Zinc in PDB 1k0w: Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase

All present enzymatic activity of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase:
5.1.3.4;

The structure of Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase, PDB code: 1k0w was solved by Y.Luo, J.Samuel, S.C.Mosimann, J.E.Lee, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.10
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	105.900, 105.900, 274.800, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.1

The binding sites of Zinc atom in the Crystal Structure of L-Ribulose-5-Phosphate 4-Epimerase (pdb code 1k0w). 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 L-Ribulose-5-Phosphate 4-Epimerase, PDB code: 1k0w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:40.9 occ:1.00 NE2 A:HIS171 2.2 23.5 1.0 NE2 A:HIS95 2.4 25.7 1.0 NE2 A:HIS97 2.4 26.8 1.0 CE1 A:HIS95 3.1 25.6 1.0 CE1 A:HIS171 3.1 22.4 1.0 CD2 A:HIS171 3.2 23.0 1.0 CD2 A:HIS97 3.3 26.0 1.0 CE1 A:HIS97 3.3 26.3 1.0 O A:HOH385 3.5 34.9 1.0 CD2 A:HIS95 3.5 25.3 1.0 ND1 A:HIS171 4.2 23.3 1.0 CG A:HIS171 4.3 21.6 1.0 ND1 A:HIS95 4.3 25.8 1.0 OD1 A:ASP76 4.4 25.8 1.0 CG A:HIS97 4.4 25.6 1.0 ND1 A:HIS97 4.4 27.2 1.0 CG A:HIS95 4.5 24.6 1.0 OD2 A:ASP76 4.7 23.5 1.0 CG A:ASP76 4.9 24.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:38.8 occ:1.00 NE2 B:HIS95 2.2 17.7 1.0 NE2 B:HIS171 2.2 20.7 1.0 NE2 B:HIS97 2.4 28.2 1.0 O B:HOH403 2.8 32.0 1.0 O B:HOH388 2.9 29.8 1.0 CE1 B:HIS95 3.0 18.0 1.0 CD2 B:HIS171 3.1 20.0 1.0 CE1 B:HIS171 3.2 19.6 1.0 CE1 B:HIS97 3.3 28.9 1.0 CD2 B:HIS95 3.3 17.6 1.0 CD2 B:HIS97 3.4 28.3 1.0 O B:HOH355 4.0 27.2 1.0 ND1 B:HIS95 4.2 18.8 1.0 CG B:HIS171 4.2 19.4 1.0 ND1 B:HIS171 4.3 21.1 1.0 ND1 B:HIS97 4.3 29.1 1.0 OD1 B:ASP76 4.3 21.6 1.0 CG B:HIS95 4.4 19.1 1.0 CG B:HIS97 4.4 26.7 1.0 OD2 B:ASP76 4.6 22.4 1.0 CG B:ASP76 4.9 20.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn303 b:39.5 occ:1.00 NE2 C:HIS95 2.2 18.1 1.0 NE2 C:HIS171 2.2 21.8 1.0 NE2 C:HIS97 2.4 30.1 1.0 O C:HOH389 2.6 25.8 1.0 CE1 C:HIS95 3.0 16.0 1.0 CE1 C:HIS171 3.2 20.1 1.0 CD2 C:HIS171 3.2 19.1 1.0 CE1 C:HIS97 3.3 30.7 1.0 CD2 C:HIS95 3.3 17.4 1.0 CD2 C:HIS97 3.4 30.5 1.0 O C:HOH444 3.7 38.8 1.0 ND1 C:HIS95 4.2 18.4 1.0 ND1 C:HIS171 4.3 20.5 1.0 CG C:HIS171 4.3 18.2 1.0 CG C:HIS95 4.4 17.3 1.0 ND1 C:HIS97 4.4 32.1 1.0 OD1 C:ASP76 4.4 19.8 1.0 O C:HOH417 4.5 33.6 1.0 CG C:HIS97 4.5 30.0 1.0 O C:HOH428 4.7 35.7 1.0 OD2 C:ASP76 4.9 21.