Manganese in PDB 5a74: Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn

The structure of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn, PDB code: 5a74 was solved by R.Molina, P.Redondo, B.Lopezmendez, M.Villate, N.Merino, F.J.Blanco, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.944 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.730, 82.030, 94.490, 90.00, 90.00, 90.00
R / Rfree (%)	18.62 / 23.38

The binding sites of Manganese atom in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn (pdb code 5a74). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn, PDB code: 5a74:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1525 b:19.5 occ:1.00 OP1 D:DC614 2.0 19.1 1.0 OP2 E:DG515 2.0 15.5 1.0 OD2 B:ASP23 2.2 14.3 1.0 O A:ALA22 2.3 13.9 1.0 OP3 E:DG515 2.4 18.5 1.0 O A:HOH2004 2.5 17.3 1.0 P E:DG515 2.7 18.1 1.0 CG B:ASP23 3.2 15.7 1.0 C A:ALA22 3.3 13.8 1.0 P D:DC614 3.5 14.1 1.0 OD1 B:ASP23 3.5 19.0 1.0 CA A:ALA22 3.7 11.1 1.0 OP1 E:DG515 3.8 13.7 1.0 O5' E:DG515 3.9 14.2 1.0 MN F:MN1626 3.9 18.9 1.0 O A:HOH2072 3.9 10.2 1.0 OE1 B:GLN50 3.9 13.4 1.0 O A:HOH2053 4.0 22.1 1.0 O3' D:DA613 4.0 15.6 1.0 NE2 B:GLN50 4.0 14.9 1.0 C5' D:DC614 4.2 16.5 1.0 O5' D:DC614 4.3 22.5 1.0 C4' D:DC614 4.3 18.2 1.0 OD1 A:ASP23 4.3 14.6 1.0 CD B:GLN50 4.4 12.9 1.0 CB A:ALA22 4.4 10.0 1.0 N A:ASP23 4.5 12.0 1.0 C5' E:DG515 4.5 14.0 1.0 OP2 D:DC614 4.5 16.4 1.0 O A:ASP21 4.5 11.3 1.0 CB B:ASP23 4.5 13.8 1.0 CA A:ASP23 4.9 11.5 1.0 N A:ALA22 4.9 11.3 1.0 O3' C:DC514 4.9 16.9 1.0 C3' D:DC614 5.0 19.5 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1625 b:19.6 occ:1.00 OD2 A:ASP23 2.1 12.5 1.0 O A:HOH2005 2.1 13.4 1.0 OP1 C:DC514 2.2 12.9 1.0 OP1 F:DG615 2.2 15.3 1.0 O B:ALA22 2.2 16.2 1.0 OP2 F:DG615 2.4 13.5 1.0 P F:DG615 2.7 12.4 1.0 CG A:ASP23 3.1 13.2 1.0 C B:ALA22 3.3 13.1 1.0 OD1 A:ASP23 3.5 14.6 1.0 P C:DC514 3.5 20.1 1.0 O B:HOH2072 3.8 10.2 1.0 O5' F:DG615 3.8 20.9 1.0 MN F:MN1626 3.8 18.9 1.0 CA B:ALA22 3.8 13.0 1.0 OP3 F:DG615 3.8 16.9 1.0 O3' C:DA513 3.9 12.8 1.0 OE1 A:GLN50 3.9 14.5 1.0 O B:HOH2053 4.1 20.8 1.0 NE2 A:GLN50 4.1 12.9 1.0 C5' C:DC514 4.1 13.8 1.0 OD1 B:ASP23 4.2 19.0 1.0 C4' C:DC514 4.3 15.8 1.0 O5' C:DC514 4.3 14.1 1.0 CD A:GLN50 4.4 13.8 1.0 N B:ASP23 4.4 12.9 1.0 C5' F:DG615 4.5 15.0 1.0 CB A:ASP23 4.5 12.2 1.0 O B:ASP21 4.5 11.7 1.0 CB B:ALA22 4.6 10.3 1.0 OP2 C:DC514 4.7 16.3 1.0 CA B:ASP23 4.8 14.9 1.0 O3' C:DC514 4.9 16.9 1.0 C3' C:DC514 5.0 17.7 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Homing Endonuclease I-Cvui in Complex with Its Target (SRO1.3) in the Presence of 2 Mm Mn within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1626 b:18.9 occ:1.00 OD1 A:ASP23 2.1 14.6 1.0 OP1 F:DG615 2.1 15.3 1.0 OD1 B:ASP23 2.2 19.0 1.0 OP2 E:DG515 2.3 15.5 1.0 O3' C:DC514 2.4 16.9 1.0 O3' D:DC614 2.5 20.4 1.0 CG B:ASP23 3.2 15.7 1.0 CG A:ASP23 3.2 13.2 1.0 C3' D:DC614 3.3 19.5 1.0 P F:DG615 3.4 12.4 1.0 P E:DG515 3.4 18.1 1.0 C3' C:DC514 3.4 17.7 1.0 OD2 B:ASP23 3.7 14.3 1.0 OD2 A:ASP23 3.7 12.5 1.0 O5' F:DG615 3.8 20.9 1.0 MN F:MN1625 3.8 19.6 1.0 O5' E:DG515 3.8 14.2 1.0 MN E:MN1525 3.9 19.5 1.0 C4' D:DC614 3.9 18.2 1.0 C4' C:DC514 3.9 15.8 1.0 OP1 E:DG515 3.9 13.7 1.0 OP3 F:DG615 4.0 16.9 1.0 O B:ALA22 4.1 16.2 1.0 O A:ALA22 4.1 13.9 1.0 CB B:ASP23 4.4 13.8 1.0 CB A:ASP23 4.5 12.2 1.0 CA B:ASP23 4.6 14.9 1.0 OP2 F:DG615 4.6 13.5 1.0 CA A:ASP23 4.6 11.5 1.0 OP3 E:DG515 4.6 18.5 1.0 C B:ALA22 4.6 13.1 1.0 O D:HOH2017 4.7 16.4 1.0 C2' D:DC614 4.7 17.9 1.0 C A:ALA22 4.7 13.8 1.0 C2' C:DC514 4.7 17.2 1.0 C5' D:DC614 4.8 16.5 1.0 C5' C:DC514 4.8 13.8 1.0 OP1 D:DC614 4.9 19.1 1.0 N B:ASP23 4.9 12.9 1.0 N A:ASP23 5.0 12.0 1.0

R.Molina, P.Redondo, B.Lopez-Mendez, M.Villate, N.Merino, F.J.Blanco, J.Valton, S.Grizot, P.Duchateau, J.Prieto, G.Montoya. Crystal Structure of the Homing Endonuclease I-Cvui Provides A New Template For Genome Modification J.Biol.Chem. V. 290 28727 2015.
ISSN: ISSN 0021-9258
PubMed: 26363068
DOI: 10.1074/JBC.M115.678342