Calcium in PDB 4q0z: The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III)

The structure of The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III), PDB code: 4q0z was solved by M.Mietus, E.Nowak, M.Jaciuk, P.Kustosz, M.Nowotny, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.33 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	110.278, 86.039, 134.440, 90.00, 110.95, 90.00
R / Rfree (%)	17.8 / 23.5

The structure of The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III) also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Calcium atom in the The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III) (pdb code 4q0z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III), PDB code: 4q0z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:53.2 occ:1.00 OE2 A:GLU794 2.4 17.2 0.5 OD2 A:ASP815 2.8 38.3 1.0 O A:HOH1117 2.8 39.6 1.0 O A:HOH1178 3.0 38.9 1.0 OD2 A:ASP813 3.0 40.2 1.0 CD A:GLU794 3.3 22.1 0.5 OE2 A:GLU794 3.4 17.4 0.5 CG A:ASP813 3.4 18.2 1.0 OD1 A:ASP813 3.4 23.8 1.0 O A:HOH1293 3.5 34.4 1.0 CG A:ASP815 3.7 24.8 1.0 CD A:GLU794 3.7 23.6 0.5 OD2 A:ASP864 3.9 38.2 1.0 CB A:ASP815 3.9 22.4 1.0 OE1 A:GLU794 4.0 20.5 0.5 NZ A:LYS84 4.0 59.1 1.0 O A:HOH1177 4.0 31.4 1.0 OE1 A:GLU794 4.1 22.0 0.5 N A:GLY2 4.2 14.8 1.0 CG A:GLU794 4.2 22.5 0.5 O A:HOH1227 4.5 48.6 1.0 CG A:GLU794 4.6 21.8 0.5 CB A:ASP813 4.6 13.4 1.0 CG A:ASP864 4.9 29.9 1.0 OD1 A:ASP815 4.9 18.8 1.0 CE A:LYS84 4.9 47.8 1.0 CA A:GLY2 5.0 13.7 1.0

Calcium binding site 2 out of 4 in the The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:56.4 occ:1.00 O B:HOH1224 2.4 53.9 1.0 OE2 B:GLU794 2.5 46.2 1.0 OD2 B:ASP813 2.5 63.6 1.0 O B:HOH1183 3.0 47.2 1.0 OD2 B:ASP815 3.0 49.9 1.0 CD B:GLU794 3.1 39.1 1.0 CG B:ASP813 3.4 33.8 1.0 OE1 B:GLU794 3.5 35.9 1.0 NZ B:LYS84 3.6 52.1 1.0 OD1 B:ASP813 3.7 18.2 1.0 OD2 B:ASP864 3.7 43.8 1.0 O B:HOH1264 3.9 34.8 1.0 CG B:ASP815 4.0 29.9 1.0 CB B:ASP815 4.1 28.1 1.0 CG B:GLU794 4.2 28.7 1.0 N B:GLY2 4.2 23.9 1.0 CG B:ASP864 4.7 54.2 1.0 CB B:ASP813 4.8 27.6 1.0 CE B:LYS84 4.8 32.6 1.0

Calcium binding site 3 out of 4 in the The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III) within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1001 b:51.5 occ:1.00 O E:HOH1149 2.6 59.0 1.0 OD2 E:ASP815 2.6 43.1 1.0 OE2 E:GLU794 2.6 46.7 1.0 OD2 E:ASP813 2.6 38.2 1.0 O E:HOH1202 3.2 46.4 1.0 CD E:GLU794 3.3 51.4 1.0 OD2 E:ASP864 3.4 57.7 1.0 CG E:ASP813 3.4 33.4 1.0 OD1 E:ASP813 3.6 33.7 1.0 CG E:ASP815 3.6 23.6 1.0 OE1 E:GLU794 3.8 49.4 1.0 CB E:ASP815 4.0 22.4 1.0 N E:GLY2 4.2 22.6 1.0 CG E:GLU794 4.4 48.9 1.0 O E:HOH1201 4.4 43.7 1.0 NZ E:LYS84 4.5 46.4 1.0 CG E:ASP864 4.5 51.0 1.0 OD1 E:ASP815 4.7 32.0 1.0 CB E:ASP813 4.8 23.5 1.0 CA E:GLY2 5.0 17.7 1.0

Calcium binding site 4 out of 4 in the The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Catalytic Core of RAD2 in Complex with Dna Substrate (Complex III) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1001 b:62.7 occ:1.00 O F:HOH1258 2.4 42.5 1.0 O F:HOH1101 2.7 29.4 1.0 OE1 F:GLU794 2.7 39.9 1.0 OD2 F:ASP864 2.8 42.8 1.0 OD2 F:ASP813 2.9 37.3 1.0 OD2 F:ASP815 3.3 56.1 1.0 CD F:GLU794 3.5 32.8 1.0 CG F:ASP813 3.6 20.5 1.0 O F:HOH1115 3.7 31.0 1.0 OD1 F:ASP813 3.8 20.8 1.0 OE2 F:GLU794 3.9 41.5 1.0 N F:GLY2 4.0 32.6 1.0 CG F:ASP864 4.0 52.3 1.0 O H:HOH120 4.1 37.3 1.0 CE F:LYS84 4.1 51.4 1.0 CG F:ASP815 4.3 38.5 1.0 CB F:ASP815 4.6 24.4 1.0 O F:HOH1182 4.6 31.9 1.0 CB F:ASP864 4.7 44.0 1.0 CG F:GLU794 4.7 26.8 1.0 CB F:ASP813 4.8 15.1 1.0 NZ F:LYS84 4.9 41.6 1.0 OD1 F:ASP864 4.9 42.7 1.0

M.Mietus, E.Nowak, M.Jaciuk, P.Kustosz, J.Studnicka, M.Nowotny. Crystal Structure of the Catalytic Core of RAD2: Insights Into the Mechanism of Substrate Binding. Nucleic Acids Res. V. 42 10762 2014.
ISSN: ISSN 0305-1048
PubMed: 25120270
DOI: 10.1093/NAR/GKU729