Magnesium in PDB 3c5c: Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp

The structure of Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp, PDB code: 3c5c was solved by L.Shen, Y.Tong, W.Tempel, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.040, 66.436, 71.943, 101.46, 90.03, 89.89
R / Rfree (%)	20.2 / 23.8

The binding sites of Magnesium atom in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp (pdb code 3c5c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp, PDB code: 3c5c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


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-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:20.8 occ:1.00 O3B A:GDP201 2.0 18.1 1.0 O A:HOH302 2.1 15.0 1.0 OG A:SER34 2.1 14.7 1.0 O A:HOH303 2.2 17.3 1.0 O A:HOH301 2.2 13.3 1.0 O A:HOH304 2.3 16.1 1.0 CB A:SER34 3.2 12.2 1.0 PB A:GDP201 3.4 20.6 1.0 O1B A:GDP201 3.7 21.4 1.0 N A:SER34 4.0 17.5 1.0 OD2 A:ASP74 4.0 20.5 1.0 OD1 A:ASP74 4.1 16.1 1.0 CA A:SER34 4.2 15.0 1.0 O2A A:GDP201 4.2 18.9 1.0 O A:ASP50 4.2 21.2 1.0 O A:PRO51 4.2 24.9 1.0 O2B A:GDP201 4.4 20.4 1.0 O A:LEU53 4.4 16.9 1.0 CG A:ASP74 4.4 15.4 1.0 O3A A:GDP201 4.4 18.9 1.0 CA A:PRO51 4.5 22.3 1.0 O A:THR75 4.5 17.8 1.0 C A:PRO51 4.6 20.5 1.0 PA A:GDP201 4.6 17.6 1.0 O1A A:GDP201 4.8 18.0 1.0 O A:TYR49 4.8 18.7 1.0 NZ A:LYS33 4.9 16.2 1.0 O A:HOH316 4.9 26.7 1.0 CB A:LYS33 4.9 16.3 1.0 CD2 A:TYR49 4.9 17.3 1.0 O A:HOH308 4.9 18.5 1.0 C A:LYS33 5.0 16.1 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


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-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:32.4 occ:1.00 O A:HOH352 2.0 21.4 1.0 OD1 A:ASP55 2.0 20.8 1.0 O A:HOH355 2.0 17.4 1.0 O A:HOH359 2.3 33.6 1.0 CG A:ASP55 3.0 20.7 1.0 OD2 A:ASP55 3.3 19.7 1.0 N A:THR56 4.2 15.8 1.0 O A:HOH322 4.3 23.7 1.0 O A:THR56 4.4 17.2 1.0 CB A:ASP55 4.4 18.7 1.0 CA A:ASP55 4.8 17.5 1.0 CB A:THR56 4.8 19.9 1.0 CA A:THR56 4.9 17.8 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


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-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:19.5 occ:1.00 O B:HOH302 2.1 17.2 1.0 OG B:SER34 2.1 14.7 1.0 O B:HOH301 2.1 12.0 1.0 O3B B:GDP201 2.2 17.5 1.0 O B:HOH304 2.2 11.6 1.0 O B:HOH303 2.3 14.5 1.0 CB B:SER34 3.1 13.5 1.0 PB B:GDP201 3.4 18.8 1.0 O1B B:GDP201 3.6 13.6 1.0 N B:SER34 3.9 15.7 1.0 OD2 B:ASP74 4.0 18.0 1.0 CA B:SER34 4.1 11.6 1.0 O2A B:GDP201 4.1 17.7 1.0 O B:PRO51 4.2 16.9 1.0 O B:ASP50 4.2 14.1 1.0 OD1 B:ASP74 4.3 11.9 1.0 CA B:PRO51 4.5 17.5 1.0 O3A B:GDP201 4.5 16.4 1.0 O2B B:GDP201 4.5 16.4 1.0 CG B:ASP74 4.5 14.1 1.0 O B:LEU53 4.6 17.4 1.0 PA B:GDP201 4.6 15.7 1.0 C B:PRO51 4.6 16.3 1.0 O B:THR75 4.7 14.6 1.0 O1A B:GDP201 4.7 16.3 1.0 O B:TYR49 4.8 17.5 1.0 O B:HOH312 4.9 14.4 1.0 CD2 B:TYR49 4.9 16.1 1.0 C B:ASP50 5.0 15.5 1.0 CB B:ALA76 5.0 19.7 1.0 CB B:LYS33 5.0 17.4 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


