Magnesium in PDB 5o2s: Human Kras in Complex with Darpin K27

The structure of Human Kras in Complex with Darpin K27, PDB code: 5o2s was solved by J.E.Debreczeni, S.Guillard, P.Kolasinska-Zwierz, J.Breed, J.Zhang, N.Bery, R.Marwood, J.Tart, P.Stocki, B.Mistry, C.Phillips, T.Rabbitts, R.Jackson, R.Minter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.57 / 3.22
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	197.140, 197.140, 84.610, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.5

The binding sites of Magnesium atom in the Human Kras in Complex with Darpin K27 (pdb code 5o2s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Kras in Complex with Darpin K27, PDB code: 5o2s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Kras in Complex with Darpin K27


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Kras in Complex with Darpin K27 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:33.1 occ:1.00 O A:HOH301 1.9 38.5 1.0 O A:HOH305 1.9 40.1 1.0 O A:HOH304 2.0 38.3 1.0 O2B A:GDP201 2.0 41.4 1.0 O A:HOH302 2.1 47.2 1.0 OG A:SER17 2.1 46.7 1.0 PB A:GDP201 3.1 40.9 1.0 O3B A:GDP201 3.3 38.4 1.0 CB A:SER17 3.4 48.3 1.0 OD1 A:ASP57 3.8 70.0 1.0 O A:ASP33 4.0 45.2 1.0 O A:PRO34 4.1 48.1 1.0 O1B A:GDP201 4.1 36.1 1.0 O1A A:GDP201 4.2 38.4 1.0 N A:SER17 4.2 49.3 1.0 O3A A:GDP201 4.3 42.2 1.0 CA A:PRO34 4.3 45.2 1.0 CB A:ALA59 4.3 55.8 1.0 CA A:SER17 4.4 48.8 1.0 C A:PRO34 4.4 48.1 1.0 OD2 A:ASP57 4.4 69.5 1.0 CD2 A:TYR32 4.6 51.9 1.0 CG A:ASP57 4.6 70.5 1.0 PA A:GDP201 4.6 41.9 1.0 O A:THR58 4.6 49.2 1.0 O2A A:GDP201 4.7 43.0 1.0 O A:ILE36 4.7 55.5 1.0 NZ A:LYS16 4.8 53.5 1.0 C A:ASP33 4.9 46.5 1.0 CE2 A:TYR32 4.9 51.0 1.0 CE A:LYS16 5.0 53.1 1.0

Magnesium binding site 2 out of 4 in the Human Kras in Complex with Darpin K27


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Kras in Complex with Darpin K27 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:41.2 occ:1.00 O C:HOH302 1.8 53.2 1.0 O C:HOH304 1.9 58.9 1.0 OG C:SER17 2.1 47.1 1.0 O C:HOH303 2.1 48.7 1.0 O3B C:GDP201 2.4 44.8 1.0 O C:HOH301 2.5 49.8 1.0 CB C:SER17 3.3 51.0 1.0 PB C:GDP201 3.5 44.2 1.0 O1B C:GDP201 3.7 44.8 1.0 O C:ASP33 3.8 53.8 1.0 OD1 C:ASP57 3.9 75.4 1.0 O C:PRO34 4.1 58.8 1.0 O1A C:GDP201 4.1 39.6 1.0 CA C:PRO34 4.2 57.9 1.0 N C:SER17 4.3 51.7 1.0 CD2 C:TYR32 4.3 57.6 1.0 CB C:ALA59 4.3 57.4 1.0 C C:PRO34 4.3 59.0 1.0 OD2 C:ASP57 4.4 76.1 1.0 CA C:SER17 4.4 52.4 1.0 O3A C:GDP201 4.5 45.2 1.0 O C:ILE36 4.6 68.3 1.0 CG C:ASP57 4.6 72.4 1.0 PA C:GDP201 4.6 44.4 1.0 O2B C:GDP201 4.6 41.4 1.0 CE2 C:TYR32 4.7 57.6 1.0 C C:ASP33 4.7 56.0 1.0 O C:THR58 4.8 53.2 1.0 O2A C:GDP201 4.8 40.7 1.0 N C:PRO34 5.0 58.1 1.0

