 3.4 11.2 1.0 N A:SER17 4.0 8.2 1.0 OD2 A:ASP57 4.1 11.4 1.0 O2A A:GDP201 4.1 12.7 1.0 OD1 A:ASP57 4.2 10.5 1.0 O A:PRO34 4.2 11.4 1.0 CA A:SER17 4.2 9.8 1.0 O A:ASP33 4.3 14.5 1.0 CD2 A:TYR32 4.3 20.8 1.0 O1B A:GDP201 4.4 13.7 1.0 O A:THR58 4.4 14.4 1.0 CA A:PRO34 4.4 12.8 1.0 O3A A:GDP201 4.5 12.9 1.0 O A:ILE36 4.5 16.7 1.0 CE2 A:TYR32 4.5 22.0 1.0 CG A:ASP57 4.6 11.9 1.0 C A:PRO34 4.6 17.6 1.0 CB A:ALA59 4.6 13.8 1.0 PA A:GDP201 4.6 13.3 1.0 CE A:LYS16 4.7 15.4 1.0 O1A A:GDP201 4.8 12.3 1.0 CB A:LYS16 4.9 8.8 1.0 NZ A:LYS16 4.9 9.8 1.0 O A:HOH358 5.0 15.3 1.0

Magnesium binding site 2 out of 2 in the Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Second-Site Screening of K-Ras in the Presence of Covalently Attached First-Site Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:33.5 occ:1.00 O B:HOH301 1.8 11.7 1.0 O B:HOH314 2.1 14.2 1.0 O B:HOH306 2.1 14.5 1.0 O3B B:GDP201 2.3 12.3 1.0 OG B:SER17 2.3 11.0 1.0 O B:HOH464 2.8 30.0 1.0 CB B:SER17 3.3 12.5 1.0 PB B:GDP201 3.4 10.5 1.0 O2B B:GDP201 3.5 13.9 1.0 OD2 B:ASP57 3.8 11.8 1.0 N B:SER17 3.9 14.0 1.0 OD1 B:ASP57 4.1 11.7 1.0 CA B:SER17 4.1 11.9 1.0 O B:PRO34 4.3 23.3 1.0 O B:ASP33 4.3 25.5 1.0 CG B:ASP57 4.3 13.6 1.0 O2A B:GDP201 4.3 16.1 1.0 O B:THR58 4.4 12.0 1.0 O1B B:GDP201 4.4 9.8 1.0 O B:ILE36 4.4 17.4 1.0 CA B:PRO34 4.4 23.9 1.0 O B:HOH320 4.5 20.1 1.0 O3A B:GDP201 4.6 9.2 1.0 CD2 B:TYR32 4.6 22.2 1.0 C B:PRO34 4.6 25.2 1.0 CB B:ALA59 4.8 17.2 1.0 PA B:GDP201 4.8 10.6 1.0 O1A B:GDP201 4.8 18.2 1.0 CB B:LYS16 4.9 15.9 1.0 C B:LYS16 5.0 12.8 1.0 CE B:LYS16 5.0 14.1 1.0

Q.Sun, J.Phan, A.R.Friberg, D.V.Camper, E.T.Olejniczak, S.W.Fesik. A Method For the Second-Site Screening of K-Ras in the Presence of A Covalently Attached First-Site Ligand. J.Biomol.uc(Nmr) V. 60 11 2014.
ISSN: ISSN 0925-2738
PubMed: 25087006
DOI: 10.1007/S10858-014-9849-8