Manganese in PDB 8yyk: Structure of Rnase J2 Wild Type at Room Temperature

The structure of Structure of Rnase J2 Wild Type at Room Temperature, PDB code: 8yyk was solved by A.K.Singh, K.Chinnasamy, B.Gopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.60 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.304, 133.38, 117.751, 90, 92.02, 90
R / Rfree (%)	20.5 / 24.8

The binding sites of Manganese atom in the Structure of Rnase J2 Wild Type at Room Temperature (pdb code 8yyk). 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 J2 Wild Type at Room Temperature, PDB code: 8yyk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Rnase J2 Wild Type at Room Temperature


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 J2 Wild Type at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:47.5 occ:1.00 OE1 A:GLU166 1.8 40.9 1.0 NE2 A:HIS80 1.9 52.6 1.0 NE2 A:HIS144 1.9 32.7 1.0 ND1 A:HIS78 2.7 30.8 1.0 CE1 A:HIS144 2.8 29.9 1.0 CD2 A:HIS80 2.9 50.6 1.0 NE2 A:HIS76 3.0 26.9 1.0 CD A:GLU166 3.0 36.2 1.0 CE1 A:HIS80 3.0 50.8 1.0 CD2 A:HIS144 3.1 28.7 1.0 CE1 A:HIS78 3.6 32.1 1.0 CD2 A:HIS76 3.6 26.9 1.0 OE2 A:GLU166 3.7 39.9 1.0 CG A:HIS78 3.8 30.1 1.0 CB A:GLU166 4.0 29.9 1.0 ND1 A:HIS144 4.0 27.9 1.0 CE1 A:HIS76 4.0 27.6 1.0 CG A:HIS80 4.1 45.2 1.0 CB A:HIS78 4.1 28.7 1.0 CG A:GLU166 4.1 32.4 1.0 ND1 A:HIS80 4.1 48.9 1.0 CG A:HIS144 4.2 27.1 1.0 CE1 A:HIS370 4.5 16.5 1.0 CG A:HIS76 4.8 26.8 1.0 NE2 A:HIS370 4.8 16.6 1.0 NE2 A:HIS78 4.8 32.1 1.0 OG A:SER145 4.8 21.4 1.0 CD2 A:HIS78 4.9 30.8 1.0 ND1 A:HIS76 4.9 27.9 1.0

Manganese binding site 2 out of 4 in the Structure of Rnase J2 Wild Type at Room Temperature


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 J2 Wild Type at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:36.9 occ:1.00 NE2 B:HIS80 1.9 49.4 1.0 OE1 B:GLU166 1.9 27.1 1.0 NE2 B:HIS144 2.0 27.7 1.0 ND1 B:HIS78 2.0 32.5 1.0 CD2 B:HIS80 2.9 50.9 1.0 NE2 B:HIS76 2.9 26.1 1.0 CE1 B:HIS144 3.0 25.4 1.0 CE1 B:HIS80 3.0 50.9 1.0 CE1 B:HIS78 3.0 31.0 1.0 CD2 B:HIS144 3.1 24.7 1.0 CG B:HIS78 3.2 29.8 1.0 CD B:GLU166 3.2 23.4 1.0 CD2 B:HIS76 3.4 26.2 1.0 CB B:HIS78 3.6 30.1 1.0 OE2 B:GLU166 4.0 22.1 1.0 CG B:HIS80 4.1 48.9 1.0 ND1 B:HIS80 4.1 52.0 1.0 CE1 B:HIS76 4.1 26.2 1.0 ND1 B:HIS144 4.1 23.4 1.0 CG B:HIS144 4.2 22.9 1.0 NE2 B:HIS78 4.2 29.7 1.0 CD2 B:HIS78 4.3 29.9 1.0 CG B:GLU166 4.3 23.1 1.0 CB B:GLU166 4.3 22.3 1.0 CG B:HIS76 4.7 27.1 1.0 OG B:SER145 4.7 19.7 1.0 CE1 B:HIS370 4.9 17.6 1.0 ND1 B:HIS76 5.0 27.1 1.0

