Zinc in PDB 5ws2: Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna

The structure of Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna, PDB code: 5ws2 was solved by D.F.Li, N.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.67 / 2.40
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	168.610, 168.610, 165.868, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.9

The binding sites of Zinc atom in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna (pdb code 5ws2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna, PDB code: 5ws2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:31.0 occ:0.49 OD2 A:ASP174 1.8 38.7 1.0 OD2 A:ASP86 1.9 48.6 1.0 O A:HOH605 2.2 42.5 1.0 NE2 A:HIS410 2.2 59.5 1.0 CG A:ASP174 2.6 41.6 1.0 CG A:ASP86 2.8 38.6 1.0 OP2 C:A2 2.8 60.0 1.0 NE2 A:HIS87 2.8 46.3 1.0 OD1 A:ASP174 2.9 53.1 1.0 CE1 A:HIS410 3.0 57.8 1.0 OD1 A:ASP86 3.1 49.5 1.0 CD2 A:HIS87 3.2 48.0 1.0 ZN A:ZN502 3.2 22.7 0.4 CD2 A:HIS410 3.3 56.0 1.0 P C:A2 3.8 61.7 1.0 OP1 C:A2 3.9 69.3 1.0 O A:HOH695 3.9 38.3 1.0 CB A:ASP174 4.0 43.7 1.0 CE1 A:HIS87 4.1 40.2 1.0 NE2 A:HIS82 4.1 37.4 1.0 OD1 A:ASN18 4.2 28.3 1.0 CB A:ASP86 4.2 29.3 1.0 ND1 A:HIS410 4.2 56.2 1.0 CG A:HIS410 4.4 51.4 1.0 CE1 A:HIS82 4.4 40.7 1.0 CE1 A:HIS388 4.5 23.1 1.0 CG A:HIS87 4.5 36.2 1.0 O5' C:A2 4.6 56.2 1.0 ND1 A:HIS87 4.9 37.3 1.0 NE2 A:HIS152 5.0 29.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:22.7 occ:0.44 O A:HOH605 1.8 42.5 1.0 NE2 A:HIS152 2.2 29.1 1.0 OP1 C:A2 2.3 69.3 1.0 OD2 A:ASP174 2.4 38.7 1.0 ND1 A:HIS84 2.5 32.8 1.0 NE2 A:HIS82 2.7 37.4 1.0 CD2 A:HIS152 3.1 27.9 1.0 CE1 A:HIS152 3.2 29.5 1.0 ZN A:ZN501 3.2 31.0 0.5 CE1 A:HIS84 3.3 27.3 1.0 CG A:ASP174 3.4 41.6 1.0 P C:A2 3.4 61.7 1.0 CD2 A:HIS82 3.5 35.8 1.0 CG A:HIS84 3.5 41.9 1.0 CE1 A:HIS82 3.5 40.7 1.0 CB A:ASP174 3.7 43.7 1.0 OP2 C:A2 3.7 60.0 1.0 CB A:HIS84 3.8 43.3 1.0 OD1 A:ASP86 4.1 49.5 1.0 CG A:HIS152 4.3 34.9 1.0 O5' C:A2 4.3 56.2 1.0 ND1 A:HIS152 4.3 24.4 1.0 C5' C:A2 4.4 54.5 1.0 O A:HOH617 4.4 39.4 1.0 ND1 A:HIS82 4.5 48.3 1.0 OD1 A:ASP174 4.5 53.1 1.0 NE2 A:HIS84 4.5 30.2 1.0 CG A:HIS82 4.5 30.7 1.0 CE1 A:HIS388 4.6 23.1 1.0 O3' C:A1 4.6 69.9 1.0 CD2 A:HIS84 4.6 36.0 1.0 OD2 A:ASP86 4.6 48.6 1.0 CD2 A:HIS87 4.7 48.0 1.0 NE2 A:HIS87 4.7 46.3 1.0 OG A:SER153 4.7 35.2 1.0 CG A:ASP86 4.8 38.6 1.0 NE2 A:HIS388 4.9 32.3 1.0 CA A:ASP174 4.9 48.