Zinc in PDB 2hbm: Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump

The structure of Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump, PDB code: 2hbm was solved by S.F.Midtgaard, J.Assenholt, A.T.Jonstrup, L.B.Van, T.H.Jensen, D.E.Brodersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 2.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.577, 110.577, 79.330, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 28.6

The structure of Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Zinc atom in the Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump (pdb code 2hbm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump, PDB code: 2hbm:

Zinc binding site 1 out of 1 in the Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Yeast Nuclear Exosome Component, RRP6P, Reveals An Interplay Between the Active Site and the Hrdc Domain; Protein in Complex with Mn, Zn, and Ump within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:63.9 occ:1.00 OD2 A:ASP365 2.0 43.0 1.0 OE2 A:GLU240 2.1 33.7 1.0 OP2 A:U3001 2.2 88.1 1.0 O A:HOH3003 2.2 37.5 1.0 OD2 A:ASP238 2.5 42.2 1.0 CG A:ASP365 3.1 40.9 1.0 CD A:GLU240 3.1 35.5 1.0 OE1 A:GLU240 3.4 32.6 1.0 CG A:ASP238 3.5 37.4 1.0 O A:HOH3002 3.5 35.2 1.0 P A:U3001 3.6 86.8 1.0 CB A:ASP365 3.9 37.0 1.0 OD1 A:ASP238 3.9 37.5 1.0 OE1 A:GLN255 4.0 37.2 1.0 OD1 A:ASP365 4.0 40.2 1.0 O A:LEU239 4.0 34.5 1.0 O5' A:U3001 4.1 86.7 1.0 C5' A:U3001 4.2 87.6 1.0 MN A:MN1002 4.2 51.3 1.0 O A:HOH3004 4.2 57.2 1.0 CG A:GLU240 4.5 36.5 1.0 OP3 A:U3001 4.5 86.6 1.0 OP1 A:U3001 4.5 87.9 1.0 NE2 A:GLN345 4.5 95.7 1.0 CB A:ASP238 4.8 35.4 1.0 C A:LEU239 4.9 36.3 1.0

S.F.Midtgaard, J.Assenholt, A.T.Jonstrup, L.B.Van, T.H.Jensen, D.E.Brodersen. Structure of the Nuclear Exosome Component RRP6P Reveals An Interplay Between the Active Site and the Hrdc Domain. Proc.Natl.Acad.Sci.Usa V. 103 11898 2006.
ISSN: ISSN 0027-8424
PubMed: 16882719
DOI: 10.1073/PNAS.0604731103