Zinc in PDB 5haa: Crystal Structure of Mpy-Rnase J, An Archaeal Rnase J From Methanolobus Psychrophilus R15

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

Resolution Low / High (Å)	39.03 / 2.90
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	162.508, 162.508, 180.659, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 27.4

The binding sites of Zinc atom in the Crystal Structure of Mpy-Rnase J, An Archaeal Rnase J From Methanolobus Psychrophilus R15 (pdb code 5haa). 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, An Archaeal Rnase J From Methanolobus Psychrophilus R15, PDB code: 5haa:
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, An Archaeal Rnase J From Methanolobus Psychrophilus R15


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, An Archaeal Rnase J From Methanolobus Psychrophilus R15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.0 occ:1.00 OD2 A:ASP86 2.0 0.8 1.0 OD1 A:ASP174 2.0 0.3 1.0 NE2 A:HIS410 2.4 96.6 1.0 OD2 A:ASP174 2.5 0.2 1.0 CG A:ASP174 2.6 0.7 1.0 ZN A:ZN502 2.7 93.4 1.0 O A:HOH601 2.8 45.4 1.0 CG A:ASP86 2.8 0.0 1.0 OD1 A:ASP86 3.0 0.2 1.0 CE1 A:HIS410 3.2 90.8 1.0 CD2 A:HIS410 3.6 98.9 1.0 NE2 A:HIS87 4.0 89.1 1.0 NE2 A:HIS388 4.0 67.5 1.0 CB A:ASP174 4.0 0.0 1.0 CD2 A:HIS87 4.2 78.4 1.0 CB A:ASP86 4.2 0.9 1.0 ND1 A:HIS410 4.4 89.6 1.0 CE1 A:HIS82 4.4 92.2 1.0 NE2 A:HIS82 4.4 98.0 1.0 NE2 A:HIS152 4.5 81.2 1.0 ND1 A:HIS84 4.6 1.0 1.0 CG A:HIS410 4.6 90.8 1.0 CE1 A:HIS87 4.6 88.4 1.0 CE1 A:HIS388 4.7 66.5 1.0 CE1 A:HIS152 4.7 79.8 1.0 CG A:HIS87 4.9 87.5 1.0 CB A:HIS84 5.0 0.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Mpy-Rnase J, An Archaeal Rnase J From Methanolobus Psychrophilus R15


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, An Archaeal Rnase J From Methanolobus Psychrophilus R15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:93.4 occ:1.00 NE2 A:HIS152 2.1 81.2 1.0 ND1 A:HIS84 2.4 1.0 1.0 NE2 A:HIS82 2.5 98.0 1.0 ZN A:ZN501 2.7 0.0 1.0 CE1 A:HIS152 3.0 79.8 1.0 CG A:ASP174 3.0 0.7 1.0 OD1 A:ASP174 3.0 0.3 1.0 CE1 A:HIS82 3.1 92.2 1.0 CD2 A:HIS152 3.2 76.0 1.0 OD2 A:ASP174 3.2 0.2 1.0 CE1 A:HIS84 3.3 0.1 1.0 CG A:HIS84 3.4 0.0 1.0 CB A:ASP174 3.6 0.0 1.0 CD2 A:HIS82 3.6 0.4 1.0 CB A:HIS84 3.7 0.8 1.0 O A:HOH601 3.7 45.4 1.0 OD1 A:ASP86 3.7 0.2 1.0 ND1 A:HIS152 4.1 73.6 1.0 CG A:HIS152 4.2 75.9 1.0 OD2 A:ASP86 4.2 0.8 1.0 ND1 A:HIS82 4.3 85.1 1.0 CG A:ASP86 4.4 0.0 1.0 NE2 A:HIS84 4.4 0.3 1.0 CD2 A:HIS84 4.5 0.2 1.0 NE2 A:HIS388 4.5 67.5 1.0 CG A:HIS82 4.6 95.0 1.0 OG A:SER153 4.6 93.8 1.0 NE2 A:HIS410 4.9 96.6 1.0 CA A:ASP174 5.0 90.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Mpy-Rnase J, An Archaeal Rnase J From Methanolobus Psychrophilus R15


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, An Archaeal Rnase J From Methanolobus Psychrophilus R15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:0.4 occ:1.00 OD1 B:ASP174 1.9 0.6 1.0 NE2 B:HIS152 2.2 78.2 1.0 ND1 B:HIS84 2.2 0.7 1.0 NE2 B:HIS82 2.6 96.1 1.0 CE1 B:HIS152 3.0 87.8 1.0 ZN B:ZN502 3.0 0.3 1.0 CG B:ASP174 3.0 0.2 1.0 CE1 B:HIS84 3.1 0.7 1.0 CE1 B:HIS82 3.2 84.2 1.0 CG B:HIS84 3.3 0.4 1.0 CD2 B:HIS152 3.3 88.9 1.0 O B:HOH601 3.3 51.2 1.0 CB B:HIS84 3.6 94.3 1.0 CD2 B:HIS82 3.7 0.5 1.0 CB B:ASP174 3.8 0.7 1.0 OD1 B:ASP86 3.8 0.6 1.0 OD2 B:ASP174 3.9 0.1 1.0 ND1 B:HIS152 4.2 88.3 1.0 NE2 B:HIS84 4.2 0.5 1.0 CD2 B:HIS84 4.3 0.9 1.0 CG B:HIS152 4.3 81.6 1.0 ND1 B:HIS82 4.4 82.2 1.0 NE2 B:HIS388 4.5 72.7 1.0 OD2 B:ASP86 4.5 1.0 1.0 CG B:ASP86 4.6 0.9 1.0 CG B:HIS82 4.7 0.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Mpy-Rnase J, An Archaeal Rnase J From Methanolobus Psychrophilus R15


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, An Archaeal Rnase J From Methanolobus Psychrophilus R15 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:0.3 occ:1.00 OD1 B:ASP174 2.0 0.6 1.0 OD2 B:ASP86 2.0 1.0 1.0 NE2 B:HIS410 2.5 0.0 1.0 CG B:ASP174 2.6 0.2 1.0 OD2 B:ASP174 2.6 0.1 1.0 CG B:ASP86 2.8 0.9 1.0 OD1 B:ASP86 2.9 0.6 1.0 ZN B:ZN501 3.0 0.4 1.0 O B:HOH601 3.1 51.2 1.0 NE2 B:HIS87 3.3 93.8 1.0 CE1 B:HIS410 3.3 0.4 1.0 CD2 B:HIS410 3.6 1.0 1.0 CD2 B:HIS87 3.6 83.8 1.0 CE1 B:HIS87 4.0 91.5 1.0 CB B:ASP174 4.0 0.7 1.0 CB B:ASP86 4.2 88.6 1.0 NE2 B:HIS388 4.3 72.7 1.0 CE1 B:HIS82 4.3 84.2 1.0 NE2 B:HIS82 4.3 96.1 1.0 OD1 B:ASN18 4.4 88.9 1.0 ND1 B:HIS410 4.5 0.4 1.0 CG B:HIS87 4.5 84.4 1.0 CG B:HIS410 4.6 0.3 1.0 NE2 B:HIS152 4.7 78.2 1.0 ND1 B:HIS87 4.7 83.1 1.0 ND1 B:HIS84 4.9 0.7 1.0 CE1 B:HIS152 4.9 87.8 1.0

X.Zheng, N.Feng, D.F.Li, J.Li, X.Z.Dong. Molecular Insights Into Catalysis and Processive Exonucleolytic Mechanisms of Prokaryotic Rnase J Revealing Striking Parallels with That of Eukaryotic XRN1 To Be Published.