Zinc in PDB 2fli: The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate

The structure of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate, PDB code: 2fli was solved by A.A.Fedorov, E.V.Fedorov, J.Akana, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.99 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.022, 199.449, 87.622, 90.00, 109.76, 90.00
R / Rfree (%)	22.4 / 25.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate (pdb code 2fli). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate, PDB code: 2fli:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1981 b:43.4 occ:1.00 OD1 A:ASP36 2.1 18.8 1.0 NE2 A:HIS34 2.2 20.3 1.0 ND1 A:HIS67 2.2 19.3 1.0 OD2 A:ASP176 2.3 28.1 1.0 O2 A:DX51901 2.6 29.6 1.0 CD2 A:HIS34 2.9 16.8 1.0 O3 A:DX51901 3.0 28.9 1.0 CE1 A:HIS67 3.1 18.2 1.0 CG A:ASP36 3.2 21.4 1.0 CG A:HIS67 3.2 19.5 1.0 CE1 A:HIS34 3.3 20.2 1.0 CG A:ASP176 3.4 25.2 1.0 CB A:HIS67 3.6 18.9 1.0 OD2 A:ASP36 3.6 23.2 1.0 C2 A:DX51901 3.7 29.7 1.0 C3 A:DX51901 3.8 29.8 1.0 OD1 A:ASP176 4.0 30.6 1.0 CG A:HIS34 4.1 19.0 1.0 CE A:MET69 4.2 21.6 1.0 NE2 A:HIS67 4.3 19.2 1.0 ND1 A:HIS34 4.3 18.7 1.0 CD2 A:HIS67 4.3 17.8 1.0 CB A:ASP176 4.5 21.3 1.0 CB A:ASP36 4.5 17.6 1.0 CD2 A:LEU136 4.8 18.7 1.0 C1 A:DX51901 4.9 29.6 1.0 CA A:ASP36 4.9 17.7 1.0 SD A:MET138 5.0 21.1 1.0

Zinc binding site 2 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1982 b:39.5 occ:1.00 OD1 B:ASP36 2.2 17.6 1.0 NE2 B:HIS34 2.3 23.5 1.0 OD2 B:ASP176 2.3 29.2 1.0 ND1 B:HIS67 2.3 22.4 1.0 O2 B:DX51902 2.5 35.1 1.0 CD2 B:HIS34 2.9 22.7 1.0 O3 B:DX51902 3.0 39.5 1.0 CG B:ASP36 3.1 22.9 1.0 CE1 B:HIS67 3.3 22.2 1.0 CG B:HIS67 3.4 21.5 1.0 CE1 B:HIS34 3.4 24.1 1.0 CG B:ASP176 3.5 27.8 1.0 OD2 B:ASP36 3.5 23.3 1.0 C2 B:DX51902 3.6 35.9 1.0 CB B:HIS67 3.7 20.2 1.0 C3 B:DX51902 3.9 37.1 1.0 OD1 B:ASP176 4.1 29.7 1.0 CE B:MET69 4.1 22.6 1.0 CG B:HIS34 4.2 22.1 1.0 ND1 B:HIS34 4.4 22.4 1.0 NE2 B:HIS67 4.4 20.1 1.0 CB B:ASP36 4.5 20.9 1.0 CD2 B:HIS67 4.5 21.5 1.0 CB B:ASP176 4.5 25.8 1.0 CD1 B:LEU136 4.8 21.8 1.0 C1 B:DX51902 4.8 35.8 1.0 CG1 B:VAL196 5.0 21.0 1.0 CA B:ASP36 5.0 21.1 1.0

