Zinc in PDB 2c20: Crystal Structure of Udp-Glucose 4-Epimerase

All present enzymatic activity of Crystal Structure of Udp-Glucose 4-Epimerase:
5.1.3.2;

The structure of Crystal Structure of Udp-Glucose 4-Epimerase, PDB code: 2c20 was solved by A.A.Lebedev, O.V.Moroz, E.V.Blagova, V.M.Levdikov, M.J.Fogg, J.A.Brannigan, A.J.Wilkinson, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.02 / 2.7
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	136.165, 136.165, 248.646, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 27.6

The binding sites of Zinc atom in the Crystal Structure of Udp-Glucose 4-Epimerase (pdb code 2c20). 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 Udp-Glucose 4-Epimerase, PDB code: 2c20:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Udp-Glucose 4-Epimerase


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 Udp-Glucose 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:13.5 occ:1.00 ND1 A:HIS185 1.8 8.4 1.0 OE2 A:GLU183 2.0 13.1 1.0 ND1 A:HIS190 2.0 14.7 1.0 OE2 A:GLU188 2.2 11.5 1.0 CE1 A:HIS190 2.7 12.8 1.0 OE1 A:GLU188 2.8 11.7 1.0 CE1 A:HIS185 2.8 8.0 1.0 CD A:GLU188 2.9 11.5 1.0 CG A:HIS185 2.9 10.3 1.0 CD A:GLU183 3.0 11.7 1.0 CG A:HIS190 3.1 13.6 1.0 CB A:HIS185 3.2 12.7 1.0 CG A:GLU183 3.5 12.5 1.0 CB A:HIS190 3.7 11.7 1.0 NE2 A:HIS190 3.9 11.8 1.0 NE2 A:HIS185 3.9 7.2 1.0 CD2 A:HIS185 4.0 8.0 1.0 OE1 A:GLU183 4.0 6.2 1.0 O A:HOH2041 4.0 12.8 1.0 CD2 A:HIS190 4.1 13.0 1.0 CG A:GLU188 4.3 11.3 1.0 N A:HIS190 4.4 11.6 1.0 N A:THR189 4.5 11.5 1.0 CG A:PRO193 4.6 8.8 1.0 CA A:HIS185 4.6 13.5 1.0 CA A:HIS190 4.7 11.9 1.0 OG1 A:THR189 4.8 11.1 1.0 CA A:GLU188 4.9 11.7 1.0 N A:HIS185 4.9 15.1 1.0 CB A:GLU183 4.9 14.1 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Udp-Glucose 4-Epimerase


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 Udp-Glucose 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:15.4 occ:1.00 ND1 B:HIS190 1.9 18.8 1.0 OE2 B:GLU183 2.0 14.4 1.0 ND1 B:HIS185 2.0 5.0 1.0 OE2 B:GLU188 2.1 12.2 1.0 CE1 B:HIS190 2.6 15.2 1.0 CD B:GLU188 2.8 11.2 1.0 OE1 B:GLU188 2.8 8.9 1.0 CE1 B:HIS185 3.0 5.1 1.0 CD B:GLU183 3.0 13.0 1.0 CG B:HIS185 3.0 9.3 1.0 CG B:HIS190 3.1 17.7 1.0 CB B:HIS185 3.4 12.2 1.0 CG B:GLU183 3.4 11.1 1.0 CB B:HIS190 3.7 15.3 1.0 NE2 B:HIS190 3.8 14.2 1.0 CD2 B:HIS190 4.1 16.0 1.0 NE2 B:HIS185 4.1 2.5 1.0 OE1 B:GLU183 4.1 8.1 1.0 CD2 B:HIS185 4.1 6.0 1.0 N B:HIS190 4.2 14.2 1.0 CG B:GLU188 4.2 12.4 1.0 OG1 B:THR189 4.3 14.7 1.0 N B:THR189 4.3 14.5 1.0 O B:HOH2041 4.4 13.2 1.0 CA B:HIS190 4.6 15.1 1.0 CA B:HIS185 4.7 12.5 1.0 N B:HIS185 4.7 13.3 1.0 CG B:PRO193 4.8 12.2 1.0 CA B:GLU188 4.9 13.4 1.0 CB B:GLU183 4.9 12.8 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Udp-Glucose 4-Epimerase


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 Udp-Glucose 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:12.1 occ:1.00 ND1 C:HIS190 1.9 10.5 1.0 OE2 C:GLU188 1.9 8.2 1.0 OE2 C:GLU183 2.0 11.5 1.0 ND1 C:HIS185 2.0 2.0 1.0 CE1 C:HIS190 2.7 11.6 1.0 CD C:GLU188 2.8 8.5 1.0 OE1 C:GLU188 2.9 9.5 1.0 CE1 C:HIS185 3.0 2.0 1.0 CG C:HIS190 3.0 10.6 1.0 CD C:GLU183 3.0 6.8 1.0 CG C:HIS185 3.0 2.1 1.0 CB C:HIS185 3.4 5.7 1.0 CG C:GLU183 3.4 4.8 1.0 CB C:HIS190 3.5 8.4 1.0 O C:HOH2031 3.8 8.1 1.0 NE2 C:HIS190 3.9 10.6 1.0 CD2 C:HIS190 4.0 10.5 1.0 N C:HIS190 4.0 8.2 1.0 NE2 C:HIS185 4.1 2.0 1.0 OE1 C:GLU183 4.1 4.8 1.0 CD2 C:HIS185 4.1 2.0 1.0 CG C:GLU188 4.2 6.8 1.0 CA C:HIS190 4.4 8.7 1.0 N C:THR189 4.5 7.7 1.0 CG C:PRO193 4.6 7.5 1.0 CA C:HIS185 4.8 6.0 1.0 N C:HIS185 4.9 6.8 1.0 OG1 C:THR189 4.9 6.6 1.0 CB C:GLU183 4.9 6.1 1.0 CA C:GLU188 5.0 6.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Udp-Glucose 4-Epimerase


