Zinc in PDB 1m68: Ycdx Protein, Trinuclear Zinc Site

The structure of Ycdx Protein, Trinuclear Zinc Site, PDB code: 1m68 was solved by A.Teplyakov, G.Obmolova, P.P.Khil, R.D.Camerini-Otero, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.30
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.350, 77.350, 80.050, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 22.5

The binding sites of Zinc atom in the Ycdx Protein, Trinuclear Zinc Site (pdb code 1m68). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ycdx Protein, Trinuclear Zinc Site, PDB code: 1m68:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ycdx Protein, Trinuclear Zinc Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ycdx Protein, Trinuclear Zinc Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:27.8 occ:1.00 NE2 A:HIS15 1.9 40.9 1.0 NE2 A:HIS40 2.1 37.2 1.0 NE2 A:HIS194 2.1 36.2 1.0 O A:HOH322 2.5 27.4 1.0 CE1 A:HIS15 2.8 24.3 1.0 CE1 A:HIS40 2.9 16.0 1.0 CD2 A:HIS194 3.0 19.9 1.0 CD2 A:HIS15 3.1 23.8 1.0 CE1 A:HIS194 3.1 33.5 1.0 CD2 A:HIS40 3.1 22.5 1.0 ND1 A:HIS15 3.9 22.3 1.0 O A:HOH441 4.1 46.3 1.0 ND1 A:HIS40 4.1 26.8 1.0 CG A:HIS15 4.1 36.9 1.0 ND1 A:HIS194 4.2 20.9 1.0 CG A:HIS194 4.2 35.7 1.0 CG A:HIS40 4.2 22.2 1.0 CE1 A:HIS9 4.3 19.8 1.0 NE2 A:HIS9 4.3 24.7 1.0 ND1 A:HIS9 4.4 27.1 1.0 CD2 A:HIS9 4.5 25.8 1.0 CG A:HIS9 4.6 37.7 1.0 ZN A:ZN302 4.9 27.5 1.0

Zinc binding site 2 out of 3 in the Ycdx Protein, Trinuclear Zinc Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ycdx Protein, Trinuclear Zinc Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:27.5 occ:1.00 NE2 A:HIS7 2.0 28.0 1.0 O A:HOH441 2.1 46.3 1.0 NE2 A:HIS9 2.1 24.7 1.0 OE1 A:GLU73 2.1 22.0 1.0 OD1 A:ASP192 2.3 32.5 1.0 CE1 A:HIS7 2.9 22.6 1.0 CE1 A:HIS9 2.9 19.8 1.0 CD A:GLU73 3.0 25.2 1.0 CD2 A:HIS7 3.1 22.5 1.0 CG A:ASP192 3.1 26.0 1.0 CD2 A:HIS9 3.2 25.8 1.0 OD2 A:ASP192 3.3 27.4 1.0 OE2 A:GLU73 3.3 25.6 1.0 ZN A:ZN303 3.4 31.6 1.0 CE1 A:HIS40 4.0 16.0 1.0 ND1 A:HIS7 4.1 27.7 1.0 ND1 A:HIS9 4.1 27.1 1.0 CG A:HIS7 4.2 28.5 1.0 CE1 A:HIS194 4.2 33.5 1.0 CG A:GLU73 4.3 35.1 1.0 CG A:HIS9 4.3 37.7 1.0 CB A:ASP192 4.4 28.1 1.0 NE2 A:HIS40 4.5 37.2 1.0 CB A:GLU73 4.6 20.5 1.0 NE2 A:HIS194 4.7 36.2 1.0 O A:HOH322 4.7 27.4 1.0 ND1 A:HIS40 4.7 26.8 1.0 CA A:ASP192 4.7 24.0 1.0 NE2 A:HIS101 4.8 44.6 1.0 ZN A:ZN301 4.9 27.8 1.0 NE2 A:HIS131 4.9 31.8 1.0

Zinc binding site 3 out of 3 in the Ycdx Protein, Trinuclear Zinc Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ycdx Protein, Trinuclear Zinc Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:31.6 occ:1.00 NE2 A:HIS101 2.0 44.6 1.0 OE2 A:GLU73 2.1 25.6 1.0 O A:HOH441 2.2 46.3 1.0 NE2 A:HIS131 2.2 31.8 1.0 CE1 A:HIS101 2.6 39.8 1.0 CD A:GLU73 2.9 25.2 1.0 OE1 A:GLU73 3.0 22.0 1.0 CE1 A:HIS131 3.2 28.6 1.0 CD2 A:HIS131 3.2 34.5 1.0 CD2 A:HIS101 3.3 41.1 1.0 ZN A:ZN302 3.4 27.5 1.0 ND1 A:HIS101 3.8 35.9 1.0 OD2 A:ASP192 4.2 27.4 1.0 CE1 A:HIS40 4.2 16.0 1.0 OG A:SER130 4.2 27.0 1.0 CG A:HIS101 4.2 45.5 1.0 CE1 A:HIS7 4.3 22.6 1.0 CG A:GLU73 4.3 35.1 1.0 ND1 A:HIS131 4.3 40.5 1.0 CG A:HIS131 4.4 40.5 1.0 O A:HOH322 4.4 27.4 1.0 NE2 A:HIS7 4.4 28.0 1.0 CB A:SER130 4.7 31.3 1.0 ND1 A:HIS40 4.7 26.8 1.0 OD1 A:ASP192 4.9 32.5 1.0 O A:HOH311 4.9 23.0 1.0 CG A:ASP192 4.9 26.0 1.0

A.Teplyakov, G.Obmolova, P.P.Khil, A.J.Howard, R.D.Camerini-Otero, G.L.Gilliland. Crystal Structure of the Escherichia Coli Ycdx Protein Reveals A Trinuclear Zinc Active Site Proteins: V. 51 315 2003STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 12661000
DOI: 10.1002/PROT.10352