Calcium in PDB 2c2h: Crystal Structure of the Human RAC3 in Complex with Gdp

The structure of Crystal Structure of the Human RAC3 in Complex with Gdp, PDB code: 2c2h was solved by J.E.Debreczeni, X.Yang, Y.Zao, J.Elkins, C.Gileadi, N.Burgess, S.Colebrook, O.Gileadi, O.Fedorov, G.Bunkoczi, F.Von Delft, D.Doyle, M.Sundstrom, C.Arrowsmith, J.Weigelt, A.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.14 / 1.85
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	110.320, 110.320, 81.790, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 22.9

The structure of Crystal Structure of the Human RAC3 in Complex with Gdp also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Human RAC3 in Complex with Gdp (pdb code 2c2h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of the Human RAC3 in Complex with Gdp, PDB code: 2c2h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1183 b:17.2 occ:1.00 O A:HOH2050 1.9 33.6 1.0 O2B A:GDP1180 2.0 20.2 1.0 N7 A:GDP1179 2.0 31.7 1.0 NE2 A:HIS104 2.1 25.9 1.0 CE1 A:HIS104 3.0 25.9 1.0 C5 A:GDP1179 3.0 31.8 1.0 C8 A:GDP1179 3.1 32.2 1.0 PB A:GDP1180 3.1 21.0 1.0 CD2 A:HIS104 3.2 24.5 1.0 O6 A:GDP1179 3.2 32.0 1.0 O3B A:GDP1180 3.3 16.8 1.0 C6 A:GDP1179 3.6 31.8 1.0 O3A A:GDP1180 3.9 22.2 1.0 ND1 A:HIS104 4.1 22.0 1.0 N9 A:GDP1179 4.2 32.0 1.0 C4 A:GDP1179 4.2 32.3 1.0 CG A:HIS104 4.3 22.0 1.0 O1B A:GDP1180 4.3 19.0 1.0 CD2 A:HIS103 4.5 20.4 1.0 NE2 A:HIS103 4.8 18.7 1.0 CA A:CA1184 4.8 8.3 1.0 N1 A:GDP1179 4.9 32.4 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1184 b:8.3 occ:1.00 O3B A:GDP1179 1.7 22.3 1.0 O3B A:GDP1180 1.8 16.8 1.0 NE2 A:HIS103 1.9 18.7 1.0 N7 A:GDP1180 2.0 16.0 1.0 CE1 A:HIS103 2.9 19.1 1.0 CD2 A:HIS103 2.9 20.4 1.0 PB A:GDP1179 3.0 18.5 1.0 C5 A:GDP1180 3.0 13.7 1.0 C8 A:GDP1180 3.0 15.5 1.0 O1B A:GDP1179 3.2 17.9 1.0 PB A:GDP1180 3.2 21.0 1.0 O6 A:GDP1180 3.4 16.8 1.0 C6 A:GDP1180 3.7 15.9 1.0 O1B A:GDP1180 3.7 19.0 1.0 O A:HOH2087 3.8 17.7 1.0 O3A A:GDP1180 3.9 22.2 1.0 O2B A:GDP1179 3.9 19.6 1.0 ND1 A:HIS103 4.0 17.7 1.0 CG A:HIS103 4.1 19.3 1.0 N9 A:GDP1180 4.2 15.2 1.0 O3A A:GDP1179 4.2 22.6 1.0 C4 A:GDP1180 