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 Udp-Glucose 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:15.5 occ:1.00 OE2 D:GLU188 1.9 5.3 1.0 ND1 D:HIS185 1.9 8.8 1.0 OE2 D:GLU183 1.9 6.6 1.0 ND1 D:HIS190 2.0 13.8 1.0 CD D:GLU188 2.7 4.2 1.0 CE1 D:HIS185 2.8 10.3 1.0 OE1 D:GLU188 2.8 2.5 1.0 CE1 D:HIS190 2.9 12.2 1.0 CG D:HIS185 3.0 9.2 1.0 CG D:HIS190 3.1 13.6 1.0 CD D:GLU183 3.1 10.0 1.0 CB D:HIS185 3.5 10.6 1.0 CB D:HIS190 3.5 11.4 1.0 CG D:GLU183 3.6 10.5 1.0 O D:HOH2031 3.8 2.0 1.0 NE2 D:HIS185 4.0 9.4 1.0 N D:HIS190 4.0 9.4 1.0 NE2 D:HIS190 4.0 11.4 1.0 CD2 D:HIS185 4.1 8.8 1.0 CG D:GLU188 4.1 5.6 1.0 OE1 D:GLU183 4.1 6.0 1.0 CD2 D:HIS190 4.1 12.1 1.0 N D:THR189 4.3 7.3 1.0 CA D:HIS190 4.4 11.7 1.0 CG D:PRO193 4.6 13.8 1.0 OG1 D:THR189 4.7 7.5 1.0 CA D:GLU188 4.8 6.2 1.0 CA D:HIS185 4.8 10.8 1.0 CB D:GLU188 5.0 5.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Udp-Glucose 4-Epimerase


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 Udp-Glucose 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:14.4 occ:1.00 OE2 E:GLU183 1.8 2.0 1.0 OE2 E:GLU188 1.9 15.2 1.0 ND1 E:HIS190 2.0 15.4 1.0 ND1 E:HIS185 2.1 14.7 1.0 CE1 E:HIS190 2.8 12.4 1.0 CD E:GLU188 2.8 15.1 1.0 CD E:GLU183 2.9 5.1 1.0 CG E:HIS185 2.9 14.4 1.0 OE1 E:GLU188 3.0 14.1 1.0 CE1 E:HIS185 3.0 15.6 1.0 CG E:HIS190 3.1 16.4 1.0 CB E:HIS185 3.3 14.4 1.0 CG E:GLU183 3.4 9.0 1.0 O E:HOH2031 3.6 11.2 1.0 CB E:HIS190 3.7 15.8 1.0 OE1 E:GLU183 4.0 2.3 1.0 NE2 E:HIS190 4.0 10.7 1.0 CD2 E:HIS185 4.0 14.2 1.0 NE2 E:HIS185 4.0 14.4 1.0 CD2 E:HIS190 4.2 14.0 1.0 CG E:GLU188 4.2 15.6 1.0 N E:HIS190 4.4 16.4 1.0 CA E:HIS185 4.6 14.4 1.0 N E:HIS185 4.6 14.6 1.0 CA E:HIS190 4.7 16.8 1.0 N E:THR189 4.7 17.5 1.0 CG E:PRO193 4.8 20.2 1.0 CB E:GLU183 4.9 12.9 1.0 CA E:GLU188 4.9 16.4 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Udp-Glucose 4-Epimerase


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 Udp-Glucose 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn601 b:14.0 occ:1.00 OE2 F:GLU188 1.8 7.6 1.0 ND1 F:HIS190 1.8 14.3 1.0 ND1 F:HIS185 2.0 4.5 1.0 OE2 F:GLU183 2.0 8.4 1.0 CE1 F:HIS190 2.5 13.9 1.0 CD F:GLU188 2.8 8.9 1.0 CE1 F:HIS185 3.0 5.4 1.0 CG F:HIS185 3.0 7.6 1.0 OE1 F:GLU188 3.1 10.0 1.0 CD F:GLU183 3.1 9.1 1.0 CG F:HIS190 3.1 13.8 1.0 CB F:HIS185 3.3 9.9 1.0 CG F:GLU183 3.6 9.2 1.0 NE2 F:HIS190 3.7 14.3 1.0 CB F:HIS190 3.8 12.4 1.0 CD2 F:HIS190 4.0 14.9 1.0 OE1 F:GLU183 4.1 4.1 1.0 NE2 F:HIS185 4.1 5.8 1.0 CD2 F:HIS185 4.1 5.7 1.0 N F:HIS190 4.1 12.0 1.0 CG F:GLU188 4.2 8.6 1.0 O F:HOH2035 4.2 11.0 1.0 OG1 F:THR189 4.3 10.4 1.0 N F:THR189 4.4 11.7 1.0 CA F:HIS190 4.6 12.2 1.0 CG F:PRO193 4.6 11.1 1.0 CA F:HIS185 4.7 10.3 1.0 N F:HIS185 4.9 11.6 1.0 CA F:GLU188 4.9 10.2 1.0

A.A.Lebedev, O.V.Moroz, E.V.Blagova, V.M.Levdikov, M.J.Fogg, J.A.Brannigan, A.J.Wilkinson, K.S.Wilson. Crystal Structure of Udp-Glucose 4-Epimerase From Bacillus Anthracis at 2.7A Resolution To Be Published.