Chlorine in PDB 6ob3: Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)

The structure of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1), PDB code: 6ob3 was solved by T.H.Tran, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.76 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.677, 97.169, 155.525, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.6

The structure of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) (pdb code 6ob3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1), PDB code: 6ob3:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1501 b:0.9 occ:1.00 ND2 B:ASN1379 2.9 65.8 1.0 CA B:PHE1376 3.3 51.8 1.0 C B:PHE1376 3.3 52.7 1.0 N B:GLN1378 3.3 64.8 1.0 N B:PRO1377 3.5 51.1 1.0 CD B:PRO1377 3.5 57.3 1.0 CB B:GLN1378 3.6 82.8 1.0 CB B:PHE1376 3.8 47.9 1.0 O B:PHE1376 3.8 51.4 1.0 O B:HOH1661 3.8 75.2 1.0 CA B:GLN1378 3.9 69.8 1.0 CG B:ASN1379 4.1 69.5 1.0 N B:ASN1379 4.1 67.0 1.0 CG B:GLN1378 4.2 99.4 1.0 C B:PRO1377 4.3 62.0 1.0 CD1 B:PHE1376 4.3 52.1 1.0 NE2 B:GLN1378 4.3 0.7 1.0 C B:GLN1378 4.3 67.4 1.0 CA B:PRO1377 4.4 53.3 1.0 CG B:PHE1376 4.6 49.2 1.0 O B:HOH1644 4.6 62.1 1.0 N B:PHE1376 4.6 51.0 1.0 O B:ARG1375 4.6 57.3 1.0 OD1 B:ASN1379 4.7 78.8 1.0 CD B:GLN1378 4.8 0.8 1.0 CG B:PRO1377 4.8 58.3 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1502 b:0.8 occ:1.00 O B:HOH1691 2.8 74.7 1.0 O B:HOH1693 3.7 86.5 1.0 O B:HOH1661 3.8 75.2 1.0 NH2 B:ARG1375 4.0 63.2 1.0 CZ B:ARG1375 4.0 58.5 1.0 NH1 B:ARG1375 4.2 59.2 1.0 CE1 B:PHE1376 4.3 55.4 1.0 CG B:ARG1375 4.4 56.6 1.0 O B:ASP1269 4.4 59.8 1.0 NE B:ARG1375 4.5 56.2 1.0 O B:ARG1375 4.6 57.3 1.0 CZ B:PHE1376 4.8 57.1 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl203 b:90.5 occ:1.00 NH1 C:ARG68 3.5 49.7 1.0 NH2 C:ARG68 3.8 50.0 1.0 CZ C:ARG68 4.1 52.0 1.0 OE2 C:GLU62 4.4 83.3 1.0 CG C:GLU62 4.6 76.1 1.0 CB C:HIS95 4.7 77.8 1.0 CD C:GLU62 4.7 85.0 1.0

D.Rabara, T.H.Tran, S.Dharmaiah, R.M.Stephens, F.Mccormick, D.K.Simanshu, M.Holderfield. Kras G13D Sensitivity to Neurofibromin-Mediated Gtp Hydrolysis. Proc.Natl.Acad.Sci.Usa V. 116 22122 2019.
ISSN: ESSN 1091-6490
PubMed: 31611389
DOI: 10.1073/PNAS.1908353116