Zinc in PDB 6llb: Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, in Complex with 6 Nt Rna

The structure of Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, in Complex with 6 Nt Rna, PDB code: 6llb was solved by D.F.Li, Y.J.Hou, L.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.60
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	168.726, 168.726, 166.427, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, in Complex with 6 Nt Rna (pdb code 6llb). 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, in Complex with 6 Nt Rna, PDB code: 6llb:
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, in Complex with 6 Nt 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, in Complex with 6 Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:58.3 occ:0.66 OD2 A:ASP174 1.9 73.4 1.0 OD2 A:ASP86 2.0 72.0 1.0 NE2 A:HIS410 2.3 73.4 1.0 CG A:ASP174 2.4 54.3 1.0 OD1 A:ASP174 2.5 53.8 1.0 CG A:ASP86 2.8 58.5 1.0 NE2 A:HIS87 2.8 52.2 1.0 OD1 A:ASP86 2.9 54.3 1.0 CD2 A:HIS87 3.1 57.1 1.0 OP2 C:A2 3.1 87.0 1.0 CE1 A:HIS410 3.2 71.8 1.0 ZN A:ZN502 3.2 59.3 0.7 CD2 A:HIS410 3.4 70.2 1.0 OP1 C:A2 3.8 98.7 1.0 CB A:ASP174 3.9 49.4 1.0 P C:A2 3.9 86.9 1.0 CE1 A:HIS87 4.0 53.7 1.0 ND2 A:ASN18 4.1 42.5 1.0 NE2 A:HIS82 4.2 54.2 1.0 CB A:ASP86 4.2 44.1 1.0 CE1 A:HIS82 4.3 51.7 1.0 ND1 A:HIS410 4.3 64.7 1.0 O5' C:A2 4.4 83.3 1.0 CG A:HIS87 4.4 57.4 1.0 CG A:HIS410 4.5 61.7 1.0 CE1 A:HIS388 4.6 48.4 1.0 ND1 A:HIS87 4.8 59.0 1.0 CA A:ASP174 4.9 57.3 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, in Complex with 6 Nt 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, in Complex with 6 Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:59.3 occ:0.72 OD2 A:ASP174 1.9 73.4 1.0 OP1 C:A2 2.2 98.7 1.0 NE2 A:HIS152 2.4 50.2 1.0 ND1 A:HIS84 2.5 56.1 1.0 NE2 A:HIS82 2.5 54.2 1.0 CG A:ASP174 3.0 54.3 1.0 ZN A:ZN501 3.2 58.3 0.7 CD2 A:HIS152 3.3 53.9 1.0 CE1 A:HIS82 3.4 51.7 1.0 CE1 A:HIS152 3.4 39.4 1.0 CD2 A:HIS82 3.4 55.7 1.0 CE1 A:HIS84 3.4 57.9 1.0 CG A:HIS84 3.4 56.5 1.0 CB A:ASP174 3.4 49.4 1.0 P C:A2 3.4 86.9 1.0 CB A:HIS84 3.7 47.5 1.0 OD1 A:ASP86 3.9 54.3 1.0 O5' C:A2 3.9 83.3 1.0 OP2 C:A2 4.0 87.0 1.0 OD1 A:ASP174 4.1 53.8 1.0 ND1 A:HIS82 4.4 56.2 1.0 CG A:HIS152 4.5 55.3 1.0 ND1 A:HIS152 4.5 45.2 1.0 CG A:HIS82 4.5 53.4 1.0 NE2 A:HIS84 4.5 60.6 1.0 CE1 A:HIS388 4.5 48.4 1.0 NE2 A:HIS87 4.5 52.2 1.0 CD2 