Zinc in PDB 5mtz: Crystal Structure of A Long Form Rnase Z From Yeast

All present enzymatic activity of Crystal Structure of A Long Form Rnase Z From Yeast:
3.1.26.11;

The structure of Crystal Structure of A Long Form Rnase Z From Yeast, PDB code: 5mtz was solved by I.Li De La Sierra-Gallay, M.Miao, H.Van Tilbeurgh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.61 / 2.99
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	136.000, 136.000, 115.810, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 26.2

The binding sites of Zinc atom in the Crystal Structure of A Long Form Rnase Z From Yeast (pdb code 5mtz). 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 A Long Form Rnase Z From Yeast, PDB code: 5mtz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Long Form Rnase Z From Yeast


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 A Long Form Rnase Z From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:83.4 occ:1.00 O1 A:PO4903 2.0 89.4 1.0 ND1 A:HIS542 2.1 67.4 1.0 OD2 A:ASP699 2.1 87.7 1.0 NE2 A:HIS540 2.2 71.7 1.0 NE2 A:HIS670 2.3 94.9 1.0 CE1 A:HIS542 3.0 66.9 1.0 CG A:HIS542 3.1 68.1 1.0 CG A:ASP699 3.1 82.8 1.0 P A:PO4903 3.2 92.0 1.0 CE1 A:HIS540 3.2 72.7 1.0 CE1 A:HIS670 3.2 97.2 1.0 CD2 A:HIS540 3.2 69.3 1.0 CD2 A:HIS670 3.3 91.2 1.0 CB A:HIS542 3.4 66.4 1.0 CB A:ASP699 3.4 91.1 1.0 ZN A:ZN902 3.5 73.2 1.0 O4 A:PO4903 3.6 0.5 1.0 O2 A:PO4903 3.7 77.7 1.0 NE2 A:HIS545 4.1 73.5 1.0 NE2 A:HIS542 4.1 68.0 1.0 CD2 A:HIS542 4.2 64.7 1.0 OD1 A:ASP699 4.2 73.2 1.0 CD2 A:HIS545 4.3 73.2 1.0 OD1 A:ASP544 4.3 86.3 1.0 ND1 A:HIS540 4.3 64.3 1.0 ND1 A:HIS670 4.4 93.9 1.0 CG A:HIS540 4.4 65.4 1.0 CG A:HIS670 4.4 87.9 1.0 O3 A:PO4903 4.4 96.0 1.0 CE1 A:HIS737 4.5 79.0 1.0 OD2 A:ASP544 4.7 84.1 1.0 CA A:HIS542 4.9 62.5 1.0 NE2 A:HIS737 4.9 80.1 1.0 CA A:ASP699 5.0 91.4 1.0 CG A:ASP544 5.0 75.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Long Form Rnase Z From Yeast


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 A Long Form Rnase Z From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:73.2 occ:1.00 O2 A:PO4903 2.0 77.7 1.0 NE2 A:HIS759 2.0 64.1 1.0 OD2 A:ASP544 2.1 84.1 1.0 OD2 A:ASP699 2.1 87.7 1.0 NE2 A:HIS545 2.2 73.5 1.0 CG A:ASP699 2.8 82.8 1.0 CE1 A:HIS759 3.0 65.9 1.0 OD1 A:ASP699 3.0 73.2 1.0 CD2 A:HIS759 3.1 63.6 1.0 P A:PO4903 3.1 92.0 1.0 CG A:ASP544 3.1 75.0 1.0 CD2 A:HIS545 3.2 73.2 1.0 CE1 A:HIS545 3.3 75.3 1.0 OD1 A:ASP544 3.5 86.3 1.0 ZN A:ZN901 3.5 83.4 1.0 O4 A:PO4903 3.5 0.5 1.0 O1 A:PO4903 3.5 89.4 1.0 ND1 A:HIS759 4.1 62.9 1.0 CG A:HIS759 4.2 60.4 1.0 CE1 A:HIS737 4.2 79.0 1.0 CB A:ASP699 4.3 91.1 1.0 CG A:HIS545 4.3 68.9 1.0 ND1 A:HIS545 4.3 72.2 1.0 O3 A:PO4903 4.4 96.0 1.0 CB A:ASP544 4.5 67.7 1.0 N A:ALA476 4.5 69.9 1.0 CE1 A:HIS540 4.6 72.7 1.0 NE2 A:HIS540 4.6 71.7 1.0 CG2 A:VAL485 4.8 75.8 1.0 OG A:SER475 4.9 82.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Long Form Rnase Z From Yeast


