Calcium in PDB 6s48: Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna

The structure of Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna, PDB code: 6s48 was solved by M.Kisiala, M.Kowalska, H.Korza, H.Czapinska, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.07 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.129, 116.210, 56.774, 90.00, 102.91, 90.00
R / Rfree (%)	17.6 / 21.7

The binding sites of Calcium atom in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna (pdb code 6s48). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna, PDB code: 6s48:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:26.5 occ:1.00 O A:HOH410 1.9 32.7 1.0 OP1 C:DG5 2.2 20.1 0.5 OD2 A:ASP147 2.3 23.3 1.0 OE1 A:GLN161 2.3 23.6 1.0 O A:VAL162 2.3 21.5 0.5 O A:VAL162 2.3 21.5 0.5 OP3 I:DG5 2.4 23.9 0.5 OP1 I:DG5 2.5 21.8 0.5 O C:HOH501 2.5 29.3 0.5 P I:DG5 3.0 22.2 0.5 CG A:ASP147 3.1 24.6 1.0 OD1 A:ASP147 3.1 24.4 1.0 CD A:GLN161 3.3 23.7 1.0 C A:VAL162 3.5 22.3 0.5 C A:VAL162 3.5 22.4 0.5 P C:DG5 3.6 20.3 0.5 CA C:CA101 3.7 46.1 1.0 OE2 A:GLU123 3.7 34.1 1.0 N A:VAL162 3.8 23.1 0.5 N A:VAL162 3.9 23.2 0.5 NE2 A:GLN161 3.9 22.6 1.0 O I:HOH110 4.0 28.4 1.0 O5' C:DG5 4.1 20.0 0.5 CG2 A:VAL162 4.1 22.5 0.5 OP2 I:DG5 4.1 21.8 0.5 CA A:VAL162 4.2 22.5 0.5 O5' I:DG5 4.2 21.2 0.5 C5' C:DG5 4.2 19.9 0.5 CA A:VAL162 4.2 22.7 0.5 C5' I:DG5 4.3 21.0 0.5 OP2 C:DG5 4.3 20.0 0.5 CD A:LYS163 4.4 24.6 1.0 CG A:GLN161 4.5 23.2 1.0 NZ A:LYS163 4.5 23.5 1.0 OP2 I:DA6 4.5 22.4 0.5 CB A:ASP147 4.5 24.8 1.0 OP2 C:DT6 4.5 21.2 0.5 O A:HOH533 4.5 29.8 1.0 N A:LYS163 4.6 22.1 1.0 CB A:VAL162 4.6 22.2 0.5 O A:HOH411 4.6 34.1 1.0 CD A:GLU123 4.7 33.7 1.0 O3' C:DG4 4.7 22.3 0.5 CB A:VAL162 4.8 22.7 0.5 CE A:LYS163 4.8 25.0 1.0 C A:GLN161 4.8 23.3 1.0 CA A:LYS163 4.9 22.8 1.0 CG1 A:VAL162 5.0 22.2 0.5

Calcium binding site 2 out of 5 in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:32.3 occ:1.00 O B:HOH518 2.2 32.0 1.0 O B:VAL162 2.4 22.0 1.0 OE1 B:GLN161 2.4 19.5 1.0 OD2 B:ASP147 2.4 23.2 1.0 OP1 G:DG5 2.4 25.0 0.5 OP3 E:DG5 2.4 22.4 0.5 OP1 E:DG5 2.4 23.5 0.5 OP3 G:DG5 2.7 27.2 0.5 P E:DG5 3.0 27.3 0.5 OD1 B:ASP147 3.1 22.4 1.0 CG B:ASP147 3.1 23.0 1.0 P G:DG5 3.2 27.2 0.5 CD B:GLN161 3.4 21.4 1.0 C B:VAL162 3.5 22.5 1.0 CA B:CA302 3.8 46.4 1.0 N B:VAL162 3.9 21.2 1.0 NE2 B:GLN161 4.0 21.4 1.0 O5' E:DG5 4.1 22.3 0.5 OP2 E:DG5 4.1 23.6 0.5 C5' G:DG5 4.1 22.5 0.5 C5' E:DG5 4.1 21.2 0.5 O5' G:DG5 4.2 24.3 0.5 OE2 B:GLU123 4.2 38.0 1.0 CA B:VAL162 4.2 23.6 1.0 O B:HOH466 4.3 27.1 1.0 OP2 G:DG5 4.3 25.3 0.5 NZ B:LYS163 4.3 26.8 1.0 OP2 G:DT6 4.4 21.8 0.5 CD B:LYS163 4.5 24.1 1.0 CG B:GLN161 4.5 22.1 1.0 CB B:ASP147 4.5 23.1 1.0 OP2 E:DA6 4.5 21.1 0.5 O B:HOH413 4.6 30.9 1.0 CB B:VAL162 4.6 26.1 1.0 N B:LYS163 4.6 22.2 1.0 O B:HOH551 4.6 27.1 1.0 CE B:LYS163 4.8 24.5 1.0 C B:GLN161 4.9 23.3 1.0 CA B:LYS163 4.9 22.5 1.0 O3' D:DG4 5.0 31.3 0.5 O3' F:DG4 5.0 29.8 0.5

