Zinc in PDB 4gcw: Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr)

All present enzymatic activity of Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr):
3.1.26.11;

The structure of Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr), PDB code: 4gcw was solved by O.Pellegrini, I.Li De La Sierra-Gallay, J.Piton, L.Gilet, C.Condon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.30 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.080, 42.550, 110.890, 90.00, 127.18, 90.00
R / Rfree (%)	22.7 / 25.6

The binding sites of Zinc atom in the Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr) (pdb code 4gcw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr), PDB code: 4gcw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr)


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 Rnase Z in Complex with Precursor Trna(Thr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:70.5 occ:1.00 NE2 A:HIS68 2.0 54.1 1.0 OD2 A:ASP211 2.0 71.8 1.0 OD2 A:ASP67 2.3 64.6 1.0 NE2 A:HIS269 2.4 61.5 1.0 CG A:ASP211 2.8 66.9 1.0 CD2 A:HIS68 3.0 54.3 1.0 OD1 A:ASP211 3.0 67.8 1.0 CE1 A:HIS68 3.1 53.8 1.0 CE1 A:HIS269 3.2 61.1 1.0 CD2 A:HIS269 3.2 61.7 1.0 CG A:ASP67 3.3 58.4 1.0 ZN A:ZN402 3.4 68.8 1.0 OD1 A:ASP67 3.5 58.5 1.0 NE2 A:HIS63 4.0 49.0 1.0 CG A:HIS68 4.1 52.4 1.0 CE1 A:HIS63 4.1 48.6 1.0 ND1 A:HIS68 4.2 54.3 1.0 OG1 A:THR20 4.2 59.2 1.0 CB A:ASP211 4.2 58.2 1.0 ND1 A:HIS269 4.3 61.7 1.0 CG A:HIS269 4.3 60.1 1.0 CB A:ASP67 4.6 49.9 1.0 N A:GLY11 4.7 51.0 1.0 CE1 A:HIS247 4.8 75.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Rnase Z in Complex with Precursor Trna(Thr)


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 Rnase Z in Complex with Precursor Trna(Thr) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:68.8 occ:1.00 NE2 A:HIS63 2.1 49.0 1.0 ND1 A:HIS65 2.4 50.9 1.0 OD2 A:ASP211 2.5 71.8 1.0 NE2 A:HIS140 2.5 63.5 1.0 CD2 A:HIS63 2.9 49.0 1.0 CG A:HIS65 3.1 48.9 1.0 CE1 A:HIS65 3.1 50.3 1.0 CE1 A:HIS63 3.2 48.6 1.0 CE1 A:HIS140 3.3 63.2 1.0 ZN A:ZN401 3.4 70.5 1.0 CG A:ASP211 3.4 66.9 1.0 CB A:HIS65 3.5 45.0 1.0 CD2 A:HIS140 3.6 63.8 1.0 CB A:ASP211 3.7 58.2 1.0 CD2 A:HIS65 4.0 50.7 1.0 NE2 A:HIS65 4.0 50.5 1.0 NE2 A:HIS68 4.1 54.1 1.0 CG A:HIS63 4.1 46.7 1.0 ND1 A:HIS63 4.3 48.9 1.0 CD2 A:HIS68 4.3 54.3 1.0 OD1 A:ASP211 4.5 67.8 1.0 OD1 A:ASP67 4.5 58.5 1.0 ND1 A:HIS140 4.5 63.8 1.0 CG A:HIS140 4.6 62.2 1.0 CE1 A:HIS247 4.7 75.1 1.0 OD2 A:ASP67 4.9 64.6 1.0 CA A:HIS65 5.0 44.1 1.0

O.Pellegrini, I.Li De La Sierra-Gallay, J.Piton, L.Gilet, C.Condon. Activation of Trna Maturation By Downstream Uracil Residues in B. Subtilis Structure V. 20 1769 2012.
ISSN: ISSN 0969-2126
PubMed: 22940585
DOI: 10.1016/J.STR.2012.08.002