Manganese in PDB 7dog: Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus

The structure of Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus, PDB code: 7dog was solved by J.Lee, N.-C.Ha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.84 / 2.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.906, 89.465, 116.575, 90, 90, 90
R / Rfree (%)	19.2 / 24.9

The binding sites of Manganese atom in the Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus (pdb code 7dog). 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 A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus, PDB code: 7dog:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus


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 A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:32.6 occ:1.00 OD2 A:ASP48 2.0 28.7 1.0 ND1 A:HIS210 2.1 36.0 1.0 OD1 A:ASN84 2.2 27.0 1.0 NE2 A:HIS172 2.5 19.9 1.0 CE1 A:HIS210 2.8 35.9 1.0 CG A:ASP48 2.9 26.7 1.0 MN A:MN402 3.1 22.6 1.0 CG A:ASN84 3.2 33.0 1.0 OD1 A:ASP48 3.3 28.1 1.0 CE1 A:HIS172 3.4 20.9 1.0 CG A:HIS210 3.4 31.1 1.0 ND2 A:ASN84 3.4 38.7 1.0 CD2 A:HIS172 3.6 25.1 1.0 CA A:HIS210 3.8 25.5 1.0 ND1 A:HIS85 3.9 31.2 1.0 CE1 A:HIS85 4.0 36.4 1.0 CB A:HIS210 4.0 24.4 1.0 NE2 A:HIS210 4.0 32.0 1.0 O A:HIS210 4.1 33.5 1.0 OD1 A:ASP8 4.1 27.5 1.0 CB A:ASP48 4.2 26.1 1.0 CD2 A:HIS210 4.3 31.0 1.0 C A:HIS210 4.4 29.7 1.0 ND1 A:HIS172 4.5 25.4 1.0 N A:ASN84 4.6 31.1 1.0 CB A:ASN84 4.6 29.1 1.0 CG A:HIS172 4.7 26.5 1.0 NE2 A:HIS10 4.7 27.4 1.0 N A:HIS210 4.9 23.9 1.0 CE1 A:HIS10 4.9 27.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus


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 A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:22.6 occ:1.00 OD2 A:ASP48 2.1 28.7 1.0 OD1 A:ASP8 2.1 27.5 1.0 NE2 A:HIS10 2.1 27.4 1.0 NE2 A:HIS212 2.4 31.4 1.0 CE1 A:HIS10 3.0 27.2 1.0 CG A:ASP48 3.0 26.7 1.0 MN A:MN401 3.1 32.6 1.0 CG A:ASP8 3.2 28.4 1.0 CD2 A:HIS10 3.2 29.4 1.0 CD2 A:HIS212 3.3 32.4 1.0 CB A:ASP48 3.4 26.1 1.0 CE1 A:HIS212 3.5 35.4 1.0 O A:HIS210 3.6 33.5 1.0 CB A:ASP8 3.8 27.4 1.0 OD1 A:ASP48 4.1 28.1 1.0 ND1 A:HIS10 4.2 27.8 1.0 OD2 A:ASP8 4.2 31.2 1.0 CA A:HIS210 4.3 25.5 1.0 C A:HIS210 4.3 29.7 1.0 CG A:HIS10 4.3 27.5 1.0 CE1 A:HIS172 4.3 20.9 1.0 CA A:ASP8 4.4 28.0 1.0 NE2 A:HIS172 4.4 19.9 1.0 CG A:HIS212 4.5 33.6 1.0 ND1 A:HIS210 4.5 36.0 1.0 ND1 A:HIS212 4.5 37.7 1.0 CE1 A:HIS85 4.6 36.4 1.0 ND1 A:HIS85 4.7 31.2 1.0 CA A:ASP48 4.9 23.0 1.0 N A:HIS210 5.0 23.9 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus


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 A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:29.2 occ:1.00 OD1 B:ASP8 1.8 25.1 1.0 OD2 B:ASP48 2.1 29.7 1.0 NE2 B:HIS10 2.3 23.1 1.0 NE2 B:HIS212 2.3 29.2 1.0 CG B:ASP8 3.0 25.5 1.0 MN B:MN402 3.0 29.0 1.0 CG B:ASP48 3.1 28.4 1.0 CD2 B:HIS212 3.2 27.7 1.0 CE1 B:HIS10 3.2 21.1 1.0 CD2 B:HIS10 3.3 24.1 1.0 CE1 B:HIS212 3.3 33.6 1.0 CB B:ASP48 3.5 25.9 1.0 O B:HIS210 3.6 31.2 1.0 CB B:ASP8 3.7 29.1 1.0 OD2 B:ASP8 3.9 26.3 1.0 CA B:HIS210 4.0 27.7 1.0 C B:HIS210 4.1 29.1 1.0 OD1 B:ASP48 4.2 27.4 1.0 NE2 B:HIS172 4.3 26.7 1.0 CE1 B:HIS172 4.3 30.1 1.0 CG B:HIS212 4.3 30.6 1.0 ND1 B:HIS10 4.4 20.4 1.0 CA B:ASP8 4.4 26.9 1.0 ND1 B:HIS212 4.4 35.8 1.0 CG B:HIS10 4.4 23.6 1.0 ND1 B:HIS210 4.4 35.1 1.0 N B:HIS210 4.6 27.9 1.0 OD1 B:ASN84 4.7 31.5 1.0 CD2 B:HIS85 5.0 30.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus


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 A Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:29.0 occ:1.00 OD2 B:ASP48 2.1 29.7 1.0 OD1 B:ASN84 2.2 31.5 1.0 ND1 B:HIS210 2.2 35.1 1.0 NE2 B:HIS172 2.4 26.7 1.0 MN B:MN401 3.0 29.2 1.0 CG B:ASN84 3.1 32.6 1.0 CG B:ASP48 3.1 28.4 1.0 CE1 B:HIS210 3.2 32.0 1.0 CG B:HIS210 3.2 27.7 1.0 CE1 B:HIS172 3.4 30.1 1.0 CA B:HIS210 3.4 27.7 1.0 ND2 B:ASN84 3.4 35.6 1.0 CD2 B:HIS172 3.4 29.0 1.0 CB B:HIS210 3.5 25.9 1.0 OD1 B:ASP48 3.5 27.4 1.0 OD1 B:ASP8 3.8 25.1 1.0 O B:HIS210 3.9 31.2 1.0 CD2 B:HIS85 4.1 30.9 1.0 C B:HIS210 4.1 29.1 1.0 CB B:ASP48 4.3 25.9 1.0 NE2 B:HIS210 4.3 26.9 1.0 CD2 B:HIS210 4.3 30.5 1.0 CB B:ASN84 4.4 30.1 1.0 N B:HIS210 4.4 27.9 1.0 ND1 B:HIS172 4.5 30.1 1.0 NE2 B:HIS85 4.6 29.2 1.0 CG B:HIS172 4.6 26.2 1.0 N B:ASN84 4.6 38.3 1.0 NE2 B:HIS10 4.6 23.1 1.0 NE2 B:HIS212 4.7 29.2 1.0 CE1 B:HIS10 4.9 21.1 1.0

J.Lee, I.Jo, J.Ahn, S.Hong, S.Jeong, A.Kwon, N.C.Ha. Crystal Structure of the Nuclease and Capping Domain of Sbcd From Staphylococcus Aureus. J.Microbiol 2021.
ISSN: ESSN 1976-3794
PubMed: 33877576
DOI: 10.1007/S12275-021-1012-0