Zinc in PDB 1d8w: L-Rhamnose Isomerase

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

The structure of L-Rhamnose Isomerase, PDB code: 1d8w was solved by I.P.Korndorfer, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.849, 163.104, 78.150, 90.00, 110.32, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Zinc atom in the L-Rhamnose Isomerase (pdb code 1d8w). 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: 1d8w:
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:31.7 occ:0.70 OE2 A:GLU234 1.9 20.4 1.0 ND1 A:HIS294 2.0 23.0 1.0 OD2 A:ASP334 2.1 39.0 1.0 OD2 A:ASP267 2.2 38.6 1.0 CD A:GLU234 2.7 18.2 1.0 OE1 A:GLU234 2.9 17.8 1.0 CG A:HIS294 3.0 24.0 1.0 CE1 A:HIS294 3.0 25.5 1.0 CG A:ASP267 3.2 32.2 1.0 CB A:HIS294 3.2 18.5 1.0 CG A:ASP334 3.3 31.6 1.0 CB A:ASP267 3.4 31.2 1.0 CB A:ASP334 3.7 18.4 1.0 NE2 A:HIS270 3.9 40.3 1.0 CG A:GLU234 4.1 11.6 1.0 NE2 A:HIS294 4.1 26.0 1.0 CD2 A:HIS294 4.1 23.4 1.0 CE1 A:HIS270 4.2 41.4 1.0 OD1 A:ASP267 4.3 39.1 1.0 O A:HOH643 4.3 42.8 1.0 OD1 A:ASP334 4.3 36.0 1.0 O A:HOH663 4.4 37.9 1.0 SG A:CYS265 4.4 18.7 1.0 CD2 A:HIS270 4.6 44.3 1.0 CA A:ASP267 4.6 23.2 1.0 O A:HOH662 4.7 49.0 1.0 CA A:HIS294 4.8 17.6 1.0 ND1 A:HIS270 4.9 35.5 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:26.0 occ:0.70 OE2 B:GLU234 1.9 19.2 1.0 ND1 B:HIS294 1.9 19.0 1.0 OD2 B:ASP267 2.0 43.6 1.0 OD2 B:ASP334 2.2 33.5 1.0 CD B:GLU234 2.9 23.1 1.0 CG B:HIS294 2.9 19.7 1.0 CE1 B:HIS294 3.0 21.0 1.0 CG B:ASP267 3.1 59.3 1.0 CB B:HIS294 3.1 15.0 1.0 OE1 B:GLU234 3.1 17.9 1.0 O B:HOH708 3.1 45.5 1.0 CG B:ASP334 3.2 25.9 1.0 CB B:ASP267 3.4 24.8 1.0 CB B:ASP334 3.5 19.6 1.0 O B:HOH653 3.9 49.9 1.0 CD2 B:HIS294 4.1 17.6 1.0 NE2 B:HIS294 4.1 20.2 1.0 OD1 B:ASP267 4.2 28.0 1.0 CG B:GLU234 4.2 13.7 1.0 NE2 B:HIS270 4.2 74.3 1.0 OD1 B:ASP334 4.2 30.3 1.0 SG B:CYS265 4.3 19.3 1.0 CA B:ASP267 4.5 16.2 1.0 CD2 B:HIS270 4.6 72.4 1.0 CA B:HIS294 4.6 14.8 1.0 CE1 B:HIS270 4.7 69.5 1.0 O B:HOH554 4.9 42.5 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:40.4 occ:0.70 OE2 C:GLU234 1.8 20.0 1.0 OD2 C:ASP267 2.0 60.1 1.0 ND1 C:HIS294 2.1 25.1 1.0 OD2 C:ASP334 2.2 45.0 1.0 CD C:GLU234 2.8 18.0 1.0 CG C:HIS294 2.9 19.9 1.0 CB C:HIS294 3.1 17.6 1.0 CG C:ASP267 3.1 32.1 1.0 OE1 C:GLU234 3.1 21.6 1.0 CE1 C:HIS294 3.2 24.4 1.0 CG C:ASP334 3.3 44.0 1.0 CB C:ASP267 3.5 22.4 1.0 CB C:ASP334 3.7 15.6 1.0 NE2 C:HIS270 3.9 63.9 1.0 CE1 C:HIS270 4.1 49.8 1.0 CG C:GLU234 4.1 15.8 1.0 CD2 C:HIS294 4.1 18.5 1.0 OD1 C:ASP267 4.1 29.0 1.0 NE2 C:HIS294 4.2 23.3 1.0 O C:HOH814 4.3 54.5 1.0 OD1 C:ASP334 4.3 38.8 1.0 SG C:CYS265 4.4 19.3 1.0 CA C:ASP267 4.6 15.8 1.0 CD2 C:HIS270 4.6 56.3 1.0 CA C:HIS294 4.6 12.2 1.0 ND1 C:HIS270 4.8 63.0 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:39.3 occ:0.70 OD2 D:ASP267 1.8 0.0 1.0 OE2 D:GLU234 2.1 24.1 1.0 ND1 D:HIS294 2.1 22.4 1.0 OD2 D:ASP334 2.1 46.0 1.0 CG D:ASP267 2.9 43.2 1.0 CD D:GLU234 2.9 27.1 1.0 CG D:HIS294 3.0 24.9 1.0 OE1 D:GLU234 3.1 20.8 1.0 CE1 D:HIS294 3.1 21.2 1.0 CB D:HIS294 3.2 18.8 1.0 CG D:ASP334 3.3 49.1 1.0 CB D:ASP267 3.5 24.9 1.0 CB D:ASP334 3.8 20.5 1.0 OD1 D:ASP267 3.9 25.6 1.0 NE2 D:HIS270 4.1 51.5 1.0 O D:HOH649 4.1 34.2 1.0 CD2 D:HIS294 4.2 26.2 1.0 NE2 D:HIS294 4.2 23.1 1.0 CG D:GLU234 4.3 16.1 1.0 OD1 D:ASP334 4.3 37.2 1.0 CE1 D:HIS270 4.3 46.8 1.0 SG D:CYS265 4.6 21.1 1.0 CA D:ASP267 4.6 28.1 1.0 CD2 D:HIS270 4.6 54.1 1.0 CA D:HIS294 4.7 15.0 1.0 ND1 D:HIS270 5.0 68.5 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