Zinc in PDB 5umf: Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate

All present enzymatic activity of Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate:
5.1.3.1;

The structure of Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate, PDB code: 5umf was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.68 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.730, 70.900, 83.500, 90.00, 109.31, 90.00
R / Rfree (%)	14.8 / 16.5

The binding sites of Zinc atom in the Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate (pdb code 5umf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate, PDB code: 5umf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate


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 A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.1 occ:0.60 OD1 A:ASP36 1.9 19.6 1.0 OD2 A:ASP180 2.1 19.8 0.5 NE2 A:HIS34 2.1 13.5 1.0 ND1 A:HIS67 2.2 13.5 1.0 OD2 A:ASP180 2.9 17.1 0.5 CG A:ASP36 3.0 20.8 1.0 CE1 A:HIS34 3.1 11.8 1.0 CD2 A:HIS34 3.1 11.7 1.0 CG A:HIS67 3.2 11.6 1.0 CE1 A:HIS67 3.2 13.8 1.0 CG A:ASP180 3.3 15.9 0.5 CB A:HIS67 3.4 10.6 1.0 OD2 A:ASP36 3.4 22.0 1.0 CG A:ASP180 3.9 15.8 0.5 OD1 A:ASP180 4.0 18.6 0.5 ND1 A:HIS34 4.2 11.8 1.0 O A:HOH412 4.2 32.3 1.0 CB A:ASP36 4.3 14.4 1.0 CG A:HIS34 4.3 11.1 1.0 CB A:ASP180 4.3 14.1 0.5 CB A:ASP180 4.3 14.4 0.5 CD2 A:LEU136 4.3 12.5 1.0 NE2 A:HIS67 4.3 12.5 1.0 CD2 A:HIS67 4.3 10.6 1.0 CE A:MET69 4.4 12.6 1.0 CA A:ASP36 4.6 13.8 1.0 O A:HOH568 4.9 18.0 0.5 SD A:MET138 4.9 16.8 1.0 CG1 A:VAL200 4.9 13.4 1.0 CA A:HIS67 5.0 9.0 1.0 OD1 A:ASP180 5.0 15.4 0.5

Zinc binding site 2 out of 3 in the Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate


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 A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.5 occ:0.57 OD1 B:ASP36 1.9 19.7 1.0 OD2 B:ASP180 2.1 20.9 0.6 NE2 B:HIS34 2.1 13.7 1.0 ND1 B:HIS67 2.3 14.1 1.0 OD2 B:ASP180 2.8 18.6 0.4 CG B:ASP36 3.0 21.5 1.0 CE1 B:HIS34 3.1 12.1 1.0 CD2 B:HIS34 3.1 10.8 1.0 CG B:HIS67 3.2 11.5 1.0 CE1 B:HIS67 3.2 15.2 1.0 CG B:ASP180 3.3 17.6 0.6 CB B:HIS67 3.5 10.3 1.0 OD2 B:ASP36 3.5 24.7 1.0 CG B:ASP180 3.8 19.3 0.4 OD1 B:ASP180 4.0 20.9 0.6 ND1 B:HIS34 4.2 12.4 1.0 O B:HOH411 4.2 29.4 1.0 CB B:ASP180 4.3 15.6 0.6 CB B:ASP180 4.3 14.8 0.4 CG B:HIS34 4.3 12.0 1.0 CB B:ASP36 4.3 16.6 1.0 CD2 B:LEU136 4.3 13.1 1.0 NE2 B:HIS67 4.4 12.8 1.0 CD2 B:HIS67 4.4 11.1 1.0 CE B:MET69 4.4 12.8 1.0 CA B:ASP36 4.7 13.9 1.0 O B:HOH569 4.8 22.0 0.6 OD1 B:ASP180 4.9 19.3 0.4 CG1 B:VAL200 4.9 12.7 1.0 SD B:MET138 4.9 17.5 1.0 CA B:HIS67 5.0 8.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate


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 A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:12.0 occ:0.59 OD1 C:ASP36 2.0 19.3 1.0 OD2 C:ASP180 2.1 18.4 0.6 NE2 C:HIS34 2.1 13.6 1.0 ND1 C:HIS67 2.3 15.0 1.0 OD2 C:ASP180 2.9 15.3 0.5 CG C:ASP36 3.1 19.5 1.0 CD2 C:HIS34 3.1 11.8 1.0 CE1 C:HIS34 3.1 11.4 1.0 CG C:HIS67 3.2 10.9 1.0 CE1 C:HIS67 3.2 13.8 1.0 CG C:ASP180 3.3 15.0 0.6 CB C:HIS67 3.5 10.1 1.0 OD2 C:ASP36 3.5 22.9 1.0 CG C:ASP180 3.9 16.9 0.5 OD1 C:ASP180 3.9 20.0 0.6 ND1 C:HIS34 4.2 12.1 1.0 CG C:HIS34 4.2 10.9 1.0 CB C:ASP180 4.3 14.0 0.5 CB C:ASP180 4.3 13.9 0.6 CD2 C:LEU136 4.3 11.7 1.0 O C:HOH441 4.3 36.6 1.0 CB C:ASP36 4.3 15.9 1.0 NE2 C:HIS67 4.4 13.2 1.0 CD2 C:HIS67 4.4 11.1 1.0 CE C:MET69 4.4 16.0 1.0 CA C:ASP36 4.7 12.9 1.0 SD C:MET138 4.9 16.1 1.0 CG1 C:VAL200 4.9 12.1 1.0 OD1 C:ASP180 5.0 15.4 0.5 O C:HOH565 5.0 31.0 1.0 CA C:HIS67 5.0 9.8 1.0

D.M.Dranow, D.G.Conrady, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Ribulose-Phosphate 3-Epimerase From Neisseria Gonorrhoeae with Bound Phosphate To Be Published.