Calcium binding site 3 out of 5 in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:46.4 occ:1.00 O B:HOH413 2.0 30.9 1.0 OP1 G:DG5 2.2 25.0 0.5 OD1 B:ASP147 2.3 22.4 1.0 O3' F:DG4 2.4 29.8 0.5 O3' D:DG4 2.4 31.3 0.5 OP1 E:DG5 2.4 23.5 0.5 O B:HOH561 2.4 35.2 1.0 O B:HOH551 2.5 27.1 1.0 CG B:ASP147 3.5 23.0 1.0 P G:DG5 3.5 27.2 0.5 C3' F:DG4 3.7 27.8 0.5 C3' D:DG4 3.7 29.0 0.5 CA B:CA301 3.8 32.3 1.0 P E:DG5 3.8 27.3 0.5 OE2 B:GLU123 3.8 38.0 1.0 O5' G:DG5 4.0 24.3 0.5 OD2 B:ASP147 4.1 23.2 1.0 C4' D:DG4 4.2 29.2 0.5 C4' F:DG4 4.2 28.2 0.5 C5' G:DG5 4.3 22.5 0.5 OP2 G:DG5 4.3 25.3 0.5 OE1 B:GLU123 4.3 37.3 1.0 O D:HOH102 4.3 31.3 1.0 C5' E:DG5 4.4 21.2 0.5 CD B:GLU123 4.4 34.6 1.0 O5' E:DG5 4.4 22.3 0.5 O B:VAL146 4.5 25.4 1.0 CB B:ASP147 4.6 23.1 1.0 OP3 G:DG5 4.6 27.2 0.5 O B:HOH518 4.6 32.0 1.0 O G:HOH103 4.6 25.1 1.0 C5' D:DG4 4.6 30.4 0.5 C5' F:DG4 4.7 29.8 0.5 NE2 B:GLN161 4.7 21.4 1.0 OP2 E:DG5 4.7 23.6 0.5 CA B:ASP147 4.7 23.2 1.0 OP3 E:DG5 4.7 22.4 0.5 OE1 B:GLN161 4.8 19.5 1.0 C2' F:DG4 4.8 26.6 0.5 C2' D:DG4 4.8 27.9 0.5 C B:VAL146 4.9 23.7 1.0 N B:ASP147 4.9 23.5 1.0

