Magnesium in PDB 5mlb: Crystal Structure of Human Ras in Complex with Darpin K27

The structure of Crystal Structure of Human Ras in Complex with Darpin K27, PDB code: 5mlb was solved by J.E.Debreczeni, S.Guillard, P.Kolasinska-Zwierz, J.Breed, J.Zhang, N.Bery, R.Marwood, J.Tart, R.Overman, 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 Crystal Structure of Human Ras in Complex with Darpin K27 (pdb code 5mlb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Ras in Complex with Darpin K27, PDB code: 5mlb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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 Crystal Structure of Human Ras 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.Minstry, C.Phillips, T.Rabbitts, R.Jackson, R.Minter. Inhibition of Ras Nucleotide Exchange By A Darpin: Structural Characterisation and Effects on Downstream Signalling By Active Ras To Be Published.