Zinc in PDB 1de6: L-Rhamnose Isomerase

All present enzymatic activity of L-Rhamnose Isomerase:
5.3.1.14;

The structure of L-Rhamnose Isomerase, PDB code: 1de6 was solved by I.P.Korndorfer, W.D.Fessner, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.179, 162.439, 77.726, 90.00, 109.89, 90.00
R / Rfree (%)	n/a / n/a

The structure of L-Rhamnose Isomerase also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Zinc atom in the L-Rhamnose Isomerase (pdb code 1de6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the L-Rhamnose Isomerase, PDB code: 1de6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn450 b:36.9 occ:1.00 OD1 A:ASP267 2.0 33.6 1.0 OD2 A:ASP334 2.0 24.7 1.0 OE2 A:GLU234 2.0 24.1 1.0 ND1 A:HIS294 2.1 30.6 1.0 O3 A:RNS1462 2.9 19.6 0.6 CD A:GLU234 2.9 15.2 1.0 CG A:ASP267 3.0 18.9 1.0 CE1 A:HIS294 3.0 22.2 1.0 CG A:ASP334 3.1 25.2 1.0 CG A:HIS294 3.1 26.9 1.0 OE1 A:GLU234 3.2 27.2 1.0 CB A:ASP267 3.3 19.1 1.0 CB A:ASP334 3.4 19.5 1.0 CB A:HIS294 3.4 26.9 1.0 O2 A:RNS1462 3.5 30.5 0.6 CE1 A:HIS270 3.9 28.5 1.0 C3 A:RNS1462 3.9 17.3 0.6 C2 A:RNS1462 4.0 21.1 0.6 OD2 A:ASP267 4.1 26.7 1.0 NE2 A:HIS270 4.1 24.2 1.0 OD1 A:ASP334 4.2 34.5 1.0 NE2 A:HIS294 4.2 24.6 1.0 CD2 A:HIS294 4.2 31.1 1.0 CG A:GLU234 4.3 16.7 1.0 ND1 A:HIS270 4.6 35.3 1.0 SG A:CYS265 4.6 20.5 1.0 CA A:ASP267 4.6 24.2 1.0 MN A:MN451 4.7 59.0 1.0 CA A:HIS294 4.9 29.6 1.0 CA A:ASP334 5.0 25.9 1.0

Zinc binding site 2 out of 4 in the L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn450 b:34.3 occ:1.00 ND1 B:HIS294 1.8 28.1 1.0 OE2 B:GLU234 2.0 24.5 1.0 OD2 B:ASP334 2.0 21.5 1.0 OD1 B:ASP267 2.0 32.1 1.0 CE1 B:HIS294 2.8 20.4 1.0 CD B:GLU234 2.8 14.9 1.0 O2 B:RNS2462 2.9 40.8 0.5 CG B:HIS294 2.9 27.7 1.0 OE1 B:GLU234 3.0 25.4 1.0 CG B:ASP267 3.1 16.4 1.0 CG B:ASP334 3.1 25.0 1.0 O3 B:RNS2462 3.3 16.1 0.5 CB B:ASP334 3.3 16.5 1.0 CB B:ASP267 3.4 14.9 1.0 CB B:HIS294 3.4 22.7 1.0 C2 B:RNS2462 3.9 22.4 0.5 NE2 B:HIS294 3.9 20.7 1.0 CE1 B:HIS270 4.0 25.7 1.0 CD2 B:HIS294 4.0 27.6 1.0 OD2 B:ASP267 4.2 22.6 1.0 C3 B:RNS2462 4.2 25.0 0.5 CG B:GLU234 4.2 13.9 1.0 NE2 B:HIS270 4.3 22.2 1.0 OD1 B:ASP334 4.3 28.5 1.0 SG B:CYS265 4.5 18.9 1.0 CA B:ASP267 4.5 21.4 1.0 O4 B:RNS2462 4.6 56.0 0.5 ND1 B:HIS270 4.7 34.3 1.0 CA B:ASP334 4.9 26.2 1.0 CA B:HIS294 4.9 26.4 1.0