A:HIS84 4.6 58.3 1.0 CD2 A:HIS87 4.6 57.1 1.0 C5' C:A2 4.6 81.2 1.0 OD2 A:ASP86 4.7 72.0 1.0 O3' C:A1 4.7 91.4 1.0 CG A:ASP86 4.7 58.5 1.0 CA A:ASP174 4.7 57.3 1.0 OG A:SER153 4.8 49.0 1.0 NE2 A:HIS388 5.0 53.6 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, in Complex with 6 Nt 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, in Complex with 6 Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:58.7 occ:0.68 OD2 B:ASP86 1.8 72.3 1.0 OD2 B:ASP174 1.9 77.2 1.0 NE2 B:HIS410 2.3 67.2 1.0 CG B:ASP174 2.5 52.3 1.0 OD1 B:ASP174 2.5 47.9 1.0 CG B:ASP86 2.7 59.7 1.0 NE2 B:HIS87 2.9 53.6 1.0 OD1 B:ASP86 3.0 57.1 1.0 CE1 B:HIS410 3.0 64.7 1.0 OP2 D:A2 3.0 89.7 1.0 CD2 B:HIS87 3.2 54.3 1.0 ZN B:ZN502 3.2 56.9 0.7 CD2 B:HIS410 3.5 64.4 1.0 OP1 D:A2 3.8 88.8 1.0 P D:A2 3.8 87.9 1.0 CB B:ASP174 3.9 48.4 1.0 ND2 B:ASN18 4.1 41.5 1.0 CB B:ASP86 4.1 47.4 1.0 CE1 B:HIS87 4.1 56.5 1.0 NE2 B:HIS82 4.2 62.1 1.0 ND1 B:HIS410 4.2 67.5 1.0 CE1 B:HIS82 4.4 50.1 1.0 O5' D:A2 4.4 86.1 1.0 CG B:HIS410 4.5 62.6 1.0 CG B:HIS87 4.5 54.1 1.0 CE1 B:HIS388 4.5 50.4 1.0 ND1 B:HIS87 4.9 54.7 1.0 CA B:ASP174 5.0 59.4 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, in Complex with 6 Nt 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, in Complex with 6 Nt Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:56.9 occ:0.70 OD2 B:ASP174 2.0 77.2 1.0 OP1 D:A2 2.3 88.8 1.0 NE2 B:HIS152 2.4 46.2 1.0 CD2 B:HIS84 2.4 52.1 1.0 NE2 B:HIS82 2.5 62.1 1.0 CG B:ASP174 3.0 52.3 1.0 ZN B:ZN501 3.2 58.7 0.7 CD2 B:HIS152 3.3 49.9 1.0 CG B:HIS84 3.3 50.7 1.0 CD2 B:HIS82 3.4 54.6 1.0 CE1 B:HIS82 3.4 50.1 1.0 CE1 B:HIS152 3.4 43.0 1.0 CB B:ASP174 3.4 48.4 1.0 P D:A2 3.5 87.9 1.0 NE2 B:HIS84 3.5 52.6 1.0 CB B:HIS84 3.7 50.5 1.0 OD1 B:ASP86 3.8 57.1 1.0 OP2 D:A2 3.9 89.7 1.0 O5' D:A2 4.0 86.1 1.0 OD1 B:ASP174 4.1 47.9 1.0 ND1 B:HIS82 4.4 58.6 1.0 CG B:HIS152 4.4 47.1 1.0 CG B:HIS82 4.4 51.9 1.0 ND1 B:HIS152 4.5 45.9 1.0 ND1 B:HIS84 4.5 56.0 1.0 OD2 B:ASP86 4.5 72.3 1.0 CE1 B:HIS84 4.6 56.9 1.0 CG B:ASP86 4.6 59.7 1.0 CE1 B:HIS388 4.6 50.4 1.0 NE2 B:HIS87 4.7 53.6 1.0 CD2 B:HIS87 4.7 54.3 1.0 O3' D:A1 4.7 87.7 1.0 C5' D:A2 4.7 84.2 1.0 CA B:ASP174 4.8 59.4 1.0 OG B:SER153 4.9 51.0 1.0

D.F.Li, Y.J.Hou, L.Guo. Crystal Structure of Mpy-Rnase J (Mutant S247A), An Archaeal Rnase J From Methanolobus Psychrophilus R15, in Complex with 6 Nt Rna To Be Published.