Zinc in PDB 1de5: L-Rhamnose Isomerase

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

The structure of L-Rhamnose Isomerase, PDB code: 1de5 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)	15.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.442, 162.693, 77.022, 90.00, 110.68, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the L-Rhamnose Isomerase (pdb code 1de5). 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: 1de5:
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:34.3 occ:1.00 OD1 A:ASP334 1.9 20.5 1.0 OE2 A:GLU234 2.1 11.4 1.0 OD1 A:ASP267 2.2 28.3 1.0 ND1 A:HIS294 2.2 25.6 1.0 O3 A:RNT1460 2.2 31.6 1.0 O2 A:RNT1460 2.3 40.1 1.0 CD A:GLU234 3.0 25.5 1.0 CG A:ASP334 3.0 23.7 1.0 CE1 A:HIS294 3.1 19.5 1.0 OE1 A:GLU234 3.1 18.3 1.0 CG A:ASP267 3.1 37.4 1.0 CG A:HIS294 3.2 23.2 1.0 C3 A:RNT1460 3.2 26.5 1.0 C2 A:RNT1460 3.3 26.9 1.0 O A:HOH1461 3.6 33.9 1.0 CB A:ASP267 3.6 24.9 1.0 CB A:HIS294 3.6 26.0 1.0 CB A:ASP334 3.8 15.3 1.0 NE2 A:HIS270 3.8 22.6 1.0 O4 A:RNT1460 3.9 25.3 1.0 OD2 A:ASP334 4.1 25.9 1.0 C4 A:RNT1460 4.2 32.6 1.0 NE2 A:HIS294 4.2 19.0 1.0 CE1 A:HIS270 4.3 25.7 1.0 CD2 A:HIS294 4.3 18.9 1.0 OD2 A:ASP267 4.3 37.9 1.0 CG A:GLU234 4.3 12.1 1.0 C1 A:RNT1460 4.4 44.1 1.0 CD2 A:HIS270 4.6 23.5 1.0 C5 A:RNT1460 4.7 28.6 1.0 CA A:ASP267 5.0 19.7 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:35.1 occ:1.00 ND1 B:HIS294 2.1 20.6 1.0 O2 B:RNT2460 2.1 35.9 1.0 OE2 B:GLU234 2.2 27.8 1.0 OD1 B:ASP267 2.2 25.1 1.0 OD1 B:ASP334 2.4 25.4 1.0 O3 B:RNT2460 2.5 25.3 1.0 CE1 B:HIS294 3.0 25.8 1.0 CD B:GLU234 3.1 25.0 1.0 C2 B:RNT2460 3.2 21.2 1.0 OE1 B:GLU234 3.2 29.8 1.0 CG B:HIS294 3.2 18.3 1.0 CG B:ASP267 3.3 37.3 1.0 C3 B:RNT2460 3.3 19.2 1.0 CG B:ASP334 3.3 28.4 1.0 CB B:HIS294 3.6 18.7 1.0 CB B:ASP334 3.7 18.7 1.0 CB B:ASP267 3.8 22.5 1.0 O B:HOH2461 3.8 23.1 1.0 NE2 B:HIS270 3.9 30.6 1.0 O4 B:RNT2460 4.0 22.2 1.0 C4 B:RNT2460 4.2 29.1 1.0 NE2 B:HIS294 4.2 23.2 1.0 C1 B:RNT2460 4.3 39.9 1.0 CE1 B:HIS270 4.3 27.8 1.0 CD2 B:HIS294 4.4 16.1 1.0 OD2 B:ASP267 4.4 32.7 1.0 CG B:GLU234 4.5 10.8 1.0 OD2 B:ASP334 4.5 32.5 1.0 CD2 B:HIS270 4.6 35.0 1.0 C5 B:RNT2460 4.8 23.5 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:33.1 occ:1.00 OE2 C:GLU234 2.0 25.1 1.0 O2 C:RNT3460 2.1 37.9 1.0 OD1 C:ASP267 2.2 28.3 1.0 OD1 C:ASP334 2.2 18.7 1.0 ND1 C:HIS294 2.3 28.1 1.0 O3 C:RNT3460 2.3 28.9 1.0 CD C:GLU234 3.1 12.8 1.0 CG C:ASP267 3.1 32.0 1.0 C2 C:RNT3460 3.2 25.9 1.0 CG C:HIS294 3.2 31.0 1.0 CG C:ASP334 3.2 30.2 1.0 C3 C:RNT3460 3.2 23.9 1.0 CE1 C:HIS294 3.3 22.8 1.0 OE1 C:GLU234 3.3 20.2 1.0 CB C:HIS294 3.4 23.5 1.0 CB C:ASP267 3.7 16.1 1.0 CB C:ASP334 3.8 22.9 1.0 O4 C:RNT3460 3.8 22.9 1.0 O C:HOH3461 3.9 20.1 1.0 NE2 C:HIS270 4.1 26.0 1.0 C4 C:RNT3460 4.2 32.4 1.0 C1 C:RNT3460 4.2 42.4 1.0 CE1 C:HIS270 4.3 24.5 1.0 OD2 C:ASP267 4.3 24.2 1.0 OD2 C:ASP334 4.3 29.8 1.0 CG C:GLU234 4.4 14.8 1.0 CD2 C:HIS294 4.4 24.0 1.0 NE2 C:HIS294 4.4 24.1 1.0 CD2 C:HIS270 4.9 25.2 1.0 C5 C:RNT3460 4.9 27.2 1.0 CA C:ASP267 4.9 19.2 1.0 CA C:HIS294 4.9 19.0 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:34.7 occ:1.00 OD1 D:ASP334 2.0 21.2 1.0 O2 D:RNT4460 2.1 34.3 1.0 ND1 D:HIS294 2.2 30.9 1.0 OD1 D:ASP267 2.3 49.3 1.0 O3 D:RNT4460 2.3 27.1 1.0 OE2 D:GLU234 2.4 25.7 1.0 CG D:ASP334 3.0 30.2 1.0 CG D:ASP267 3.1 33.0 1.0 CE1 D:HIS294 3.1 27.4 1.0 C2 D:RNT4460 3.1 22.2 1.0 C3 D:RNT4460 3.2 22.1 1.0 CG D:HIS294 3.3 30.2 1.0 CD D:GLU234 3.3 24.1 1.0 OE1 D:GLU234 3.5 27.9 1.0 O D:HOH4461 3.5 25.9 1.0 CB D:ASP267 3.6 24.3 1.0 CB D:HIS294 3.6 17.9 1.0 CB D:ASP334 3.6 25.3 1.0 NE2 D:HIS270 4.0 25.6 1.0 O4 D:RNT4460 4.0 22.0 1.0 OD2 D:ASP334 4.1 27.7 1.0 C4 D:RNT4460 4.1 29.6 1.0 CE1 D:HIS270 4.2 26.2 1.0 OD2 D:ASP267 4.2 21.3 1.0 C1 D:RNT4460 4.2 40.5 1.0 NE2 D:HIS294 4.3 28.1 1.0 CD2 D:HIS294 4.4 29.6 1.0 CG D:GLU234 4.7 12.4 1.0 C5 D:RNT4460 4.7 24.8 1.0 CD2 D:HIS270 4.9 27.1 1.0 CA D:ASP267 5.0 27.8 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