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-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:37.5 occ:1.00 OD1 B:ASP55 2.1 15.2 1.0 O B:HOH371 2.1 31.1 1.0 O B:HOH370 2.1 27.4 1.0 CG B:ASP55 3.0 17.0 1.0 OD2 B:ASP55 3.3 17.4 1.0 N B:THR56 4.4 19.5 1.0 CB B:ASP55 4.4 19.6 1.0 O B:THR56 4.5 19.8 1.0 O B:HOH308 4.7 21.7 1.0 CA B:ASP55 4.8 17.6 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:18.3 occ:1.00 O C:HOH302 2.1 16.9 1.0 O3B C:GDP201 2.1 15.7 1.0 OG C:SER34 2.1 15.0 1.0 O C:HOH304 2.2 16.4 1.0 O C:HOH303 2.2 15.6 1.0 O C:HOH301 2.4 19.5 1.0 CB C:SER34 3.1 10.2 1.0 PB C:GDP201 3.4 17.2 1.0 O1B C:GDP201 3.6 20.0 1.0 OD2 C:ASP74 4.0 23.1 1.0 N C:SER34 4.0 14.8 1.0 CA C:SER34 4.1 11.9 1.0 O C:ASP50 4.1 18.9 1.0 O C:PRO51 4.1 21.3 1.0 O2A C:GDP201 4.2 22.4 1.0 OD1 C:ASP74 4.2 20.1 1.0 O2B C:GDP201 4.4 19.9 1.0 O C:LEU53 4.4 18.1 1.0 CA C:PRO51 4.5 24.5 1.0 O3A C:GDP201 4.5 17.9 1.0 CG C:ASP74 4.5 19.5 1.0 O C:THR75 4.5 21.6 1.0 C C:PRO51 4.5 21.4 1.0 PA C:GDP201 4.6 19.6 1.0 O1A C:GDP201 4.6 17.7 1.0 O C:TYR49 4.7 18.6 1.0 O C:HOH321 4.8 26.3 1.0 CD2 C:TYR49 4.8 17.6 1.0 C C:ASP50 5.0 15.7 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:35.0 occ:1.00 OD1 C:ASP55 2.3 17.8 1.0 CG C:ASP55 3.2 21.6 1.0 OD2 C:ASP55 3.4 21.2 1.0 N C:THR56 4.4 20.4 1.0 O C:THR56 4.5 21.4 1.0 CB C:ASP55 4.6 22.9 1.0 O C:HOH310 4.7 19.7 1.0 CA C:ASP55 5.0 20.7 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:21.7 occ:1.00 O3B D:GDP201 2.0 17.3 1.0 O D:HOH303 2.1 14.9 1.0 O D:HOH301 2.2 16.8 1.0 OG D:SER34 2.2 17.2 1.0 O D:HOH304 2.2 12.7 1.0 O D:HOH302 2.3 16.6 1.0 CB D:SER34 3.3 17.3 1.0 PB D:GDP201 3.3 18.9 1.0 O1B D:GDP201 3.5 16.2 1.0 N D:SER34 3.9 17.2 1.0 O2A D:GDP201 4.1 21.2 1.0 OD2 D:ASP74 4.1 20.5 1.0 CA D:SER34 4.1 15.3 1.0 OD1 D:ASP74 4.1 22.8 1.0 O D:PRO51 4.2 19.1 1.0 O D:ASP50 4.2 17.9 1.0 O2B D:GDP201 4.3 18.0 1.0 O3A D:GDP201 4.3 18.6 1.0 PA D:GDP201 4.5 21.0 1.0 CG D:ASP74 4.5 17.8 1.0 O D:LEU53 4.5 18.0 1.0 O D:THR75 4.5 15.8 1.0 CA D:PRO51 4.6 17.7 1.0 C D:PRO51 4.6 20.9 1.0 O1A D:GDP201 4.7 20.7 1.0 CB D:LYS33 4.8 16.3 1.0 O D:HOH314 4.8 20.1 1.0 O D:HOH309 4.9 19.7 1.0 NZ D:LYS33 4.9 18.6 1.0 C D:LYS33 4.9 19.3 1.0 CD2 D:TYR49 4.9 24.8 1.0 CB D:ALA76 4.9 24.2 1.0 CE D:LYS33 4.9 17.5 1.0 O D:TYR49 5.0 20.7 1.0

L.Shen, Y.Tong, W.Tempel, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park. Crystal Structure of Human Ras-Like, Family 12 Protein in Complex with Gdp. To Be Published.