Zinc in PDB 2xev: Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf

The structure of Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf, PDB code: 2xev was solved by A.M.Krachler, A.Sharma, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.75 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.360, 37.120, 90.610, 90.00, 117.14, 90.00
R / Rfree (%)	20.407 / 22.813

The structure of Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf (pdb code 2xev). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf, PDB code: 2xev:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1123 b:16.5 occ:0.80 OE1 A:GLU88 1.9 19.6 1.0 OE2 A:GLU58 1.9 21.4 1.0 OE1 A:GLU93 2.2 29.6 1.0 CD A:GLU58 2.8 18.7 1.0 CD A:GLU88 2.9 21.9 1.0 OE1 A:GLU58 3.2 19.6 1.0 OE2 A:GLU88 3.3 20.6 1.0 CD A:GLU93 3.4 35.9 1.0 O A:HOH2033 3.9 22.8 1.0 CG A:GLN85 3.9 21.3 1.0 OE2 A:GLU93 4.0 38.8 1.0 CG A:GLU58 4.2 16.3 1.0 CG A:GLU88 4.3 22.8 1.0 CG A:LYS90 4.3 30.9 1.0 NE2 A:GLN85 4.4 26.6 1.0 NH2 A:ARG62 4.6 32.0 1.0 CB A:GLN85 4.6 19.2 1.0 CG A:GLU93 4.6 32.6 1.0 CD A:GLN85 4.7 25.1 1.0 CB A:GLU88 4.7 23.5 1.0 CA A:GLN85 4.7 19.0 1.0 CB A:LYS90 4.8 29.3 1.0 CB A:GLU58 4.9 13.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1125 b:17.6 occ:0.50 O B:HOH2036 2.8 35.0 1.0 OE1 A:GLN22 3.2 25.5 1.0 C B:ASN53 3.2 11.7 1.0 CA B:ASN53 3.3 12.1 1.0 N B:GLN55 3.3 11.9 1.0 N B:LEU56 3.3 11.4 1.0 OD1 B:ASN53 3.5 16.1 1.0 CB B:ASN53 3.5 12.0 1.0 N B:PHE54 3.5 11.7 1.0 O B:ASN53 3.6 12.6 1.0 CG B:LEU56 3.6 9.1 1.0 CB B:GLN55 3.6 13.1 1.0 CA B:GLN55 3.8 11.9 1.0 CG B:ASN53 3.9 12.5 1.0 CB B:LEU56 4.1 9.8 1.0 C B:GLN55 4.1 11.5 1.0 CD A:GLN22 4.1 22.4 1.0 C B:PHE54 4.2 11.5 1.0 CG B:GLN55 4.3 14.5 1.0 OE1 B:GLN55 4.3 21.6 1.0 CD1 B:LEU56 4.3 10.8 1.0 CA B:LEU56 4.3 10.1 1.0 CG A:GLN22 4.4 19.8 1.0 CA B:PHE54 4.4 11.1 1.0 CD B:GLN55 4.7 19.0 1.0 N B:ASN53 4.7 13.1 1.0 CD2 B:LEU56 4.7 11.8 1.0 CB A:GLN22 4.9 14.7 1.0 O B:ARG52 4.9 14.5 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1126 b:15.9 occ:0.70 OE2 B:GLU88 1.9 24.9 1.0 OE1 B:GLU58 2.1 20.6 1.0 OD1 A:ASP19 2.1 17.1 1.0 OD2 A:ASP19 2.5 17.5 1.0 CG A:ASP19 2.6 17.2 1.0 CD B:GLU88 2.9 22.8 1.0 ZN B:ZN1127 3.0 16.7 0.7 OE1 B:GLU88 3.2 22.0 1.0 CD B:GLU58 3.2 17.4 1.0 OE2 B:GLU58 3.6 17.5 1.0 NZ B:LYS90 3.8 28.9 1.0 O B:HOH2037 4.0 13.8 1.0 CB A:ASP19 4.1 14.2 1.0 CG B:GLU88 4.3 21.5 1.0 CG B:GLN55 4.3 14.5 1.0 CG B:GLU58 4.5 14.1 1.0 CE B:LYS90 4.6 30.0 1.0 O A:HOH2010 4.6 16.9 1.0 NE2 B:GLN55 4.7 18.3 1.0 CB B:GLN55 4.7 13.1 1.0 CA B:GLN55 4.8 11.9 1.0 CD B:LYS90 4.8 27.7 1.0 CA A:ASP19 4.9 14.1 1.0 CB B:GLU58 4.9 12.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


