Chlorine in PDB 7yuz: Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784, PDB code: 7yuz was solved by M.Irie, T.A.Fukami, M.Tanada, A.Ohta, T.Torizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.45 / 1.88
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.012, 66.012, 86.33, 90, 90, 120
R / Rfree (%)	25.9 / 29.9

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Iodine	(I)	1 atom

The binding sites of Chlorine atom in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 (pdb code 7yuz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784, PDB code: 7yuz:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl5 b:52.8 occ:1.00 CL I:7T25 0.0 52.8 1.0 CZ I:7T25 1.7 49.2 1.0 CE1 I:7T25 2.7 47.6 1.0 CE2 I:7T25 2.7 47.7 1.0 C1 I:MEA9 3.6 57.9 1.0 CA I:MAA1 3.9 57.6 1.0 CB I:MAA1 3.9 58.3 1.0 CD1 I:7T25 4.0 46.5 1.0 CD2 I:7T25 4.0 46.6 1.0 C I:MAA1 4.1 55.4 1.0 O I:MAA1 4.1 55.4 1.0 CN I:MVA10 4.3 58.8 1.0 CG I:7T25 4.5 46.0 1.0 O I:ILE2 4.7 50.1 1.0 N I:MEA9 4.8 57.7 1.0 N I:ILE2 4.8 53.1 1.0 C I:ILE2 4.9 50.4 1.0 OD1 I:7TK11 4.9 60.7 1.0

Chlorine binding site 2 out of 2 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 within 5.0Å range: probe atom residue distance (Å) B Occ I:Cl7 b:58.4 occ:1.00 CL1 I:FCL7 0.0 58.4 1.0 CE1 I:FCL7 1.8 56.2 1.0 CZ I:FCL7 2.7 55.5 1.0 CD1 I:FCL7 2.7 54.4 1.0 NE2 A:GLN61 3.1 57.6 1.0 CD A:GLN61 3.4 58.3 1.0 OG1 A:THR58 3.5 40.8 1.0 OE1 A:GLN61 3.6 59.4 1.0 NH1 A:ARG68 3.9 61.4 1.0 C A:ALA59 3.9 46.7 1.0 N A:ALA59 3.9 42.7 1.0 CA A:ALA59 4.0 44.6 1.0 N A:GLN61 4.0 50.2 1.0 CE2 I:FCL7 4.0 55.0 1.0 CA A:GLN61 4.0 50.8 1.0 CB A:THR58 4.0 40.5 1.0 CG I:FCL7 4.0 53.3 1.0 O A:ALA59 4.0 47.9 1.0 C A:THR58 4.2 42.0 1.0 C A:GLY60 4.2 49.4 1.0 CG A:GLN61 4.2 55.8 1.0 N A:GLY60 4.3 47.6 1.0 NZ A:LYS16 4.3 53.9 1.0 O A:HOH301 4.3 34.7 1.0 O A:GLY60 4.3 50.0 1.0 O A:THR58 4.5 41.8 1.0 CD2 I:FCL7 4.5 54.1 1.0 CD A:ARG68 4.6 59.9 1.0 CB A:GLN61 4.6 52.3 1.0 O A:GLY10 4.7 42.1 1.0 CA A:THR58 4.8 41.0 1.0 CZ A:ARG68 4.8 61.8 1.0 CA A:GLY60 4.9 48.2 1.0

M.Tanada, A.Ohta. Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP8784 To Be Published.