Manganese binding site 3 out of 4 in the Structure of Rnase J2 Wild Type at Room Temperature


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 J2 Wild Type at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:85.7 occ:1.00 OE1 C:GLU166 1.8 54.5 1.0 NE2 C:HIS80 1.9 87.7 1.0 NE2 C:HIS144 1.9 46.0 1.0 ND1 C:HIS78 2.7 72.4 1.0 CE1 C:HIS144 2.7 38.6 1.0 CD2 C:HIS80 2.9 84.8 1.0 CD C:GLU166 3.0 44.2 1.0 CE1 C:HIS80 3.0 81.2 1.0 NE2 C:HIS76 3.0 37.3 1.0 CD2 C:HIS144 3.1 36.2 1.0 CE1 C:HIS78 3.6 74.7 1.0 CD2 C:HIS76 3.7 36.5 1.0 OE2 C:GLU166 3.7 45.2 1.0 CG C:HIS78 3.8 66.2 1.0 CB C:GLU166 3.9 38.6 1.0 ND1 C:HIS144 4.0 34.3 1.0 CG C:HIS80 4.1 75.6 1.0 CB C:HIS78 4.1 56.9 1.0 CG C:GLU166 4.1 41.8 1.0 CE1 C:HIS76 4.1 38.8 1.0 ND1 C:HIS80 4.1 78.4 1.0 CG C:HIS144 4.2 33.7 1.0 CE1 C:HIS370 4.4 23.1 1.0 NE2 C:HIS370 4.7 23.4 1.0 NE2 C:HIS78 4.8 76.6 1.0 OG C:SER145 4.9 42.7 1.0 CD2 C:HIS78 4.9 71.7 1.0 CG C:HIS76 4.9 38.0 1.0 CB C:SER369 4.9 35.6 1.0

Manganese binding site 4 out of 4 in the Structure of Rnase J2 Wild Type at Room Temperature


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 J2 Wild Type at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:55.0 occ:1.00 OE1 D:GLU166 1.8 43.2 1.0 NE2 D:HIS80 1.9 61.5 1.0 ND1 D:HIS78 1.9 43.8 1.0 NE2 D:HIS144 2.0 41.4 1.0 CE1 D:HIS78 2.9 41.9 1.0 NE2 D:HIS76 2.9 33.6 1.0 CD2 D:HIS80 2.9 60.7 1.0 CE1 D:HIS144 3.0 37.4 1.0 CE1 D:HIS80 3.0 59.4 1.0 CG D:HIS78 3.0 38.5 1.0 CD2 D:HIS144 3.1 36.1 1.0 CD D:GLU166 3.1 37.3 1.0 CD2 D:HIS76 3.4 33.5 1.0 CB D:HIS78 3.5 37.9 1.0 OE2 D:GLU166 3.9 37.9 1.0 CE1 D:HIS76 4.0 34.7 1.0 NE2 D:HIS78 4.1 39.1 1.0 CG D:HIS80 4.1 55.0 1.0 ND1 D:HIS144 4.1 34.0 1.0 ND1 D:HIS80 4.1 57.4 1.0 CD2 D:HIS78 4.1 38.9 1.0 CG D:HIS144 4.2 32.9 1.0 CG D:GLU166 4.2 34.9 1.0 CB D:GLU166 4.3 33.5 1.0 CG D:HIS76 4.6 33.8 1.0 OG D:SER145 4.7 26.8 1.0 CE1 D:HIS370 4.8 28.6 1.0 ND1 D:HIS76 4.9 35.8 1.0

A.K.Singh, K.Chinnasamy, N.R.Pahelkar, B.Gopal. A Physicochemical Rationale For the Varied Catalytic Efficiency in Rnase J Paralogues. J.Biol.Chem. V. 301 08152 2024.
ISSN: ESSN 1083-351X
PubMed: 39742998
DOI: 10.1016/J.JBC.2024.108152