Zinc binding site 3 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1983 b:36.5 occ:1.00 NE2 C:HIS34 2.1 15.0 1.0 OD1 C:ASP36 2.2 18.0 1.0 OD2 C:ASP176 2.3 24.3 1.0 ND1 C:HIS67 2.3 15.6 1.0 O2 C:DX51903 2.6 33.4 1.0 CD2 C:HIS34 2.8 16.9 1.0 O3 C:DX51903 2.9 33.4 1.0 CG C:ASP36 3.2 15.4 1.0 CE1 C:HIS67 3.2 14.8 1.0 CE1 C:HIS34 3.2 16.2 1.0 CG C:HIS67 3.3 15.9 1.0 CG C:ASP176 3.4 23.4 1.0 OD2 C:ASP36 3.5 16.9 1.0 CB C:HIS67 3.6 14.4 1.0 C2 C:DX51903 3.6 31.1 1.0 C3 C:DX51903 3.7 31.3 1.0 OD1 C:ASP176 4.0 22.9 1.0 CG C:HIS34 4.0 14.6 1.0 ND1 C:HIS34 4.2 15.6 1.0 CE C:MET69 4.2 20.2 1.0 NE2 C:HIS67 4.4 16.9 1.0 CB C:ASP176 4.4 19.0 1.0 CD2 C:HIS67 4.4 16.1 1.0 CB C:ASP36 4.5 10.8 1.0 CD2 C:LEU136 4.7 17.2 1.0 C1 C:DX51903 4.9 33.3 1.0 CA C:ASP36 4.9 12.3 1.0 CG1 C:VAL196 5.0 18.3 1.0

Zinc binding site 4 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1984 b:40.5 occ:1.00 NE2 D:HIS34 2.1 20.6 1.0 OD1 D:ASP36 2.3 20.0 1.0 ND1 D:HIS67 2.3 18.9 1.0 OD2 D:ASP176 2.3 27.2 1.0 O2 D:DX51904 2.5 35.7 1.0 CD2 D:HIS34 2.9 18.1 1.0 O3 D:DX51904 3.1 33.2 1.0 CE1 D:HIS34 3.2 20.3 1.0 CE1 D:HIS67 3.2 19.6 1.0 CG D:ASP36 3.3 22.2 1.0 CG D:HIS67 3.3 18.0 1.0 CG D:ASP176 3.4 29.5 1.0 CB D:HIS67 3.6 14.8 1.0 OD2 D:ASP36 3.7 23.0 1.0 C2 D:DX51904 3.7 35.8 1.0 OD1 D:ASP176 3.9 26.8 1.0 C3 D:DX51904 4.0 34.6 1.0 CG D:HIS34 4.1 20.6 1.0 ND1 D:HIS34 4.2 19.8 1.0 CE D:MET69 4.3 24.9 1.0 NE2 D:HIS67 4.4 17.4 1.0 CB D:ASP176 4.4 24.6 1.0 CD2 D:HIS67 4.4 16.6 1.0 CB D:ASP36 4.6 19.9 1.0 CD2 D:LEU136 4.6 19.9 1.0 C1 D:DX51904 4.9 36.2 1.0 SD D:MET138 5.0 21.6 1.0 CA D:ASP36 5.0 17.8 1.0 CG1 D:VAL196 5.0 18.4 1.0

Zinc binding site 5 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1985 b:37.6 occ:1.00 NE2 E:HIS34 2.2 17.4 1.0 ND1 E:HIS67 2.2 16.9 1.0 OD1 E:ASP36 2.3 17.4 1.0 OD2 E:ASP176 2.4 32.3 1.0 O2 E:DX51905 2.6 32.2 1.0 O3 E:DX51905 2.7 37.6 1.0 CD2 E:HIS34 2.9 17.4 1.0 CE1 E:HIS67 3.2 18.9 1.0 CG E:ASP36 3.2 16.3 1.0 CG E:HIS67 3.3 20.3 1.0 CG E:ASP176 3.3 29.0 1.0 CE1 E:HIS34 3.3 20.4 1.0 OD2 E:ASP36 3.5 20.3 1.0 CB E:HIS67 3.6 17.2 1.0 C3 E:DX51905 3.6 34.7 1.0 C2 E:DX51905 3.6 35.8 1.0 OD1 E:ASP176 3.8 31.2 1.0 CG E:HIS34 4.1 19.4 1.0 ND1 E:HIS34 4.3 20.2 1.0 NE2 E:HIS67 4.3 19.0 1.0 CE E:MET69 4.3 24.2 1.0 CD2 E:HIS67 4.4 20.1 1.0 CB E:ASP176 4.4 24.0 1.0 CB E:ASP36 4.6 18.5 1.0 CD2 E:LEU136 4.8 17.0 1.0 C1 E:DX51905 4.8 36.7 1.0 C4 E:DX51905 4.9 32.2 1.0 CG1 E:VAL196 5.0 22.0 1.0