Zinc binding site 3 out of 4 in the L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn450 b:36.6 occ:1.00 ND1 C:HIS294 1.9 30.4 1.0 OD1 C:ASP267 2.0 35.5 1.0 OE2 C:GLU234 2.0 23.9 1.0 OD2 C:ASP334 2.1 23.6 1.0 CE1 C:HIS294 2.9 19.0 1.0 CD C:GLU234 3.0 17.6 1.0 CG C:HIS294 3.0 27.6 1.0 O2 C:RNS3462 3.0 38.6 0.5 CG C:ASP267 3.1 17.2 1.0 CG C:ASP334 3.2 23.5 1.0 OE1 C:GLU234 3.2 26.8 1.0 CB C:ASP267 3.3 14.4 1.0 CB C:HIS294 3.4 21.1 1.0 CB C:ASP334 3.5 12.0 1.0 O3 C:RNS3462 3.6 31.7 0.5 CE1 C:HIS270 3.9 27.0 1.0 NE2 C:HIS294 4.0 22.0 1.0 C2 C:RNS3462 4.0 21.6 0.5 OD2 C:ASP267 4.1 22.1 1.0 CD2 C:HIS294 4.1 28.0 1.0 NE2 C:HIS270 4.2 25.3 1.0 OD1 C:ASP334 4.3 31.4 1.0 CG C:GLU234 4.3 15.6 1.0 C3 C:RNS3462 4.4 31.8 0.5 CA C:ASP267 4.6 22.3 1.0 ND1 C:HIS270 4.6 36.1 1.0 SG C:CYS265 4.7 17.9 1.0 CA C:HIS294 4.8 25.6 1.0 O4 C:RNS3462 4.8 45.7 0.5 MN C:MN451 4.9 51.4 1.0 CA C:ASP334 5.0 23.6 1.0

Zinc binding site 4 out of 4 in the L-Rhamnose Isomerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn450 b:41.8 occ:1.00 OD2 D:ASP334 2.0 29.0 1.0 ND1 D:HIS294 2.1 31.3 1.0 OD1 D:ASP267 2.1 36.1 1.0 OE2 D:GLU234 2.2 28.7 1.0 O2 D:RNS4462 2.8 29.2 0.5 O3 D:RNS4462 2.9 18.1 0.5 CE1 D:HIS294 2.9 18.2 1.0 CD D:GLU234 3.0 20.7 1.0 CG D:ASP334 3.1 27.5 1.0 CG D:ASP267 3.1 19.5 1.0 CG D:HIS294 3.1 29.5 1.0 OE1 D:GLU234 3.2 27.7 1.0 CB D:ASP334 3.4 18.9 1.0 CB D:ASP267 3.5 20.0 1.0 CB D:HIS294 3.5 24.7 1.0 C2 D:RNS4462 3.8 20.7 0.5 C3 D:RNS4462 4.0 19.3 0.5 CE1 D:HIS270 4.0 29.9 1.0 NE2 D:HIS294 4.1 25.4 1.0 NE2 D:HIS270 4.1 24.6 1.0 OD2 D:ASP267 4.2 25.2 1.0 OD1 D:ASP334 4.2 34.7 1.0 CD2 D:HIS294 4.3 32.2 1.0 CG D:GLU234 4.4 15.8 1.0 O4 D:RNS4462 4.7 37.6 0.5 CA D:ASP267 4.7 27.6 1.0 MN D:MN451 4.7 61.0 1.0 ND1 D:HIS270 4.8 37.5 1.0 SG D:CYS265 4.8 21.6 1.0 C4 D:RNS4462 4.9 18.3 0.5 CA D:ASP334 5.0 28.6 1.0

I.P.Korndorfer, W.D.Fessner, B.W.Matthews. The Structure of Rhamnose Isomerase From Escherichia Coli and Its Relation with Xylose Isomerase Illustrates A Change Between Inter and Intra-Subunit Complementation During Evolution. J.Mol.Biol. V. 300 917 2000.
ISSN: ISSN 0022-2836
PubMed: 10891278
DOI: 10.1006/JMBI.2000.3896