Magnesium binding site 3 out of 4 in the Human Kras in Complex with Darpin K27


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Kras in Complex with Darpin K27 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:50.4 occ:1.00 O E:HOH301 1.8 54.8 1.0 O E:HOH303 1.9 56.1 1.0 O E:HOH302 2.0 39.4 1.0 O3B E:GDP201 2.1 47.6 1.0 OG E:SER17 2.2 56.6 1.0 O E:HOH304 2.2 56.0 1.0 PB E:GDP201 3.2 46.4 1.0 O1B E:GDP201 3.2 46.6 1.0 CB E:SER17 3.3 56.9 1.0 OD1 E:ASP57 4.0 73.3 1.0 O1A E:GDP201 4.0 52.2 1.0 O E:ASP33 4.0 53.0 1.0 O E:PRO34 4.1 59.4 1.0 N E:SER17 4.2 59.9 1.0 CA E:PRO34 4.2 57.1 1.0 O3A E:GDP201 4.3 49.2 1.0 O2B E:GDP201 4.3 38.6 1.0 C E:PRO34 4.3 60.3 1.0 CA E:SER17 4.3 58.7 1.0 PA E:GDP201 4.4 52.8 1.0 CD2 E:TYR32 4.5 63.0 1.0 CB E:ALA59 4.5 80.0 1.0 OD2 E:ASP57 4.5 68.8 1.0 CG E:ASP57 4.7 70.8 1.0 O2A E:GDP201 4.7 51.1 1.0 O E:THR58 4.8 66.7 1.0 C E:ASP33 4.9 56.2 1.0 O E:ILE36 4.9 68.1 1.0 NZ E:LYS16 4.9 65.8 1.0 CE2 E:TYR32 4.9 60.2 1.0

Magnesium binding site 4 out of 4 in the Human Kras in Complex with Darpin K27


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Kras in Complex with Darpin K27 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg202 b:53.4 occ:1.00 O G:HOH303 2.0 53.5 1.0 O G:HOH304 2.0 70.6 1.0 O G:HOH301 2.2 0.9 1.0 OG G:SER17 2.6 97.7 1.0 O3B G:GDP201 2.6 79.3 1.0 O G:HOH302 2.9 74.8 1.0 O1B G:GDP201 3.3 84.2 1.0 PB G:GDP201 3.4 81.6 1.0 O G:PRO34 3.6 99.5 1.0 O G:ASP33 3.7 0.4 1.0 CA G:PRO34 3.7 98.0 1.0 CB G:SER17 3.8 0.0 1.0 C G:PRO34 3.8 0.5 1.0 O1A G:GDP201 3.9 86.6 1.0 CB G:ALA59 4.2 0.8 1.0 OD1 G:ASP57 4.3 0.4 1.0 C G:ASP33 4.5 99.8 1.0 O3A G:GDP201 4.5 80.5 1.0 O2B G:GDP201 4.5 74.4 1.0 PA G:GDP201 4.5 88.2 1.0 CD2 G:TYR32 4.6 0.3 1.0 N G:PRO34 4.6 98.0 1.0 N G:SER17 4.7 0.5 1.0 O2A G:GDP201 4.7 89.7 1.0 O G:ILE36 4.8 0.8 1.0 N G:THR35 4.8 0.9 1.0 CB G:PRO34 4.8 95.6 1.0 OD2 G:ASP57 4.8 0.2 1.0 O G:THR58 4.8 0.5 1.0 CA G:SER17 4.9 0.2 1.0 NZ G:LYS16 4.9 0.3 1.0

S.Guillard, P.Kolasinska-Zwierz, J.Debreczeni, J.Breed, J.Zhang, N.Bery, R.Marwood, J.Tart, R.Overman, P.Stocki, B.Mistry, C.Phillips, T.Rabbitts, R.Jackson, R.Minter. Structural and Functional Characterization of A Darpin Which Inhibits Ras Nucleotide Exchange. Nat Commun V. 8 16111 2017.
ISSN: ESSN 2041-1723
PubMed: 28706291
DOI: 10.1038/NCOMMS16111