Calcium binding site 4 out of 5 in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:46.1 occ:1.00 O A:HOH411 2.1 34.1 1.0 OP1 I:DG5 2.3 21.8 0.5 OD1 A:ASP147 2.3 24.4 1.0 OP1 C:DG5 2.3 20.1 0.5 O A:HOH533 2.4 29.8 1.0 O3' H:DG4 2.4 27.1 0.5 O3' C:DG4 2.6 22.3 0.5 O H:HOH105 2.7 32.3 1.0 O A:HOH531 2.7 59.4 1.0 P C:DG5 3.0 20.3 0.5 CG A:ASP147 3.5 24.6 1.0 C3' H:DG4 3.6 27.2 0.5 OE2 A:GLU123 3.6 34.1 1.0 CA A:CA301 3.7 26.5 1.0 P I:DG5 3.7 22.2 0.5 C3' C:DG4 3.9 22.7 0.5 OP2 C:DG5 4.1 20.0 0.5 OE1 A:GLU123 4.1 38.6 1.0 O5' C:DG5 4.1 20.0 0.5 OD2 A:ASP147 4.1 23.3 1.0 C5' C:DG5 4.2 19.9 0.5 CD A:GLU123 4.2 33.7 1.0 C4' C:DG4 4.2 23.6 0.5 O H:HOH102 4.2 25.2 1.0 O5' I:DG5 4.2 21.2 0.5 O A:HOH410 4.3 32.7 1.0 C5' I:DG5 4.3 21.0 0.5 C4' H:DG4 4.3 28.1 0.5 O A:HOH521 4.3 41.2 1.0 O C:HOH502 4.4 24.9 1.0 O A:VAL146 4.4 25.2 1.0 NE2 A:GLN161 4.5 22.6 1.0 OE1 A:GLN161 4.5 23.6 1.0 OP3 I:DG5 4.6 23.9 0.5 OP2 I:DG5 4.6 21.8 0.5 CB A:ASP147 4.6 24.8 1.0 C5' H:DG4 4.7 28.7 0.5 CA A:ASP147 4.7 24.5 1.0 C5' C:DG4 4.7 24.2 0.5 C2' C:DG4 4.7 22.8 0.5 C2' H:DG4 4.8 26.9 0.5 C A:VAL146 4.9 23.5 1.0 N A:ASP147 4.9 23.1 1.0 CD A:GLN161 5.0 23.7 1.0

Calcium binding site 5 out of 5 in the Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Avaii Restriction Endonuclease in Complex with Partially Cleaved Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca101 b:32.1 occ:1.00 O C:HOH503 2.2 19.1 1.0 O A:HOH412 2.2 18.7 1.0 O G:HOH114 2.2 20.1 1.0 O B:HOH449 2.2 19.6 1.0 O C:HOH506 2.2 20.8 1.0 O G:HOH101 2.2 18.6 1.0 O4' I:DC7 4.0 20.6 0.5 O4' C:DC7 4.0 21.9 0.5 O2 G:DT6 4.0 21.5 0.5 O2 C:DT6 4.1 20.0 0.5 O4' G:DC7 4.1 20.2 0.5 O4' E:DC7 4.1 20.0 0.5 C2 E:DA6 4.1 22.3 0.5 C2 I:DA6 4.2 21.1 0.5 SD B:MET112 4.2 22.8 1.0 OE1 A:GLU115 4.2 22.8 1.0 N3 E:DA6 4.2 22.5 0.5 N3 I:DA6 4.2 21.5 0.5 SD A:MET112 4.2 24.3 1.0 CG B:MET112 4.2 21.4 1.0 O A:HOH471 4.3 17.3 1.0 O B:HOH512 4.3 24.9 1.0 CG A:MET112 4.3 24.2 1.0 OE1 B:GLU115 4.3 21.4 1.0 O2 C:DC7 4.4 20.2 0.5 O2 I:DC7 4.4 18.9 0.5 O2 G:DC7 4.5 18.1 0.5 O2 E:DC7 4.5 17.8 0.5 C1' C:DC7 4.5 21.6 0.5 C1' I:DC7 4.6 20.3 0.5 C1' E:DC7 4.6 19.4 0.5 C1' G:DC7 4.7 19.7 0.5 N1 C:DC7 4.7 21.7 0.5 C2 C:DC7 4.7 20.9 0.5 C2 I:DC7 4.7 19.6 0.5 N1 I:DC7 4.8 20.2 0.5 C2 G:DC7 4.8 18.5 0.5 C2 E:DC7 4.8 18.2 0.5 N1 E:DC7 4.8 18.3 0.5 N1 G:DC7 4.8 18.6 0.5

M.Kisiala, M.Kowalska, M.Pastor, H.Korza, H.Czapinska, M.Bochtler. Restriction Endonucleases That Cleave Rna/Dna Heteroduplexes Bind Dsdna in A-Like Conformation Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962