Manganese in PDB 7yzp: Hairpin-Bound State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and A Dna Hairpin

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

Magnesium

(Mg)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hairpin-Bound State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and A Dna Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:78.8 occ:1.00 NE2 A:HIS224 2.1 64.8 1.0 NE2 A:HIS10 2.3 64.8 1.0 CE1 A:HIS224 2.9 64.8 1.0 CD2 A:HIS224 3.0 64.8 1.0 CE1 A:HIS10 3.0 64.8 1.0 OD1 A:ASP8 3.1 64.8 1.0 CG A:ASP8 3.2 64.8 1.0 OD2 A:ASP48 3.2 64.8 1.0 CD2 A:HIS10 3.4 64.8 1.0 OD2 A:ASP8 3.5 64.8 1.0 CB A:ASP8 3.8 64.8 1.0 ND1 A:HIS224 4.0 64.8 1.0 CG A:HIS224 4.0 64.8 1.0 CG A:ASP48 4.2 64.8 1.0 ND1 A:HIS10 4.2 64.8 1.0 CG A:HIS10 4.4 64.8 1.0 CA A:ASP8 4.6 64.8 1.0 CB A:ASP48 4.6 64.8 1.0 CD1 A:LEU244 4.8 64.8 1.0 CD2 A:HIS222 4.8 64.8 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hairpin-Bound State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and A Dna Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:69.5 occ:1.00 OD1 A:ASN83 1.6 64.8 1.0 CD2 A:HIS222 2.1 64.8 1.0 NE2 A:HIS222 2.4 64.8 1.0 CG A:ASN83 2.4 64.8 1.0 ND2 A:ASN83 2.9 64.8 1.0 NE2 A:HIS184 3.0 64.8 1.0 CG A:HIS222 3.1 64.8 1.0 OD2 A:ASP48 3.2 64.8 1.0 CE1 A:HIS222 3.4 64.8 1.0 CD2 A:HIS184 3.5 64.8 1.0 OD1 A:ASP48 3.7 64.8 1.0 CB A:ASN83 3.7 64.8 1.0 ND1 A:HIS222 3.8 64.8 1.0 CG A:ASP48 3.8 64.8 1.0 N A:ASN83 3.9 64.8 1.0 CB A:HIS222 4.0 64.8 1.0 CE1 A:HIS184 4.1 64.8 1.0 CA A:ASN83 4.3 64.8 1.0 N A:GLN84 4.6 64.8 1.0 CA A:HIS222 4.7 64.8 1.0 CG A:HIS184 4.8 64.8 1.0 CG A:GLN84 4.8 30.0 1.0 C A:GLY82 4.9 64.8 1.0 C A:ASN83 5.0 64.8 1.0 ND1 A:HIS184 5.0 64.8 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hairpin-Bound State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and A Dna Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:104.2 occ:1.00 OD1 B:ASP8 2.0 84.2 1.0 CG B:ASP8 2.1 84.2 1.0 CE1 B:HIS224 2.2 85.1 1.0 OD2 B:ASP8 2.6 84.2 1.0 NE2 B:HIS10 2.7 72.7 1.0 ND1 B:HIS224 2.7 85.1 1.0 CB B:ASP8 2.9 84.2 1.0 CD2 B:HIS10 3.2 72.7 1.0 NE2 B:HIS224 3.2 85.1 1.0 OD2 B:ASP48 3.6 83.9 1.0 CA B:ASP8 3.8 84.2 1.0 CE1 B:HIS10 3.9 72.7 1.0 CG B:HIS224 3.9 85.1 1.0 CD2 B:HIS224 4.2 85.1 1.0 CG B:ASP48 4.4 83.9 1.0 O B:HIS222 4.4 86.9 1.0 CG B:HIS10 4.5 72.7 1.0 C B:HIS222 4.5 86.9 1.0 CB B:ASP48 4.5 83.9 1.0 CA B:HIS222 4.7 86.9 1.0 C B:ASP8 4.8 84.2 1.0 ND1 B:HIS10 4.8 72.7 1.0 N B:ASP8 4.8 84.2 1.0 O B:ASP8 4.9 84.2 1.0 N B:HIS224 5.0 85.1 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hairpin-Bound State of the E. Coli MRE11-RAD50 (Sbccd) Head Complex Bound to Adp and A Dna Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:102.6 occ:1.00 N B:ASN83 2.0 87.5 1.0 OD1 B:ASN83 2.0 87.5 1.0 NE2 B:HIS184 2.1 90.9 1.0 CG B:ASN83 2.2 87.5 1.0 OD2 B:ASP48 2.3 83.9 1.0 OD1 B:ASP48 2.4 83.9 1.0 CG B:ASP48 2.5 83.9 1.0 CD2 B:HIS184 2.8 90.9 1.0 ND2 B:ASN83 2.8 87.5 1.0 C B:GLY82 3.0 85.8 1.0 CA B:ASN83 3.0 87.5 1.0 CB B:ASN83 3.0 87.5 1.0 CA B:GLY82 3.1 85.8 1.0 CE1 B:HIS184 3.2 90.9 1.0 N B:GLN84 3.7 84.8 1.0 C B:ASN83 3.8 87.5 1.0 CB B:ASP48 3.9 83.9 1.0 CG B:HIS184 3.9 90.9 1.0 ND1 B:HIS184 4.1 90.9 1.0 O B:GLY82 4.1 85.8 1.0 CA B:ASP48 4.5 83.9 1.0 N B:ASP48 4.6 83.9 1.0 N B:GLY82 4.6 85.8 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