Magnesium in PDB 4q01: 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: 4q01 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)	25.01 / 1.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.314, 83.671, 104.835, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.3

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 4q01). 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: 4q01:
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:10.9 occ:1.00 O1B A:GDP201 2.0 10.1 1.0 O A:HOH303 2.0 11.6 1.0 O A:HOH302 2.1 12.1 1.0 O A:HOH304 2.1 10.7 1.0 OG A:SER17 2.1 10.0 1.0 O A:HOH301 2.1 12.6 1.0 HB2 A:SER17 3.1 13.4 1.0 CB A:SER17 3.2 11.2 1.0 PB A:GDP201 3.3 10.4 1.0 H A:SER17 3.4 11.0 1.0 HA A:PRO34 3.5 15.9 1.0 O2B A:GDP201 3.6 11.8 1.0 HD2 A:TYR32 3.7 19.5 1.0 HB3 A:SER17 3.8 13.4 1.0 N A:SER17 4.0 9.2 1.0 HB2 A:LYS16 4.0 11.8 1.0 OD2 A:ASP57 4.1 11.0 1.0 CA A:SER17 4.1 9.3 1.0 O1A A:GDP201 4.1 14.8 1.0 HE2 A:LYS16 4.2 15.2 1.0 OD1 A:ASP57 4.2 11.9 1.0 O A:ASP33 4.3 14.0 1.0 O A:PRO34 4.3 12.8 1.0 O3A A:GDP201 4.3 10.6 1.0 CA A:PRO34 4.4 13.2 1.0 O3B A:GDP201 4.4 10.7 1.0 HA A:SER17 4.4 11.1 1.0 O A:THR58 4.5 12.9 1.0 O A:ILE36 4.5 13.3 1.0 CG A:ASP57 4.5 10.8 1.0 CD2 A:TYR32 4.6 16.3 1.0 PA A:GDP201 4.6 11.8 1.0 C A:PRO34 4.6 13.1 1.0 HZ1 A:LYS16 4.7 13.2 1.0 O2A A:GDP201 4.7 12.2 1.0 HB3 A:TYR32 4.8 21.6 1.0 HZ3 A:LYS16 4.8 13.2 1.0 HE2 A:TYR32 4.9 24.3 1.0 O A:TYR32 4.9 16.5 1.0 CB A:LYS16 4.9 9.8 1.0 O A:HOH307 5.0 15.5 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:10.4 occ:1.00 O2B B:GDP201 2.0 10.7 1.0 O B:HOH303 2.0 10.8 1.0 O B:HOH301 2.1 10.8 1.0 O B:HOH302 2.1 10.7 1.0 OG B:SER17 2.1 10.6 1.0 O B:HOH304 2.1 11.7 1.0 HB2 B:SER17 3.2 13.9 1.0 CB B:SER17 3.2 11.6 1.0 PB B:GDP201 3.3 10.2 1.0 H B:SER17 3.4 11.9 1.0 HA B:PRO34 3.4 16.1 1.0 HD2 B:TYR32 3.5 16.1 1.0 O3B B:GDP201 3.6 10.3 1.0 HB3 B:SER17 3.8 13.9 1.0 N B:SER17 3.9 9.9 1.0 HB2 B:LYS16 4.0 12.1 1.0 HE2 B:TYR32 4.0 18.3 1.0 OD2 B:ASP57 4.1 12.1 1.0 O2A B:GDP201 4.1 12.6 1.0 CA B:SER17 4.1 9.7 1.0 HE2 B:LYS16 4.2 16.9 1.0 OD1 B:ASP57 4.2 12.8 1.0 CD2 B:TYR32 4.3 13.4 1.0 O B:PRO34 4.3 12.2 1.0 CA B:PRO34 4.3 13.5 1.0 O3A B:GDP201 4.3 10.5 1.0 O B:ASP33 4.3 13.3 1.0 O1B B:GDP201 4.4 10.0 1.0 O B:THR58 4.4 12.8 1.0 HA B:SER17 4.4 11.6 1.0 O B:ILE36 4.5 13.0 1.0 CG B:ASP57 4.5 11.7 1.0 PA B:GDP201 4.5 10.8 1.0 CE2 B:TYR32 4.6 15.3 1.0 C B:PRO34 4.6 12.4 1.0 O1A B:GDP201 4.7 11.9 1.0 HZ1 B:LYS16 4.8 12.1 1.0 O B:TYR32 4.9 15.7 1.0 HZ3 B:LYS16 4.9 12.1 1.0 CB B:LYS16 4.9 10.1 1.0 O B:HOH306 4.9 13.9 1.0 HB3 B:TYR32 5.0 18.6 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