4.3 14.7 1.0 C8 A:GDP1179 4.3 32.2 1.0 O4' A:GDP1179 4.3 31.8 1.0 O2B A:GDP1180 4.3 20.2 1.0 O5' A:GDP1179 4.4 26.9 1.0 MG A:MG1191 4.4 20.4 1.0 N7 A:GDP1179 4.5 31.7 1.0 N9 A:GDP1179 4.5 32.0 1.0 MG A:MG1192 4.8 23.9 1.0 CA A:CA1183 4.8 17.2 1.0 PA A:GDP1179 4.8 23.1 1.0 C4 A:GDP1179 4.9 32.3 1.0 C5 A:GDP1179 4.9 31.8 1.0 O1A A:GDP1179 4.9 19.7 1.0 NE2 A:HIS104 4.9 25.9 1.0 C5' A:GDP1179 5.0 30.5 1.0 O1A A:GDP1180 5.0 20.1 1.0 C1' A:GDP1179 5.0 32.8 1.0 O A:HIS103 5.0 19.2 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1185 b:6.7 occ:1.00 O2B A:GDP1181 1.9 16.2 1.0 PB A:GDP1181 3.2 14.9 1.0 O A:HOH2105 3.3 14.2 0.3 O1B A:GDP1181 3.5 18.3 1.0 N2 A:GDP1180 3.7 14.3 1.0 CA A:CA1187 3.9 24.1 0.3 O4 A:SO41188 4.0 20.1 1.0 O1A A:GDP1181 4.0 15.8 1.0 O3A A:GDP1181 4.1 16.4 1.0 O3B A:GDP1181 4.4 15.7 1.0 PA A:GDP1181 4.4 16.7 1.0 CA A:CA1193 4.4 10.3 1.0 C2 A:GDP1180 4.5 15.8 1.0 O2 A:SO41189 4.7 16.0 1.0 O4 A:SO41189 4.7 20.4 1.0 O2A A:GDP1181 4.8 14.9 1.0 N1 A:GDP1180 4.8 14.9 1.0 S A:SO41188 5.0 23.1 1.0 O1 A:SO41188 5.0 22.3 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1186 b:8.8 occ:1.00 O2 A:SO41188 1.9 18.2 1.0 O3B A:GDP1181 1.9 15.7 1.0 O1 A:SO41189 2.0 21.0 1.0 NE2 A:HIS107 2.0 19.3 1.0 CD2 A:HIS107 3.0 15.3 1.0 CE1 A:HIS107 3.0 18.8 1.0 S A:SO41189 3.1 19.3 1.0 S A:SO41188 3.2 23.1 1.0 PB A:GDP1181 3.2 14.9 1.0 O2 A:SO41189 3.2 16.0 1.0 O4 A:SO41188 3.4 20.1 1.0 O2B A:GDP1181 3.7 16.2 1.0 O4 A:SO41189 3.8 20.4 1.0 CG A:PRO106 4.0 21.7 1.0 O1B A:GDP1181 4.1 18.3 1.0 N7 A:GDP1181 4.1 15.6 1.0 CG A:HIS107 4.1 18.6 1.0 ND1 A:HIS107 4.1 17.5 1.0 O3 A:SO41188 4.1 21.8 1.0 O1 A:SO41188 4.2 22.3 1.0 CA A:CA1193 4.2 10.3 1.0 O3A A:GDP1181 4.2 16.4 1.0 CB A:PRO106 4.3 20.5 1.0 O3 A:SO41189 4.4 21.8 1.0 O6 A:GDP1181 4.4 16.4 1.0 C5 A:GDP1181 4.5 14.1 1.0 O A:HOH2099 4.6 17.9 1.0 C6 A:GDP1181 4.8 15.9 1.0 O A:HOH2103 4.8 35.6 1.0 C8 A:GDP1181 4.8 14.7 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1187 b:24.1 occ:0.33 O1A A:GDP1181 2.0 15.8 1.0 O1B A:GDP1181 2.2 18.3 1.0 PA A:GDP1181 3.2 16.7 1.0 PB A:GDP1181 3.3 14.9 1.0 O A:HOH2105 3.5 14.2 0.3 O3A A:GDP1181 3.5 