Calcium in PDB 3l8y: Complex of Ras with Cyclen

The structure of Complex of Ras with Cyclen, PDB code: 3l8y 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)	19.92 / 2.02
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.000, 88.000, 134.000, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 23.8

The structure of Complex of Ras with Cyclen also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Complex of Ras with Cyclen (pdb code 3l8y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex of Ras with Cyclen, PDB code: 3l8y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex of Ras with Cyclen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Ras with Cyclen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:30.5 occ:0.33 O A:HOH298 2.3 21.1 1.0 O A:HOH285 2.4 25.2 1.0 NE2 A:GLN129 3.9 20.1 1.0 O A:THR124 4.1 13.9 1.0 OE1 A:GLN129 4.4 18.7 1.0 O A:HOH290 4.5 22.9 1.0 CD A:GLN129 4.6 18.2 1.0

Calcium binding site 2 out of 4 in the Complex of Ras with Cyclen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Ras with Cyclen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:11.4 occ:1.00 O A:PHE28 2.3 13.4 1.0 O A:HOH269 2.3 21.4 1.0 OD1 A:ASP30 2.3 13.8 1.0 O A:HOH200 2.3 12.0 1.0 C A:PHE28 3.5 13.1 1.0 CG A:ASP30 3.5 13.9 1.0 N A:ASP30 3.9 13.1 1.0 CA A:VAL29 4.3 13.3 1.0 CB A:ASP30 4.3 13.4 1.0 O A:HOH196 4.3 19.1 1.0 N A:VAL29 4.3 13.2 1.0 O A:HOH179 4.4 28.1 1.0 OD2 A:ASP30 4.5 15.1 1.0 CA A:PHE28 4.5 13.1 1.0 C A:VAL29 4.6 13.2 1.0 N A:PHE28 4.6 13.1 1.0 CA A:ASP30 4.8 13.4 1.0 CB A:PHE28 4.8 12.9 1.0 ND1 A:HIS27 5.0 12.6 1.0

Calcium binding site 3 out of 4 in the Complex of Ras with Cyclen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Ras with Cyclen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:28.6 occ:0.50 O A:HOH288 1.8 12.6 0.5 O A:ARG102 2.3 23.2 1.0 OD1 A:ASP105 2.5 26.5 1.0 CG A:ASP105 3.2 25.7 1.0 OD2 A:ASP105 3.4 26.9 1.0 C A:ARG102 3.4 23.2 1.0 CA A:ARG102 4.2 23.3 1.0 N A:VAL103 4.3 23.1 1.0 CA A:VAL103 4.4 23.0 1.0 CB A:ASP105 4.5 25.1 1.0 N A:ASP105 4.6 24.4 1.0 C A:VAL103 4.6 23.1 1.0 CB A:ARG102 4.7 23.4 1.0 CA A:ASP105 4.7 24.9 1.0 O A:VAL103 4.7 22.7 1.0

Calcium binding site 4 out of 4 in the Complex of Ras with Cyclen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Ras with Cyclen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:78.9 occ:1.00 OE2 A:GLU153 2.9 19.1 1.0 O A:HOH232 3.6 24.9 1.0 CD A:GLU153 3.6 15.1 1.0 OE1 A:GLU153 3.7 18.5 1.0 NH1 A:ARG149 4.5 21.9 1.0 CG A:GLU153 5.0 14.3 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