Manganese in PDB 7yzo: Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna

The structure of Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna (pdb code 7yzo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna, PDB code: 7yzo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:63.9 occ:1.00 OD2 A:ASP48 1.5 58.1 1.0 OP1 F:DC56 2.1 85.4 1.0 MN A:MN502 2.2 58.2 1.0 NE2 A:HIS10 2.4 58.1 1.0 CG A:ASP48 2.5 58.1 1.0 CB A:ASP48 3.1 58.1 1.0 P F:DC56 3.2 85.4 1.0 CE1 A:HIS10 3.2 58.1 1.0 NE2 A:HIS224 3.3 58.1 1.0 OD1 A:ASP8 3.3 58.1 1.0 CD2 A:HIS10 3.4 58.1 1.0 OD1 A:ASP48 3.6 58.1 1.0 O5' F:DC56 3.7 85.4 1.0 CG A:ASP8 3.7 58.1 1.0 OP2 F:DC56 3.7 85.4 1.0 CD2 A:HIS224 4.1 58.1 1.0 OD2 A:ASP8 4.1 58.1 1.0 CE1 A:HIS224 4.2 58.1 1.0 CB A:ASP8 4.2 58.1 1.0 OD1 A:ASN83 4.3 58.1 1.0 ND1 A:HIS10 4.4 58.1 1.0 CE1 A:HIS184 4.4 58.1 1.0 CG A:HIS10 4.5 58.1 1.0 NE2 A:HIS184 4.5 58.1 1.0 O3' F:DC55 4.5 83.2 1.0 CA A:ASP8 4.6 58.1 1.0 CA A:ASP48 4.6 58.1 1.0 C5' F:DC56 4.9 85.4 1.0 ND1 A:HIS222 5.0 58.1 1.0

Manganese binding site 2 out of 4 in the Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:58.2 occ:1.00 OD2 A:ASP48 1.6 58.1 1.0 MN A:MN501 2.2 63.9 1.0 OP2 F:DC56 2.3 85.4 1.0 OD1 A:ASN83 2.4 58.1 1.0 CG A:ASP48 2.6 58.1 1.0 OP1 F:DC56 2.6 85.4 1.0 P F:DC56 2.8 85.4 1.0 NE2 A:HIS184 2.9 58.1 1.0 OD1 A:ASP48 2.9 58.1 1.0 ND1 A:HIS222 3.0 58.1 1.0 CE1 A:HIS184 3.4 58.1 1.0 CG A:ASN83 3.5 58.1 1.0 CE1 A:HIS222 3.6 58.1 1.0 O5' F:DC56 3.7 85.4 1.0 CB A:ASP48 3.9 58.1 1.0 CA A:HIS222 4.0 58.1 1.0 CG A:HIS222 4.1 58.1 1.0 CD2 A:HIS184 4.1 58.1 1.0 ND2 A:ASN83 4.1 58.1 1.0 O3' F:DC55 4.3 83.2 1.0 OD1 A:ASP8 4.3 58.1 1.0 NE2 A:HIS10 4.4 58.1 1.0 CB A:HIS222 4.5 58.1 1.0 C5' F:DC56 4.6 85.4 1.0 ND1 A:HIS184 4.7 58.1 1.0 N A:ASN83 4.7 58.1 1.0 CB A:ASN83 4.7 58.1 1.0 N A:HIS222 4.8 58.1 1.0 C3' F:DC55 4.8 83.2 1.0 C A:HIS222 4.8 58.1 1.0 NE2 A:HIS224 4.9 58.1 1.0 NE2 A:HIS222 4.9 58.1 1.0 O A:HIS222 4.9 58.1 1.0 OE1 A:GLN84 5.0 52.7 1.0 CE1 A:HIS10 5.0 58.1 1.0 CG A:ASP8 5.0 58.1 1.0 N A:GLN84 5.0 58.1 1.0

Manganese binding site 3 out of 4 in the Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:65.4 occ:1.00 OD1 B:ASP8 2.1 60.4 1.0 OD2 B:ASP48 2.3 64.3 1.0 CG B:ASP8 2.6 60.4 1.0 NE2 B:HIS224 2.8 63.5 1.0 CE1 B:HIS10 2.9 58.1 1.0 MN B:MN502 3.0 76.2 1.0 OD2 B:ASP8 3.0 60.4 1.0 CG B:ASP48 3.3 64.3 1.0 O B:HIS222 3.3 67.1 1.0 CD2 B:HIS224 3.5 63.5 1.0 CB B:ASP8 3.5 60.4 1.0 CB B:ASP48 3.7 64.3 1.0 NE2 B:HIS10 3.8 58.1 1.0 ND1 B:HIS10 3.8 58.1 1.0 CE1 B:HIS224 3.8 63.5 1.0 CA B:HIS222 3.9 67.1 1.0 C B:HIS222 4.0 67.1 1.0 CA B:ASP8 4.2 60.4 1.0 N B:HIS222 4.3 67.1 1.0 OD1 B:ASP48 4.4 64.3 1.0 CE1 B:HIS184 4.4 68.2 1.0 CG B:HIS224 4.6 63.5 1.0 OD1 B:ASN83 4.6 71.2 1.0 NE2 B:HIS184 4.7 68.2 1.0 ND1 B:HIS224 4.7 63.5 1.0 OE1 B:GLN84 4.8 68.6 1.0 ND1 B:HIS222 4.9 67.1 1.0 CD2 B:HIS10 5.0 58.1 1.0 CG B:HIS10 5.0 58.1 1.0

Manganese binding site 4 out of 4 in the Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Endonuclease State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and Dsdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:76.2 occ:1.00 OD1 B:ASN83 1.8 71.2 1.0 OD2 B:ASP48 1.9 64.3 1.0 NE2 B:HIS184 2.5 68.2 1.0 CG B:ASN83 2.6 71.2 1.0 ND2 B:ASN83 2.9 71.2 1.0 ND1 B:HIS222 2.9 67.1 1.0 CG B:ASP48 2.9 64.3 1.0 MN B:MN501 3.0 65.4 1.0 CE1 B:HIS184 3.1 68.2 1.0 OD1 B:ASP48 3.3 64.3 1.0 CA B:HIS222 3.5 67.1 1.0 CD2 B:HIS184 3.7 68.2 1.0 CE1 B:HIS222 3.8 67.1 1.0 OD1 B:ASP8 3.8 60.4 1.0 CG B:HIS222 3.8 67.1 1.0 CB B:HIS222 4.0 67.1 1.0 CB B:ASN83 4.1 71.2 1.0 O B:HIS222 4.1 67.1 1.0 CB B:ASP48 4.3 64.3 1.0 N B:ASN83 4.3 71.2 1.0 N B:HIS222 4.3 67.1 1.0 ND1 B:HIS184 4.3 68.2 1.0 C B:HIS222 4.3 67.1 1.0 CG B:HIS184 4.6 68.2 1.0 CA B:ASN83 4.8 71.2 1.0 CG B:ASP8 4.8 60.4 1.0 CE1 B:HIS10 4.9 58.1 1.0 N B:GLN84 5.0 68.6 1.0 NE2 B:HIS222 5.0 67.1 1.0

F.Gut, L.Kashammer, K.Lammens, J.D.Bartho, A.M.Boggusch, E.Van De Logt, B.Kessler, K.P.Hopfner. Structural Mechanism of Endonucleolytic Processing of Blocked Dna Ends and Hairpins By MRE11-RAD50. Mol.Cell V. 82 3513 2022.
ISSN: ISSN 1097-2765
PubMed: 35987200
DOI: 10.1016/J.MOLCEL.2022.07.019