Manganese in PDB 8yyg: Rnase J2 Mutant H78A

The structure of Rnase J2 Mutant H78A, PDB code: 8yyg 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)	44.70 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.83, 72.28, 105.61, 90, 90, 90
R / Rfree (%)	16.6 / 19.7

The binding sites of Manganese atom in the Rnase J2 Mutant H78A (pdb code 8yyg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Rnase J2 Mutant H78A, PDB code: 8yyg:

Manganese binding site 1 out of 1 in the Rnase J2 Mutant H78A


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 H78A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:11.2 occ:0.41 OE1 A:GLU166 1.9 17.5 0.9 NE2 A:HIS144 2.1 20.2 1.0 O A:HOH882 2.2 31.5 1.0 O A:HOH878 2.2 35.4 1.0 CE1 A:HIS76 2.3 22.9 1.0 O A:HOH871 2.3 28.8 1.0 NE2 A:HIS76 2.5 20.8 1.0 CE1 A:HIS144 3.1 21.7 1.0 CD2 A:HIS144 3.2 22.7 1.0 CD A:GLU166 3.2 15.3 0.7 ND1 A:HIS76 3.4 21.7 1.0 CB A:GLU166 3.9 13.2 1.0 CD2 A:HIS76 4.0 15.2 1.0 CB A:ALA78 4.0 18.5 1.0 CG A:GLU166 4.1 18.6 1.0 OE2 A:GLU166 4.2 18.4 1.0 O A:HOH838 4.3 20.9 1.0 ND1 A:HIS144 4.3 16.5 1.0 O A:HOH824 4.3 33.2 1.0 CG A:HIS144 4.4 14.4 1.0 CD2 A:HIS80 4.4 16.0 0.8 CG A:HIS76 4.4 13.3 1.0 CB A:HIS80 4.5 19.4 1.0 CE1 A:HIS370 4.6 14.2 1.0 CG A:HIS80 4.6 17.1 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