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 A Long Form Rnase Z From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:73.5 occ:1.00 O1 B:PO4903 2.0 78.9 1.0 OD2 B:ASP699 2.1 82.7 1.0 ND1 B:HIS542 2.2 61.6 1.0 NE2 B:HIS540 2.2 61.0 1.0 NE2 B:HIS670 2.3 70.5 1.0 CE1 B:HIS542 3.1 64.6 1.0 CG B:HIS542 3.1 60.5 1.0 CG B:ASP699 3.1 74.8 1.0 CD2 B:HIS540 3.2 58.9 1.0 P B:PO4903 3.2 85.2 1.0 CE1 B:HIS540 3.2 58.8 1.0 CE1 B:HIS670 3.3 70.3 1.0 CD2 B:HIS670 3.3 69.3 1.0 CB B:ASP699 3.5 73.0 1.0 CB B:HIS542 3.5 60.5 1.0 O2 B:PO4903 3.5 75.0 1.0 ZN B:ZN902 3.6 68.8 1.0 O4 B:PO4903 3.7 86.2 1.0 NE2 B:HIS545 4.1 54.9 1.0 NE2 B:HIS542 4.2 63.2 1.0 CD2 B:HIS542 4.2 60.0 1.0 OD1 B:ASP544 4.2 70.8 1.0 ND1 B:HIS540 4.3 58.3 1.0 CG B:HIS540 4.3 55.2 1.0 OD1 B:ASP699 4.3 69.3 1.0 ND1 B:HIS670 4.4 66.1 1.0 CE1 B:HIS737 4.4 61.4 1.0 CG B:HIS670 4.4 70.8 1.0 O3 B:PO4903 4.4 82.5 1.0 CD2 B:HIS545 4.4 52.6 1.0 OD2 B:ASP544 4.8 86.6 1.0 NE2 B:HIS737 4.9 65.0 1.0 CA B:HIS542 4.9 56.6 1.0 CG B:ASP544 4.9 73.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Long Form Rnase Z From Yeast


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 A Long Form Rnase Z From Yeast within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:68.8 occ:1.00 O2 B:PO4903 2.0 75.0 1.0 NE2 B:HIS759 2.0 62.2 1.0 OD2 B:ASP544 2.0 86.6 1.0 OD2 B:ASP699 2.1 82.7 1.0 NE2 B:HIS545 2.2 54.9 1.0 CG B:ASP699 2.8 74.8 1.0 OD1 B:ASP699 2.9 69.3 1.0 CE1 B:HIS759 2.9 63.0 1.0 CG B:ASP544 3.1 73.2 1.0 CD2 B:HIS759 3.1 65.0 1.0 CE1 B:HIS545 3.1 57.1 1.0 CD2 B:HIS545 3.1 52.6 1.0 P B:PO4903 3.3 85.2 1.0 OD1 B:ASP544 3.4 70.8 1.0 ZN B:ZN901 3.6 73.5 1.0 O1 B:PO4903 3.8 78.9 1.0 O4 B:PO4903 3.9 86.2 1.0 ND1 B:HIS759 4.1 61.0 1.0 CG B:HIS759 4.2 65.0 1.0 ND1 B:HIS545 4.2 55.4 1.0 CG B:HIS545 4.3 50.5 1.0 CE1 B:HIS737 4.3 61.4 1.0 CB B:ASP699 4.3 73.0 1.0 CE1 B:HIS540 4.4 58.8 1.0 CB B:ASP544 4.4 64.3 1.0 NE2 B:HIS540 4.5 61.0 1.0 OG B:SER475 4.5 73.4 1.0 O3 B:PO4903 4.5 82.5 1.0 N B:ALA476 4.7 69.5 1.0 NE2 B:HIS737 4.9 65.0 1.0 CA B:SER475 5.0 74.8 1.0

M.Ma, I.Li De La Sierra-Gallay, N.Lazar, O.Pellegrini, D.Durand, A.Marchfelder, C.Condon, H.Van Tilbeurgh. The Crystal Structure of TRZ1, the Long Form Rnase Z From Yeast. Nucleic Acids Res. V. 45 6209 2017.
ISSN: ESSN 1362-4962
PubMed: 28379452
DOI: 10.1093/NAR/GKX216