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 the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1127 b:16.7 occ:0.70 OE1 B:GLU88 1.9 22.0 1.0 OE2 B:GLU58 2.0 17.5 1.0 OE1 B:GLU93 2.1 23.9 1.0 CD B:GLU58 2.8 17.4 1.0 CD B:GLU93 2.9 25.8 1.0 CD B:GLU88 2.9 22.8 1.0 OE2 B:GLU93 3.0 28.9 1.0 ZN B:ZN1126 3.0 15.9 0.7 OE1 B:GLU58 3.0 20.6 1.0 OE2 B:GLU88 3.2 24.9 1.0 CD B:LYS90 3.6 27.7 1.0 CG B:GLN85 3.7 17.2 1.0 NZ B:LYS90 4.1 28.9 1.0 NE2 B:GLN85 4.1 20.0 1.0 CG B:GLU58 4.2 14.1 1.0 CB B:GLN85 4.3 15.0 1.0 CG B:GLU88 4.3 21.5 1.0 CD B:GLN85 4.3 19.5 1.0 CG B:GLU93 4.3 24.5 1.0 CE B:LYS90 4.3 30.0 1.0 CG B:LYS90 4.5 24.1 1.0 CA B:GLN85 4.6 15.5 1.0 OD2 A:ASP19 4.7 17.5 1.0 CB B:LYS90 4.7 23.4 1.0 NH2 B:ARG62 4.7 30.7 1.0 CB B:GLU88 4.8 20.3 1.0 CB B:GLU93 5.0 22.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1126 b:12.7 occ:1.00 OE1 C:GLU88 1.9 18.1 1.0 OE1 C:GLU58 2.0 9.2 1.0 OD2 B:ASP19 2.0 8.5 0.5 OD2 B:ASP19 2.0 7.0 0.5 CL C:CL1125 2.2 15.0 1.0 CD C:GLU58 2.8 8.1 1.0 CD C:GLU88 2.8 18.3 1.0 CG B:ASP19 2.9 9.9 0.5 CG B:ASP19 2.9 11.1 0.5 OD1 B:ASP19 3.1 10.1 0.5 OE2 C:GLU58 3.1 11.1 1.0 OE2 C:GLU88 3.1 17.9 1.0 OD1 B:ASP19 3.1 12.9 0.5 NZ B:LYS16 3.7 18.3 1.0 NZ C:LYS90 3.9 17.8 1.0 O C:HOH2032 4.1 10.4 1.0 CG C:GLN55 4.2 13.3 1.0 CG C:GLU88 4.2 20.7 1.0 CG C:GLU58 4.2 10.0 1.0 CG C:GLN85 4.2 12.4 1.0 CB B:ASP19 4.3 10.2 0.5 CB B:ASP19 4.3 10.7 0.5 O B:HOH2015 4.4 30.0 1.0 CB C:GLU58 4.5 10.3 1.0 CG C:LYS90 4.7 20.3 1.0 CE B:LYS16 4.7 19.4 1.0 CA C:GLN55 4.8 10.5 1.0 NE2 C:GLN85 4.9 15.4 1.0 CB C:GLN55 4.9 11.4 1.0 CB C:GLU88 4.9 18.6 1.0 CA C:GLN85 4.9 11.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Tpr Domain of Xanthomonas Campestris Ybgf within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1127 b:18.9 occ:1.00 OD1 C:ASP19 2.2 17.5 1.0 OD2 C:ASP19 2.3 17.5 1.0 CG C:ASP19 2.5 15.3 1.0 CB C:ASP19 4.0 14.4 1.0 O C:HOH2011 4.2 28.3 1.0 O C:HOH2014 4.4 19.6 1.0 O C:HOH2013 4.7 22.9 1.0 CA C:ASP19 4.9 14.3 1.0

A.M.Krachler, A.Sharma, A.Cauldwell, G.Papadakos, C.Kleanthous. Tola Modulates the Oligomeric Status of Ybgf in the Bacterial Periplasm. J.Mol.Biol. V. 403 270 2010.
ISSN: ISSN 0022-2836
PubMed: 20816983
DOI: 10.1016/J.JMB.2010.08.050