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Calcium in PDB 3l8y: Complex of Ras with Cyclen

Protein crystallography data

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

Other elements in 3l8y:

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

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

Calcium Binding Sites:

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 3l8y

Go back to Calcium Binding Sites List in 3l8y
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 3l8y

Go back to Calcium Binding Sites List in 3l8y
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 3l8y

Go back to Calcium Binding Sites List in 3l8y
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 3l8y

Go back to Calcium Binding Sites List in 3l8y
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

Reference:

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
Page generated: Sat Dec 12 04:18:34 2020

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