Manganese in PDB 6k6s: Structure of Rnase J1 From Staphylococcus Epidermidis

The structure of Structure of Rnase J1 From Staphylococcus Epidermidis, PDB code: 6k6s was solved by R.Raj, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.58 / 2.99
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	86.068, 86.068, 486.839, 90.00, 90.00, 120.00
R / Rfree (%)	29.7 / 33.7

The binding sites of Manganese atom in the Structure of Rnase J1 From Staphylococcus Epidermidis (pdb code 6k6s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Rnase J1 From Staphylococcus Epidermidis, PDB code: 6k6s:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Rnase J1 From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Rnase J1 From Staphylococcus Epidermidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:65.2 occ:1.00 OD2 A:ASP164 1.9 76.6 1.0 OD2 A:ASP78 2.0 80.3 1.0 NE2 A:HIS390 2.3 0.4 1.0 CE1 A:HIS79 2.6 78.7 1.0 CG A:ASP164 2.8 80.3 1.0 OD1 A:ASP164 3.1 80.5 1.0 CE1 A:HIS390 3.2 0.0 1.0 ND1 A:HIS79 3.2 74.1 1.0 CG A:ASP78 3.2 88.7 1.0 CD2 A:HIS390 3.3 96.4 1.0 MN A:MN602 3.4 59.8 1.0 NE2 A:HIS79 3.7 80.5 1.0 CE1 A:HIS368 3.8 96.0 1.0 OD1 A:ASP78 3.9 0.8 1.0 NE2 A:HIS74 4.2 56.9 1.0 CB A:ASP164 4.2 93.9 1.0 NE2 A:HIS368 4.3 92.5 1.0 ND1 A:HIS390 4.3 0.8 1.0 CB A:ASP78 4.3 90.2 1.0 CG A:HIS390 4.3 96.8 1.0 CE1 A:HIS74 4.5 80.9 1.0 CG A:HIS79 4.5 64.6 1.0 ND2 A:ASN23 4.5 99.9 1.0 CD2 A:HIS79 4.8 63.2 1.0 ND1 A:HIS76 4.9 73.1 1.0 ND1 A:HIS368 5.0 82.5 1.0

Manganese binding site 2 out of 4 in the Structure of Rnase J1 From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Rnase J1 From Staphylococcus Epidermidis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:59.8 occ:1.00 ND1 A:HIS76 2.0 73.1 1.0 OD2 A:ASP164 2.4 76.6 1.0 NE2 A:HIS142 2.5 92.1 1.0 NE2 A:HIS74 2.7 56.9 1.0 CE1 A:HIS76 2.8 66.0 1.0 CG A:HIS76 3.1 67.1 1.0 CD2 A:HIS74 3.3 76.1 1.0 CG A:ASP164 3.3 80.3 1.0 CE1 A:HIS142 3.4 87.5 1.0 MN A:MN601 3.4 65.2 1.0 CD2 A:HIS142 3.4 90.3 1.0 CB A:ASP164 3.5 93.9 1.0 CB A:HIS76 3.6 78.5 1.0 CE1 A:HIS74 3.8 80.9 1.0 NE2 A:HIS76 4.0 63.1 1.0 CD2 A:HIS76 4.1 54.4 1.0 OD2 A:ASP78 4.2 80.3 1.0 NE2 A:HIS368 4.2 92.5 1.0 CE1 A:HIS368 4.3 96.0 1.0 OD1 A:ASP164 4.5 80.5 1.0 ND1 A:HIS142 4.5 75.8 1.0 CG A:HIS74 4.5 75.5 1.0 OD1 A:ASP78 4.6 0.8 1.0 CG A:HIS142 4.6 81.8 1.0 CE1 A:HIS79 4.7 78.7 1.0 ND1 A:HIS79 4.7 74.1 1.0 ND1 A:HIS74 4.7 81.9 1.0 CG A:ASP78 4.8 88.7 1.0

Manganese binding site 3 out of 4 in the Structure of Rnase J1 From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Rnase J1 From Staphylococcus Epidermidis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:82.2 occ:1.00 OD2 B:ASP164 1.9 96.3 1.0 OD2 B:ASP78 2.0 0.3 1.0 NE2 B:HIS390 2.5 92.5 1.0 CE1 B:HIS79 3.0 71.0 1.0 CG B:ASP164 3.0 96.1 1.0 MN B:MN602 3.0 77.8 1.0 CG B:ASP78 3.1 0.3 1.0 CE1 B:HIS390 3.3 95.7 1.0 OD1 B:ASP164 3.4 0.9 1.0 ND1 B:HIS79 3.5 70.9 1.0 CD2 B:HIS390 3.6 86.3 1.0 CE1 B:HIS368 3.7 89.0 1.0 OD1 B:ASP78 3.7 0.4 1.0 NE2 B:HIS368 4.0 92.5 1.0 NE2 B:HIS79 4.1 97.8 1.0 NE2 B:HIS74 4.3 73.6 1.0 CB B:ASP78 4.3 0.2 1.0 CB B:ASP164 4.3 91.4 1.0 ND1 B:HIS390 4.4 94.9 1.0 ND1 B:HIS76 4.6 89.0 1.0 CG B:HIS390 4.6 85.8 1.0 CE1 B:HIS74 4.7 87.6 1.0 CG B:HIS79 4.8 0.7 1.0 ND2 B:ASN23 4.8 96.2 1.0 ND1 B:HIS368 4.9 86.4 1.0 CB B:HIS76 4.9 96.5 1.0

Manganese binding site 4 out of 4 in the Structure of Rnase J1 From Staphylococcus Epidermidis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Rnase J1 From Staphylococcus Epidermidis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:77.8 occ:1.00 ND1 B:HIS76 1.9 89.0 1.0 OD2 B:ASP164 2.3 96.3 1.0 NE2 B:HIS74 2.7 73.6 1.0 NE2 B:HIS142 2.8 78.0 1.0 CE1 B:HIS76 2.8 89.6 1.0 CG B:HIS76 3.0 90.6 1.0 MN B:MN601 3.0 82.2 1.0 CG B:ASP164 3.3 96.1 1.0 CD2 B:HIS74 3.3 75.1 1.0 CB B:HIS76 3.4 96.5 1.0 CB B:ASP164 3.6 91.4 1.0 CD2 B:HIS142 3.7 90.1 1.0 CE1 B:HIS142 3.7 79.2 1.0 CE1 B:HIS74 3.8 87.6 1.0 OD2 B:ASP78 3.9 0.3 1.0 NE2 B:HIS76 3.9 88.9 1.0 CD2 B:HIS76 4.1 92.3 1.0 NE2 B:HIS368 4.2 92.5 1.0 CE1 B:HIS368 4.3 89.0 1.0 OD1 B:ASP78 4.3 0.4 1.0 OD1 B:ASP164 4.4 0.9 1.0 CE1 B:HIS79 4.5 71.0 1.0 ND1 B:HIS79 4.5 70.9 1.0 CG B:HIS74 4.6 83.8 1.0 CG B:ASP78 4.6 0.3 1.0 ND1 B:HIS74 4.7 92.2 1.0 ND1 B:HIS142 4.8 84.1 1.0 CG B:HIS142 4.9 86.8 1.0 CA B:HIS76 4.9 98.7 1.0

R.Raj, B.Gopal. Structure of Rnase J1 From Staphylococcus Epidermidis J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X