Calcium in PDB 3l8z: H-Ras Wildtype New Crystal Form

The structure of H-Ras Wildtype New Crystal Form, PDB code: 3l8z was solved by I.C.Rosnizeck, T.Graf, M.Spoerner, J.Traenkle, D.Filchtinski, C.Herrmann, L.Gremer, I.R.Vetter, A.Wittinghofer, B.Koenig, H.R.Kalbitzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.44
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.082, 88.082, 133.391, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 22

The structure of H-Ras Wildtype New Crystal Form also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the H-Ras Wildtype New Crystal Form (pdb code 3l8z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the H-Ras Wildtype New Crystal Form, PDB code: 3l8z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the H-Ras Wildtype New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of H-Ras Wildtype New Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:27.1 occ:0.33 O A:HOH355 2.2 25.3 1.0 O A:HOH232 2.3 22.3 1.0 NE2 A:GLN129 4.0 28.0 1.0 O A:THR124 4.1 17.8 1.0 O A:HOH241 4.3 22.8 1.0 OE1 A:GLN129 4.4 25.5 1.0 CD A:GLN129 4.6 25.0 1.0

Calcium binding site 2 out of 4 in the H-Ras Wildtype New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of H-Ras Wildtype New Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:14.6 occ:1.00 O A:HOH246 2.3 19.1 1.0 O A:PHE28 2.3 13.8 1.0 OD1 A:ASP30 2.3 16.5 1.0 O A:HOH293 2.5 21.3 1.0 C A:PHE28 3.5 13.7 1.0 CG A:ASP30 3.5 15.5 1.0 N A:ASP30 3.9 13.3 1.0 CA A:VAL29 4.3 13.6 0.5 CA A:VAL29 4.3 12.7 0.5 O A:HOH225 4.3 30.1 1.0 CB A:ASP30 4.3 14.7 1.0 N A:VAL29 4.4 12.8 1.0 O A:HOH261 4.4 22.7 1.0 OD2 A:ASP30 4.5 18.8 1.0 O A:HOH396 4.5 37.6 1.0 CA A:PHE28 4.5 13.7 1.0 C A:VAL29 4.6 13.3 1.0 N A:PHE28 4.6 14.4 1.0 O A:HOH237 4.6 29.1 1.0 CB A:PHE28 4.8 13.8 1.0 CA A:ASP30 4.8 14.2 1.0 O A:HOH399 4.9 31.1 1.0 ND1 A:HIS27 4.9 16.1 1.0 CD2 A:PHE28 5.0 14.4 1.0

Calcium binding site 3 out of 4 in the H-Ras Wildtype New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of H-Ras Wildtype New Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:24.7 occ:1.00 O A:ASP107 2.2 24.6 1.0 O A:HOH292 2.2 27.1 1.0 O A:TYR137 2.3 18.4 1.0 O A:HOH338 2.4 27.1 1.0 O A:HOH334 2.4 28.5 1.0 O A:HOH428 2.4 34.4 1.0 O A:HOH339 2.6 32.1 1.0 C A:ASP107 3.3 25.1 1.0 C A:TYR137 3.5 17.5 1.0 CA A:ASP108 4.0 24.0 0.5 CA A:ASP108 4.1 24.1 0.5 N A:ASP108 4.1 24.3 1.0 CA A:TYR137 4.2 17.7 1.0 OD1 A:ASP107 4.2 33.2 1.0 CE A:MET111 4.3 17.5 0.5 CA A:ASP107 4.4 26.2 1.0 NH1 A:ARG97 4.4 16.6 0.5 CG A:ASP107 4.4 29.4 1.0 NH2 A:ARG97 4.5 27.1 0.5 CB A:TYR137 4.5 17.6 1.0 N A:GLY138 4.5 17.0 1.0 O A:HOH297 4.5 36.0 1.0 N A:VAL109 4.5 21.6 1.0 CG2 A:ILE139 4.6 15.2 1.0 O A:HOH264 4.7 65.5 1.0 OD2 A:ASP107 4.7 32.8 1.0 O A:HOH409 4.7 29.9 1.0 C A:ASP108 4.7 23.3 1.0 CA A:GLY138 4.8 16.6 1.0 O A:VAL109 4.8 17.7 1.0 OD1 A:ASP108 4.9 26.7 0.5 CB A:ASP107 4.9 27.1 1.0 NE A:ARG97 5.0 15.3 0.5

Calcium binding site 4 out of 4 in the H-Ras Wildtype New Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of H-Ras Wildtype New Crystal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:36.6 occ:1.00 OE1 A:GLN165 2.4 17.6 0.5 O A:HOH401 2.4 42.7 1.0 O A:HOH361 2.5 22.2 0.5 O A:HOH420 3.4 53.4 1.0 CD A:GLN165 3.5 14.0 0.5 NE2 A:GLN165 4.0 14.4 0.5 OE2 A:GLU162 4.5 15.0 0.5 CG A:GLN165 4.7 13.6 0.5 OE1 A:GLU162 4.7 14.4 0.5 CB A:GLN165 4.9 13.5 0.5 OE2 A:GLU162 4.9 20.2 0.5 O A:HOH408 4.9 0.2 1.0

I.C.Rosnizeck, T.Graf, M.Spoerner, J.Trankle, D.Filchtinski, C.Herrmann, L.Gremer, I.R.Vetter, A.Wittinghofer, B.Konig, H.R.Kalbitzer. Stabilizing A Weak Binding State For Effectors in the Human Ras Protein By Cyclen Complexes Angew.Chem.Int.Ed.Engl. V. 49 3830 2010.
ISSN: ISSN 1433-7851
PubMed: 20401883
DOI: 10.1002/ANIE.200907002