16.4 1.0 O2B A:GDP1181 3.8 16.2 1.0 O A:HOH2097 3.8 17.8 0.3 CA A:CA1185 3.9 6.7 1.0 O5' A:GDP1181 4.0 14.5 1.0 C8 A:GDP1181 4.2 14.7 1.0 O2A A:GDP1181 4.5 14.9 1.0 O3B A:GDP1181 4.6 15.7 1.0 O2 A:SO41189 4.6 16.0 1.0 N7 A:GDP1181 4.7 15.6 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1193 b:10.3 occ:1.00 O4 A:SO41189 1.9 20.4 1.0 O4 A:SO41188 2.0 20.1 1.0 O A:HOH2103 2.1 35.6 1.0 S A:SO41189 3.2 19.3 1.0 O A:HOH2104 3.2 10.3 0.3 S A:SO41188 3.2 23.1 1.0 O1 A:SO41189 3.5 21.0 1.0 O3 A:SO41188 3.6 21.8 1.0 O2 A:SO41188 3.8 18.2 1.0 O2 A:SO41189 4.1 16.0 1.0 CA A:CA1186 4.2 8.8 1.0 O3 A:SO41189 4.2 21.8 1.0 O A:HOH2105 4.3 14.2 0.3 O1 A:SO41188 4.3 22.3 1.0 O2B A:GDP1181 4.4 16.2 1.0 CA A:CA1185 4.4 6.7 1.0 O A:HOH2102 4.6 25.5 1.0 O3B A:GDP1181 5.0 15.7 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1182 b:14.2 occ:1.00 O3 B:SO41188 1.8 31.4 1.0 O1B B:GDP1181 2.0 23.2 1.0 O4 B:SO41187 2.0 27.5 1.0 NE2 B:HIS107 2.1 20.9 1.0 CD2 B:HIS107 3.0 20.2 1.0 CE1 B:HIS107 3.1 21.4 1.0 S B:SO41188 3.1 34.1 1.0 S B:SO41187 3.2 30.1 1.0 PB B:GDP1181 3.3 20.8 1.0 O3 B:SO41187 3.3 26.5 1.0 O1 B:SO41188 3.4 30.3 1.0 O1 B:SO41187 3.8 25.5 1.0 O3B B:GDP1181 3.9 16.8 1.0 CG B:PRO106 3.9 20.0 1.0 O4 B:SO41188 4.0 30.6 1.0 O2B B:GDP1181 4.1 22.5 1.0 N7 B:GDP1181 4.1 21.5 1.0 O2 B:SO41188 4.1 34.8 1.0 CG B:HIS107 4.1 21.5 1.0 CA B:CA1191 4.1 17.4 1.0 ND1 B:HIS107 4.2 18.9 1.0 CB B:PRO106 4.2 20.2 1.0 O3A B:GDP1181 4.3 23.2 1.0 O2 B:SO41187 4.4 26.5 1.0 O6 B:GDP1181 4.5 20.4 1.0 C5 B:GDP1181 4.6 19.0 1.0 O B:HOH2061 4.8 30.6 1.0 C6 B:GDP1181 4.8 20.2 1.0 C8 B:GDP1181 4.8 21.0 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1183 b:12.8 occ:1.00 O3B B:GDP1181 1.8 16.8 1.0 PB B:GDP1181 3.2 20.8 1.0 O B:HOH2059 3.3 18.7 0.3 O2B B:GDP1181 3.6 22.5 1.0 N2 B:GDP1180 3.8 22.9 1.0 O1A B:GDP1181 3.9 19.6 1.0 O1 B:SO41188 3.9 30.3 1.0 CA B:CA1186 4.0 30.0 0.3 O3A B:GDP1181 4.2 23.2 1.0 O1B B:GDP1181 4.3 23.2 1.0 CA B:CA1191 4.4 17.4 1.0 PA B:GDP1181 4.5 23.5 1.0 C2 B:GDP1180 4.5 24.3 1.0 O3 B:SO41187 4.6 26.5 1.0 O2A B:GDP1181 4.7 19.7 1.0 N1 B:GDP1180 4.8 25.0 1.0 O1 B:SO41187 4.8 25.5 