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:34.3 occ:1.00 NE2 D:HIS95 2.2 17.0 1.0 NE2 D:HIS171 2.2 20.7 1.0 O D:HOH371 2.3 25.3 1.0 NE2 D:HIS97 2.3 27.5 1.0 CE1 D:HIS95 3.1 16.4 1.0 CD2 D:HIS171 3.1 21.1 1.0 CD2 D:HIS97 3.2 26.4 1.0 CE1 D:HIS171 3.3 20.9 1.0 CE1 D:HIS97 3.3 26.6 1.0 CD2 D:HIS95 3.3 17.6 1.0 O D:HOH402 3.9 30.7 1.0 ND1 D:HIS95 4.2 18.1 1.0 OD1 D:ASP76 4.3 17.8 1.0 CG D:HIS171 4.3 19.6 1.0 ND1 D:HIS171 4.3 20.4 1.0 ND1 D:HIS97 4.3 26.1 1.0 CG D:HIS97 4.4 25.2 1.0 CG D:HIS95 4.4 18.2 1.0 OD2 D:ASP76 4.5 18.4 1.0 O D:HOH363 4.5 24.5 1.0 CG D:ASP76 4.8 17.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn305 b:49.3 occ:1.00 NE2 E:HIS95 2.3 26.2 1.0 NE2 E:HIS171 2.3 25.2 1.0 NE2 E:HIS97 2.5 31.5 1.0 CE1 E:HIS95 3.1 26.3 1.0 CD2 E:HIS171 3.2 24.2 1.0 CD2 E:HIS95 3.3 25.6 1.0 CE1 E:HIS171 3.4 24.9 1.0 CD2 E:HIS97 3.4 30.9 1.0 CE1 E:HIS97 3.4 31.1 1.0 O E:HOH354 3.7 28.9 1.0 OD1 E:ASP76 4.2 32.9 1.0 ND1 E:HIS95 4.3 25.1 1.0 CG E:HIS171 4.4 23.5 1.0 ND1 E:HIS97 4.4 31.4 1.0 CG E:HIS95 4.4 25.3 1.0 ND1 E:HIS171 4.4 24.8 1.0 CG E:HIS97 4.5 29.7 1.0 OD2 E:ASP76 4.7 33.4 1.0 CG E:ASP76 4.9 31.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of L-Ribulose-5-Phosphate 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 L-Ribulose-5-Phosphate 4-Epimerase within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn306 b:48.7 occ:1.00 NE2 F:HIS171 2.2 34.8 1.0 NE2 F:HIS95 2.3 29.3 1.0 NE2 F:HIS97 2.5 34.7 1.0 CD2 F:HIS171 3.1 33.0 1.0 CE1 F:HIS95 3.2 29.8 1.0 CE1 F:HIS171 3.2 32.9 1.0 CD2 F:HIS95 3.3 29.8 1.0 CD2 F:HIS97 3.3 34.5 1.0 CE1 F:HIS97 3.4 34.0 1.0 CG F:HIS171 4.3 31.7 1.0 ND1 F:HIS171 4.3 33.2 1.0 ND1 F:HIS95 4.3 30.1 1.0 ND1 F:HIS97 4.4 34.5 1.0 CG F:HIS97 4.4 34.0 1.0 CG F:HIS95 4.4 30.6 1.0 OD1 F:ASP76 4.4 37.1 1.0 OD2 F:ASP76 4.7 37.1 1.0 CG F:ASP76 5.0 36.0 1.0

Y.Luo, J.Samuel, S.C.Mosimann, J.E.Lee, M.E.Tanner, N.C.J.Strynadka. The Structure of L-Ribulose-5-Phosphate 4-Epimerase: An Aldolase-Like Platform For Epimerization Biochemistry V. 40 14763 2001.
ISSN: ISSN 0006-2960
PubMed: 11732895
DOI: 10.1021/BI0112513