Zinc binding site 6 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1986 b:48.8 occ:1.00 NE2 F:HIS34 2.1 20.2 1.0 OD1 F:ASP36 2.2 24.8 1.0 ND1 F:HIS67 2.3 24.9 1.0 OD2 F:ASP176 2.3 31.6 1.0 O2 F:DX51906 2.8 36.7 1.0 CD2 F:HIS34 3.0 19.9 1.0 CE1 F:HIS34 3.1 20.7 1.0 CG F:HIS67 3.2 23.8 1.0 CG F:ASP36 3.2 23.3 1.0 CE1 F:HIS67 3.3 24.7 1.0 O3 F:DX51906 3.4 39.0 1.0 CB F:HIS67 3.4 21.0 1.0 CG F:ASP176 3.5 29.6 1.0 OD2 F:ASP36 3.6 22.4 1.0 C2 F:DX51906 3.9 36.9 1.0 CG F:HIS34 4.1 21.3 1.0 ND1 F:HIS34 4.2 20.6 1.0 OD1 F:ASP176 4.2 30.4 1.0 C3 F:DX51906 4.2 37.7 1.0 CE F:MET69 4.3 26.2 1.0 CD2 F:HIS67 4.4 24.6 1.0 NE2 F:HIS67 4.4 25.6 1.0 CB F:ASP176 4.5 26.4 1.0 CB F:ASP36 4.5 22.3 1.0 CD1 F:LEU136 4.7 28.9 1.0 CA F:HIS67 4.9 21.1 1.0 SD F:MET138 5.0 23.4 1.0

Zinc binding site 7 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1991 b:49.3 occ:1.00 NE2 G:HIS34 2.2 26.6 1.0 OD1 G:ASP36 2.2 23.8 1.0 ND1 G:HIS67 2.3 21.6 1.0 OD2 G:ASP176 2.5 38.0 1.0 O2 G:DX51911 2.7 39.9 1.0 O3 G:DX51911 2.9 38.8 1.0 CD2 G:HIS34 3.0 26.0 1.0 CG G:ASP36 3.2 24.3 1.0 CE1 G:HIS67 3.3 23.0 1.0 CG G:ASP176 3.3 33.4 1.0 CG G:HIS67 3.3 24.0 1.0 CE1 G:HIS34 3.3 24.4 1.0 OD2 G:ASP36 3.5 24.1 1.0 CB G:HIS67 3.6 23.8 1.0 C2 G:DX51911 3.8 39.1 1.0 C3 G:DX51911 3.8 37.4 1.0 OD1 G:ASP176 3.8 35.7 1.0 CG G:HIS34 4.2 26.2 1.0 CB G:ASP176 4.3 30.8 1.0 ND1 G:HIS34 4.4 25.7 1.0 CE G:MET69 4.4 25.0 1.0 NE2 G:HIS67 4.4 23.9 1.0 CD2 G:HIS67 4.4 24.1 1.0 CB G:ASP36 4.6 22.1 1.0 CD2 G:LEU136 4.8 24.5 1.0 SD G:MET138 4.9 28.7 1.0 C1 G:DX51911 5.0 39.4 1.0

Zinc binding site 8 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1992 b:37.7 occ:1.00 OD1 H:ASP36 2.0 20.7 1.0 NE2 H:HIS34 2.2 16.2 1.0 ND1 H:HIS67 2.2 17.2 1.0 OD2 H:ASP176 2.3 23.9 1.0 O2 H:DX51912 2.5 31.5 1.0 CD2 H:HIS34 2.9 18.4 1.0 O3 H:DX51912 2.9 32.8 1.0 CG H:ASP36 3.0 16.3 1.0 CE1 H:HIS67 3.1 15.7 1.0 CG H:HIS67 3.2 18.3 1.0 CE1 H:HIS34 3.3 19.0 1.0 CG H:ASP176 3.4 25.0 1.0 OD2 H:ASP36 3.4 21.4 1.0 CB H:HIS67 3.5 18.6 1.0 C2 H:DX51912 3.5 32.8 1.0 C3 H:DX51912 3.7 32.2 1.0 OD1 H:ASP176 4.0 25.2 1.0 CG H:HIS34 4.1 19.7 1.0 NE2 H:HIS67 4.2 15.6 1.0 ND1 H:HIS34 4.3 18.6 1.0 CD2 H:HIS67 4.3 17.4 1.0 CB H:ASP36 4.4 15.5 1.0 CE H:MET69 4.4 16.5 1.0 CB H:ASP176 4.5 19.3 1.0 CD1 H:LEU136 4.8 19.7 1.0 C1 H:DX51912 4.8 33.1 1.0 CA H:ASP36 4.8 14.5 1.0 SD H:MET138 4.9 20.8 1.0

