Manganese in PDB 9bi4: Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex

The structure of Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex (pdb code 9bi4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex, PDB code: 9bi4:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:6.3 occ:1.00 OD2 B:ASP16 2.0 3.1 1.0 NE2 B:HIS18 2.0 1.2 1.0 NE2 B:HIS243 2.3 2.9 1.0 OD2 B:ASP56 2.8 1.5 1.0 CE1 B:HIS18 2.8 1.2 1.0 CE1 B:HIS243 3.0 2.9 1.0 MN B:MN1002 3.0 6.9 1.0 CG B:ASP16 3.0 3.1 1.0 CD2 B:HIS18 3.2 1.2 1.0 CD2 B:HIS243 3.4 2.9 1.0 CG B:ASP56 3.6 1.5 1.0 CB B:ASP16 3.9 3.1 1.0 OD1 B:ASP16 3.9 3.1 1.0 CB B:ASP56 4.0 1.5 1.0 ND1 B:HIS18 4.0 1.2 1.0 ND1 B:HIS243 4.1 2.9 1.0 CG B:HIS18 4.2 1.2 1.0 CG B:HIS243 4.4 2.9 1.0 CA B:ASP16 4.5 3.1 1.0 CD2 B:HIS125 4.5 2.0 1.0 OD1 B:ASP56 4.7 1.5 1.0 CE1 B:HIS213 4.7 3.5 1.0 NE2 B:HIS213 4.7 3.5 1.0 OD1 B:ASN124 4.8 2.3 1.0 CA B:HIS241 4.8 3.1 1.0 O B:HIS241 4.8 3.1 1.0

Manganese binding site 2 out of 4 in the Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1002 b:6.9 occ:1.00 OD1 B:ASN124 1.9 2.3 1.0 OD2 B:ASP56 2.0 1.5 1.0 NE2 B:HIS213 2.3 3.5 1.0 ND1 B:HIS241 2.8 3.1 1.0 CE1 B:HIS213 3.0 3.5 1.0 MN B:MN1001 3.0 6.3 1.0 CG B:ASN124 3.0 2.3 1.0 CG B:ASP56 3.2 1.5 1.0 CD2 B:HIS213 3.4 3.5 1.0 ND2 B:ASN124 3.5 2.3 1.0 CE1 B:HIS241 3.6 3.1 1.0 CG B:HIS241 3.7 3.1 1.0 CA B:HIS241 3.8 3.1 1.0 OD2 B:ASP16 3.8 3.1 1.0 OD1 B:ASP56 3.9 1.5 1.0 CB B:HIS241 4.0 3.1 1.0 ND1 B:HIS213 4.1 3.5 1.0 CB B:ASP56 4.2 1.5 1.0 N B:ASN124 4.2 2.3 1.0 CB B:ASN124 4.3 2.3 1.0 CG B:HIS213 4.4 3.5 1.0 O B:HIS241 4.5 3.1 1.0 CG B:ASP16 4.5 3.1 1.0 OD1 B:ASP16 4.5 3.1 1.0 NE2 B:HIS18 4.6 1.2 1.0 CD2 B:HIS125 4.6 2.0 1.0 C B:HIS241 4.6 3.1 1.0 N B:HIS241 4.7 3.1 1.0 NE2 B:HIS243 4.7 2.9 1.0 NE2 B:HIS241 4.7 3.1 1.0 CD2 B:HIS241 4.8 3.1 1.0 CE1 B:HIS18 4.8 1.2 1.0 CA B:ASN124 4.8 2.3 1.0

Manganese binding site 3 out of 4 in the Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:6.3 occ:1.00 OD1 A:ASP16 2.0 3.1 1.0 NE2 A:HIS243 2.1 2.9 1.0 NE2 A:HIS18 2.2 1.2 1.0 OD2 A:ASP56 2.8 1.5 1.0 CE1 A:HIS243 2.8 2.9 1.0 CE1 A:HIS18 2.9 1.2 1.0 CG A:ASP16 3.2 3.1 1.0 CD2 A:HIS243 3.3 2.9 1.0 CD2 A:HIS18 3.5 1.2 1.0 MN A:MN1002 3.5 6.9 1.0 CG A:ASP56 3.8 1.5 1.0 CB A:ASP16 4.0 3.1 1.0 ND1 A:HIS243 4.1 2.9 1.0 OD2 A:ASP16 4.1 3.1 1.0 CB A:ASP56 4.1 1.5 1.0 ND1 A:HIS18 4.1 1.2 1.0 CD2 A:HIS125 4.3 2.0 1.0 CG A:HIS243 4.3 2.9 1.0 CG A:HIS18 4.4 1.2 1.0 NE2 A:HIS125 4.6 2.0 1.0 CA A:HIS241 4.6 3.1 1.0 CA A:ASP16 4.7 3.1 1.0 OD1 A:ASP56 4.9 1.5 1.0 OD1 A:ASN124 4.9 2.3 1.0 O A:HIS241 4.9 3.1 1.0 ND1 A:HIS241 4.9 3.1 1.0 C A:HIS241 4.9 3.1 1.0

Manganese binding site 4 out of 4 in the Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Cryo Em Structure of Dsdna Bound MRE11-RAD50 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1002 b:6.9 occ:1.00 OD1 A:ASN124 2.0 2.3 1.0 OD2 A:ASP56 2.1 1.5 1.0 NE2 A:HIS213 2.2 3.5 1.0 ND1 A:HIS241 2.5 3.1 1.0 CE1 A:HIS213 2.9 3.5 1.0 CG A:ASP56 3.2 1.5 1.0 CB A:HIS241 3.2 3.1 1.0 CG A:ASN124 3.2 2.3 1.0 CG A:HIS241 3.2 3.1 1.0 CD2 A:HIS213 3.3 3.5 1.0 CA A:HIS241 3.5 3.1 1.0 MN A:MN1001 3.5 6.3 1.0 OD1 A:ASP56 3.6 1.5 1.0 CE1 A:HIS241 3.6 3.1 1.0 OD1 A:ASP16 3.8 3.1 1.0 ND1 A:HIS213 4.1 3.5 1.0 ND2 A:ASN124 4.1 2.3 1.0 N A:ASN124 4.2 2.3 1.0 CB A:ASN124 4.2 2.3 1.0 CD2 A:HIS125 4.2 2.0 1.0 CG A:HIS213 4.3 3.5 1.0 N A:HIS241 4.3 3.1 1.0 CB A:ASP56 4.4 1.5 1.0 CD2 A:HIS241 4.5 3.1 1.0 C A:HIS241 4.5 3.1 1.0 O A:HIS241 4.6 3.1 1.0 NE2 A:HIS241 4.6 3.1 1.0 CA A:ASN124 4.7 2.3 1.0 CG A:ASP16 4.8 3.1 1.0 OD2 A:ASP16 4.9 3.1 1.0 NE2 A:HIS125 5.0 2.0 1.0

J.Petrini, M.Hohl, Y.Yu, V.Kuryavyi, D.Patel. Structure Guided Functional Analysis of the S. Cerevisiae MRE11 Complex. Res Sq 2024.
ISSN: ESSN 2693-5015
PubMed: 39711558
DOI: 10.21203/RS.3.RS-5390974/V1