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1184 b:24.6 occ:1.00 O B:HOH2049 1.8 48.8 1.0 O1B B:GDP1180 1.9 25.0 1.0 N7 B:GDP1179 2.0 42.1 1.0 NE2 B:HIS104 2.1 20.0 1.0 C8 B:GDP1179 3.0 42.9 1.0 CE1 B:HIS104 3.0 20.9 1.0 C5 B:GDP1179 3.0 42.1 1.0 PB B:GDP1180 3.0 24.4 1.0 CD2 B:HIS104 3.1 20.6 1.0 O2B B:GDP1180 3.4 22.1 1.0 O6 B:GDP1179 3.4 42.8 1.0 C6 B:GDP1179 3.7 42.5 1.0 O3A B:GDP1180 3.8 26.9 1.0 ND1 B:HIS104 4.1 21.4 1.0 N9 B:GDP1179 4.1 42.8 1.0 C4 B:GDP1179 4.2 42.4 1.0 CG B:HIS104 4.2 20.5 1.0 O3B B:GDP1180 4.3 26.3 1.0 CD2 B:HIS103 4.4 19.9 1.0 CA B:CA1185 4.8 14.9 1.0 NE2 B:HIS103 4.9 18.8 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of the Human RAC3 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Human RAC3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1185 b:14.9 occ:1.00 O2B B:GDP1180 1.7 22.1 1.0 O2B B:GDP1179 1.8 30.8 1.0 NE2 B:HIS103 2.0 18.8 1.0 N7 B:GDP1180 2.1 22.7 1.0 CD2 B:HIS103 2.9 19.9 1.0 PB B:GDP1179 3.0 28.3 1.0 CE1 B:HIS103 3.0 20.1 1.0 C8 B:GDP1180 3.1 22.5 1.0 C5 B:GDP1180 3.1 23.0 1.0 PB B:GDP1180 3.2 24.4 1.0 O3B B:GDP1179 3.2 26.9 1.0 O6 B:GDP1180 3.4 24.5 1.0 C6 B:GDP1180 3.7 23.1 1.0 O3B B:GDP1180 3.8 26.3 1.0 O B:HOH2047 3.8 21.0 1.0 O1B B:GDP1179 3.8 26.8 1.0 O3A B:GDP1180 3.8 26.9 1.0 O4' B:GDP1179 4.0 42.1 1.0 CG B:HIS103 4.0 20.7 1.0 ND1 B:HIS103 4.0 18.1 1.0 O3A B:GDP1179 4.2 31.9 1.0 C8 B:GDP1179 4.2 42.9 1.0 N9 B:GDP1180 4.3 24.5 1.0 O1B B:GDP1180 4.3 25.0 1.0 O5' B:GDP1179 4.3 38.4 1.0 C4 B:GDP1180 4.3 22.5 1.0 MG B:MG1190 4.4 26.1 1.0 N9 B:GDP1179 4.5 42.8 1.0 N7 B:GDP1179 4.6 42.1 1.0 C5' B:GDP1179 4.7 40.8 1.0 O B:HOH2054 4.8 21.9 1.0 PA B:GDP1179 4.8 35.9 1.0 CA B:CA1184 4.8 24.6 1.0 C1' B:GDP1179 4.8 43.0 1.0 O B:HIS103 4.8 19.2 1.0 O1A B:GDP1179 4.9 32.6 1.0 NE2 B:HIS104 4.9 20.0 1.0 O1A B:GDP1180 4.9 26.2 1.0 C4 B:GDP1179 5.0 42.4 1.0 PA B:GDP1180 5.0 27.8 1.0

J.E.Debreczeni, X.Yang, Y.Zao, J.Elkins, C.Gileadi, N.Burgess, S.Colebrook, O.Gileadi, O.Fedorov, G.Bunkoczi, F.Von Delft, D.Doyle, M.Sundstrom, C.Arrowsmith, J.Weigelt, A.Edwards. Crystal Structure of the Human RAC3 in Complex with Gdp To Be Published.