Zinc binding site 9 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn1993 b:50.9 occ:1.00 OD1 I:ASP36 2.2 27.1 1.0 NE2 I:HIS34 2.2 27.6 1.0 OD2 I:ASP176 2.3 33.4 1.0 ND1 I:HIS67 2.4 21.8 1.0 O2 I:DX51913 2.7 42.2 1.0 CD2 I:HIS34 3.1 27.5 1.0 CG I:ASP36 3.1 26.7 1.0 CE1 I:HIS34 3.3 27.5 1.0 CG I:HIS67 3.3 21.2 1.0 CE1 I:HIS67 3.3 22.0 1.0 O3 I:DX51913 3.3 40.3 1.0 OD2 I:ASP36 3.3 28.9 1.0 CG I:ASP176 3.4 34.8 1.0 CB I:HIS67 3.5 22.0 1.0 C2 I:DX51913 3.9 41.4 1.0 OD1 I:ASP176 4.0 35.1 1.0 C3 I:DX51913 4.2 41.0 1.0 CG I:HIS34 4.3 25.9 1.0 ND1 I:HIS34 4.3 27.4 1.0 CE I:MET69 4.4 30.2 1.0 CB I:ASP176 4.4 31.7 1.0 NE2 I:HIS67 4.4 22.6 1.0 CD2 I:HIS67 4.5 21.6 1.0 CB I:ASP36 4.5 27.7 1.0 CD2 I:LEU136 4.7 26.1 1.0 SD I:MET138 4.9 26.5 1.0 CE I:MET138 5.0 22.7 1.0

Zinc binding site 10 out of 12 in the The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of D-Ribulose 5-Phosphate 3-Epimerase From Streptococus Pyogenes Complexed with D-Xylitol 5- Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1994 b:45.4 occ:1.00 NE2 J:HIS34 2.1 18.2 1.0 OD1 J:ASP36 2.2 21.4 1.0 ND1 J:HIS67 2.3 23.7 1.0 OD2 J:ASP176 2.3 29.8 1.0 O2 J:DX51914 2.5 28.7 1.0 O3 J:DX51914 2.9 31.1 1.0 CD2 J:HIS34 3.0 17.0 1.0 CE1 J:HIS67 3.1 22.8 1.0 CG J:ASP36 3.2 21.9 1.0 CE1 J:HIS34 3.2 20.8 1.0 CG J:HIS67 3.3 22.1 1.0 CG J:ASP176 3.5 27.5 1.0 C2 J:DX51914 3.5 27.4 1.0 OD2 J:ASP36 3.6 24.1 1.0 CB J:HIS67 3.6 19.3 1.0 C3 J:DX51914 3.7 30.0 1.0 CE J:MET69 4.2 23.4 1.0 CG J:HIS34 4.2 20.0 1.0 OD1 J:ASP176 4.3 27.5 1.0 ND1 J:HIS34 4.3 21.2 1.0 NE2 J:HIS67 4.3 21.1 1.0 CD2 J:HIS67 4.4 20.2 1.0 CB J:ASP176 4.5 24.8 1.0 CB J:ASP36 4.5 19.7 1.0 CD2 J:LEU136 4.7 20.0 1.0 C1 J:DX51914 4.8 28.6 1.0

J.Akana, A.A.Fedorov, E.Fedorov, W.R.Novak, P.C.Babbitt, S.C.Almo, J.A.Gerlt. D-Ribulose 5-Phosphate 3-Epimerase: Functional and Structural Relationships to Members of the Ribulose-Phosphate Binding (Beta/Alpha)(8)-Barrel Superfamily(,). Biochemistry V. 45 2493 2006.
ISSN: ISSN 0006-2960
PubMed: 16489742
DOI: 10.1021/BI052474M