Manganese in PDB 4yke: Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum

The structure of Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum, PDB code: 4yke was solved by F.U.Seifert, K.Lammens, K.-P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 2.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.722, 56.555, 304.562, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.1

The binding sites of Manganese atom in the Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum (pdb code 4yke). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum, PDB code: 4yke:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum


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 Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:57.6 occ:1.00 OD2 A:ASP17 1.9 47.8 1.0 OD2 A:ASP57 1.9 80.0 1.0 NE2 A:HIS19 2.2 40.0 1.0 NE2 A:HIS243 2.3 49.4 1.0 MN A:MN602 2.6 76.6 1.0 CG A:ASP57 2.9 64.5 1.0 CE1 A:HIS19 2.9 46.1 1.0 CG A:ASP17 3.0 58.9 1.0 CE1 A:HIS243 3.2 48.6 1.0 CD2 A:HIS243 3.4 54.2 1.0 CB A:ASP57 3.4 64.2 1.0 CD2 A:HIS19 3.4 49.1 1.0 CB A:ASP17 3.7 61.0 1.0 OD1 A:ASP57 4.0 53.4 1.0 OD1 A:ASP17 4.0 68.2 1.0 ND1 A:HIS19 4.1 43.2 1.0 OD1 A:ASN124 4.2 98.9 1.0 NE2 A:HIS213 4.3 47.2 1.0 O A:HIS241 4.3 38.5 1.0 CE1 A:HIS213 4.3 44.6 1.0 ND1 A:HIS243 4.3 54.5 1.0 ND1 A:HIS125 4.3 62.8 1.0 ND1 A:HIS241 4.3 56.9 1.0 CG A:HIS19 4.4 38.9 1.0 CG A:HIS243 4.5 55.3 1.0 CA A:ASP17 4.5 58.3 1.0 CE1 A:HIS125 4.5 69.7 1.0 CE1 A:HIS241 4.7 59.7 1.0 ND2 A:ASN124 4.7 88.7 1.0 CA A:ASP57 4.9 62.5 1.0 CG A:ASN124 4.9 89.0 1.0 C A:HIS241 5.0 46.5 1.0 CA A:HIS241 5.0 55.4 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum


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 Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:76.6 occ:1.00 OD2 A:ASP57 2.0 80.0 1.0 ND1 A:HIS241 2.0 56.9 1.0 OD1 A:ASN124 2.0 98.9 1.0 NE2 A:HIS213 2.5 47.2 1.0 CE1 A:HIS241 2.5 59.7 1.0 MN A:MN601 2.6 57.6 1.0 CG A:ASN124 2.9 89.0 1.0 CG A:ASP57 3.1 64.5 1.0 ND2 A:ASN124 3.1 88.7 1.0 CG A:HIS241 3.2 57.7 1.0 CE1 A:HIS213 3.3 44.6 1.0 OD2 A:ASP17 3.4 47.8 1.0 CD2 A:HIS213 3.5 47.8 1.0 OD1 A:ASP57 3.6 53.4 1.0 NE2 A:HIS241 3.7 60.0 1.0 O A:HIS241 3.9 38.5 1.0 CA A:HIS241 3.9 55.4 1.0 CB A:HIS241 3.9 57.6 1.0 CD2 A:HIS241 4.1 52.5 1.0 NE2 A:HIS243 4.2 49.4 1.0 CB A:ASN124 4.3 82.2 1.0 CB A:ASP57 4.3 64.2 1.0 C A:HIS241 4.4 46.5 1.0 ND1 A:HIS125 4.4 62.8 1.0 ND1 A:HIS213 4.4 44.5 1.0 N A:ASN124 4.5 83.1 1.0 CG A:HIS213 4.6 55.4 1.0 NE2 A:HIS19 4.6 40.0 1.0 CG A:ASP17 4.6 58.9 1.0 CE1 A:HIS125 4.6 69.7 1.0 O A:GLY240 4.7 57.9 1.0 CE1 A:HIS19 4.8 46.1 1.0 CD2 A:HIS243 4.9 54.2 1.0 CA A:ASN124 5.0 79.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum


