Manganese in PDB 8yyj: Rnase J2 Mutant H80A

The structure of Rnase J2 Mutant H80A, PDB code: 8yyj 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)	66.00 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.89, 131.91, 116.19, 90, 91.77, 90
R / Rfree (%)	24.7 / 30

The binding sites of Manganese atom in the Rnase J2 Mutant H80A (pdb code 8yyj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Rnase J2 Mutant H80A, PDB code: 8yyj:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Rnase J2 Mutant H80A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rnase J2 Mutant H80A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:24.4 occ:0.60 OE2 A:GLU166 1.8 33.2 1.0 ND1 A:HIS78 1.9 22.7 1.0 OE1 A:GLU166 1.9 27.0 1.0 NE2 A:HIS144 2.0 34.2 1.0 CD A:GLU166 2.2 29.7 1.0 CE1 A:HIS78 2.5 23.0 1.0 NE2 A:HIS76 2.9 27.3 1.0 CE1 A:HIS144 2.9 33.7 1.0 CD2 A:HIS144 3.2 33.2 1.0 CG A:HIS78 3.2 22.6 1.0 CD2 A:HIS76 3.5 29.6 1.0 CG A:GLU166 3.7 28.6 1.0 NE2 A:HIS78 3.8 21.1 1.0 CB A:GLU166 3.9 28.9 1.0 CB A:HIS78 3.9 24.7 1.0 CE1 A:HIS76 4.1 27.1 1.0 ND1 A:HIS144 4.1 32.7 1.0 CD2 A:HIS78 4.1 20.6 1.0 CG A:HIS144 4.2 31.6 1.0 CE1 A:HIS370 4.4 23.4 1.0 O A:HOH701 4.5 0.5 1.0 OG A:SER145 4.6 25.1 1.0 NE2 A:HIS370 4.7 24.0 1.0 CG A:HIS76 4.8 30.5 1.0 CB A:SER369 4.8 25.0 1.0 ND1 A:HIS76 5.0 27.5 1.0

Manganese binding site 2 out of 4 in the Rnase J2 Mutant H80A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rnase J2 Mutant H80A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:18.5 occ:0.60 OE1 B:GLU166 1.7 21.9 1.0 ND1 B:HIS78 1.8 24.4 1.0 NE2 B:HIS144 1.9 24.5 1.0 CE1 B:HIS78 2.6 25.3 1.0 CE1 B:HIS76 2.7 27.9 1.0 CE1 B:HIS144 2.8 25.6 1.0 CD2 B:HIS144 3.0 23.6 1.0 CG B:HIS78 3.0 24.2 1.0 CD B:GLU166 3.0 23.0 1.0 ND1 B:HIS76 3.3 28.0 1.0 CB B:HIS78 3.6 25.1 1.0 NE2 B:HIS76 3.8 28.2 1.0 NE2 B:HIS78 3.8 24.2 1.0 OE2 B:GLU166 3.8 23.3 1.0 ND1 B:HIS144 4.0 24.5 1.0 CD2 B:HIS78 4.0 23.8 1.0 CB B:GLU166 4.1 22.2 1.0 CG B:HIS144 4.1 22.4 1.0 CG B:GLU166 4.1 21.9 1.0 O B:HOH702 4.3 0.5 1.0 CG B:HIS76 4.5 26.3 1.0 CE1 B:HIS370 4.7 27.0 1.0 CD2 B:HIS76 4.7 26.9 1.0 OG B:SER145 4.9 20.0 1.0 NE2 B:HIS370 4.9 27.7 1.0

Manganese binding site 3 out of 4 in the Rnase J2 Mutant H80A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rnase J2 Mutant H80A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:29.9 occ:0.80 OE1 C:GLU166 1.7 31.4 1.0 ND1 C:HIS78 1.8 31.6 1.0 NE2 C:HIS144 1.9 32.1 1.0 CE1 C:HIS78 2.5 31.1 1.0 NE2 C:HIS76 2.6 36.3 1.0 CE1 C:HIS144 2.9 30.9 1.0 CD2 C:HIS144 3.0 29.9 1.0 CD C:GLU166 3.0 33.9 1.0 CG C:HIS78 3.0 30.1 1.0 CD2 C:HIS76 3.3 35.6 1.0 O C:HOH701 3.6 22.4 1.0 CB C:HIS78 3.7 29.6 1.0 NE2 C:HIS78 3.8 29.4 1.0 CE1 C:HIS76 3.8 36.6 1.0 OE2 C:GLU166 3.8 37.0 1.0 CD2 C:HIS78 4.0 28.6 1.0 ND1 C:HIS144 4.0 28.6 1.0 CG C:GLU166 4.0 32.5 1.0 CB C:GLU166 4.0 32.4 1.0 CG C:HIS144 4.1 28.0 1.0 CG C:HIS76 4.6 34.9 1.0 CE1 C:HIS370 4.6 30.9 1.0 ND1 C:HIS76 4.8 34.2 1.0 OG C:SER145 4.9 28.8 1.0 NE2 C:HIS370 4.9 31.3 1.0

Manganese binding site 4 out of 4 in the Rnase J2 Mutant H80A


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Rnase J2 Mutant H80A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:26.9 occ:0.60 OE1 D:GLU166 1.8 26.9 1.0 ND1 D:HIS78 1.8 27.1 1.0 NE2 D:HIS144 1.9 31.7 1.0 NE2 D:HIS76 1.9 29.8 1.0 CD2 D:HIS76 2.7 30.5 1.0 CE1 D:HIS78 2.8 27.3 1.0 CD2 D:HIS144 2.8 28.9 1.0 CG D:HIS78 2.9 27.3 1.0 CD D:GLU166 3.0 28.7 1.0 CE1 D:HIS144 3.0 31.1 1.0 CE1 D:HIS76 3.1 30.0 1.0 O D:HOH701 3.3 9.7 1.0 CB D:HIS78 3.4 29.6 1.0 OE2 D:GLU166 3.8 31.3 1.0 NE2 D:HIS78 3.9 25.6 1.0 CG D:HIS76 3.9 30.6 1.0 CD2 D:HIS78 3.9 25.8 1.0 CG D:GLU166 3.9 27.5 1.0 CB D:GLU166 3.9 27.9 1.0 CG D:HIS144 4.0 27.2 1.0 ND1 D:HIS144 4.1 29.2 1.0 ND1 D:HIS76 4.1 29.7 1.0 CA D:HIS78 4.8 30.8 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