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:31.1 occ:0.44 OD2 B:ASP86 1.8 42.5 1.0 OD2 B:ASP174 1.8 45.0 1.0 NE2 B:HIS410 2.2 65.5 1.0 O B:HOH601 2.4 36.3 1.0 CG B:ASP174 2.6 40.9 1.0 CE1 B:HIS410 2.7 62.3 1.0 OD1 B:ASP174 2.7 37.6 1.0 CG B:ASP86 2.7 43.2 1.0 OP2 D:A2 2.9 56.0 1.0 OD1 B:ASP86 3.1 50.2 1.0 NE2 B:HIS87 3.1 48.0 1.0 CD2 B:HIS87 3.3 50.6 1.0 ZN B:ZN502 3.4 24.9 0.5 CD2 B:HIS410 3.5 62.0 1.0 P D:A2 3.9 58.8 1.0 OP1 D:A2 3.9 61.9 1.0 ND2 B:ASN18 3.9 28.3 1.0 ND1 B:HIS410 4.0 62.2 1.0 CB B:ASP174 4.0 42.8 1.0 CB B:ASP86 4.1 39.7 1.0 O B:HOH647 4.2 45.7 1.0 NE2 B:HIS82 4.2 37.3 1.0 CE1 B:HIS87 4.4 42.7 1.0 CG B:HIS410 4.4 51.6 1.0 CE1 B:HIS82 4.5 37.5 1.0 CE1 B:HIS388 4.6 30.8 1.0 CG B:HIS87 4.6 42.4 1.0 O5' D:A2 4.8 51.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, Complex with Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:24.9 occ:0.45 O B:HOH601 1.7 36.3 1.0 OD2 B:ASP174 2.2 45.0 1.0 CE1 B:HIS152 2.2 27.3 1.0 OP1 D:A2 2.3 61.9 1.0 ND1 B:HIS84 2.4 33.1 1.0 NE2 B:HIS82 2.8 37.3 1.0 CG B:ASP174 3.0 40.9 1.0 NE2 B:HIS152 3.1 36.3 1.0 ND1 B:HIS152 3.1 37.7 1.0 CE1 B:HIS84 3.2 36.7 1.0 CB B:ASP174 3.3 42.8 1.0 ZN B:ZN501 3.4 31.1 0.4 CG B:HIS84 3.5 42.8 1.0 CE1 B:HIS82 3.5 37.5 1.0 P D:A2 3.5 58.8 1.0 CD2 B:HIS82 3.6 44.8 1.0 CB B:HIS84 3.9 38.9 1.0 OP2 D:A2 3.9 56.0 1.0 OD1 B:ASP174 4.1 37.6 1.0 OD1 B:ASP86 4.1 50.2 1.0 CD2 B:HIS152 4.3 27.0 1.0 CG B:HIS152 4.3 30.9 1.0 NE2 B:HIS84 4.4 37.2 1.0 O5' D:A2 4.4 51.5 1.0 ND1 B:HIS82 4.5 47.4 1.0 O B:HOH641 4.5 38.8 1.0 C5' D:A2 4.5 49.4 1.0 CG B:HIS82 4.5 42.1 1.0 CD2 B:HIS84 4.6 34.3 1.0 CE1 B:HIS388 4.6 30.8 1.0 OG B:SER153 4.7 30.6 1.0 OD2 B:ASP86 4.7 42.5 1.0 CA B:ASP174 4.7 42.5 1.0 O3' D:A1 4.7 68.3 1.0 CD2 B:HIS87 4.8 50.6 1.0 CG B:ASP86 4.8 43.2 1.0 NE2 B:HIS87 4.8 48.0 1.0 NE2 B:HIS388 4.9 35.9 1.0

X.Zheng, N.Feng, D.Li, X.Dong, J.Li. New Molecular Insights Into An Archaeal Rnase J Reveal A Conserved Processive Exoribonucleolysis Mechanism of the Rnase J Family Mol. Microbiol. V. 106 351 2017.
ISSN: ESSN 1365-2958
PubMed: 28795788
DOI: 10.1111/MMI.13769