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 Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:49.9 occ:1.00 OD2 B:ASP17 1.7 57.9 1.0 NE2 B:HIS243 2.0 74.7 1.0 NE2 B:HIS19 2.1 56.6 1.0 OD2 B:ASP57 2.4 56.1 1.0 CE1 B:HIS243 2.8 76.0 1.0 CG B:ASP17 2.8 67.6 1.0 CE1 B:HIS19 2.9 61.9 1.0 MN B:MN602 3.0 56.0 1.0 CD2 B:HIS243 3.1 72.1 1.0 CG B:ASP57 3.3 52.9 1.0 CD2 B:HIS19 3.3 68.2 1.0 CB B:ASP17 3.4 61.0 1.0 CB B:ASP57 3.5 48.7 1.0 OD1 B:ASP17 3.8 70.1 1.0 ND1 B:HIS243 4.0 78.2 1.0 ND1 B:HIS19 4.1 61.3 1.0 CG B:HIS243 4.2 73.8 1.0 O B:HIS241 4.3 45.8 1.0 CA B:ASP17 4.3 56.0 1.0 CG B:HIS19 4.3 68.3 1.0 OD1 B:ASP57 4.4 47.2 1.0 NE2 B:HIS213 4.4 67.8 1.0 ND1 B:HIS241 4.5 71.5 1.0 CE1 B:HIS213 4.5 64.5 1.0 ND1 B:HIS125 4.5 59.0 1.0 CE1 B:HIS125 4.6 57.3 1.0 OD1 B:ASN124 4.6 53.0 1.0 CE1 B:HIS241 4.8 82.6 1.0 C B:HIS241 4.9 59.9 1.0 CA B:HIS241 5.0 66.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Eukaryotic MRE11 Catalytic Domain From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:56.0 occ:1.00 OD2 B:ASP57 1.8 56.1 1.0 OD1 B:ASN124 2.0 53.0 1.0 ND1 B:HIS241 2.0 71.5 1.0 NE2 B:HIS213 2.3 67.8 1.0 CE1 B:HIS241 2.7 82.6 1.0 CG B:ASP57 2.9 52.9 1.0 CG B:ASN124 2.9 44.9 1.0 MN B:MN601 3.0 49.9 1.0 CE1 B:HIS213 3.2 64.5 1.0 CG B:HIS241 3.2 67.9 1.0 CD2 B:HIS213 3.2 58.9 1.0 ND2 B:ASN124 3.3 47.5 1.0 OD2 B:ASP17 3.3 57.9 1.0 OD1 B:ASP57 3.4 47.2 1.0 CA B:HIS241 3.7 66.6 1.0 CB B:HIS241 3.8 75.2 1.0 NE2 B:HIS241 3.9 73.2 1.0 O B:HIS241 4.0 45.8 1.0 CB B:ASP57 4.1 48.7 1.0 CD2 B:HIS241 4.2 66.4 1.0 ND1 B:HIS213 4.3 57.5 1.0 CB B:ASN124 4.3 45.3 1.0 CG B:HIS213 4.3 60.0 1.0 C B:HIS241 4.3 59.9 1.0 N B:ASN124 4.4 57.6 1.0 ND1 B:HIS125 4.4 59.0 1.0 CG B:ASP17 4.4 67.6 1.0 NE2 B:HIS243 4.4 74.7 1.0 ND2 B:ASN179 4.7 71.5 1.0 NE2 B:HIS19 4.7 56.6 1.0 CE1 B:HIS125 4.7 57.3 1.0 OD1 B:ASP17 4.8 70.1 1.0 CE1 B:HIS19 4.8 61.9 1.0 N B:HIS241 4.8 68.3 1.0 CA B:ASN124 5.0 54.3 1.0

F.U.Seifert, K.Lammens, K.P.Hopfner. Structure of the Catalytic Domain of MRE11 From Chaetomium Thermophilum. Acta Crystallogr.,Sect.F V. 71 752 2015.
ISSN: ESSN 2053-230X
PubMed: 26057807
DOI: 10.1107/S2053230X15007566