Manganese 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:

Zinc

(Zn)

4 atoms

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn451 b:59.0 occ:1.00 OD1 A:ASP302 2.3 38.5 1.0 O2 A:RNS1462 2.4 30.5 0.6 OD2 A:ASP302 2.6 44.9 1.0 NE2 A:HIS270 2.7 24.2 1.0 CG A:ASP302 2.8 34.4 1.0 OD1 A:ASP304 3.0 54.4 1.0 OD2 A:ASP304 3.2 30.2 1.0 CD2 A:HIS270 3.3 19.5 1.0 CG A:ASP304 3.5 35.6 1.0 C2 A:RNS1462 3.8 21.1 0.6 O4 A:RNS1462 3.8 36.3 0.6 CE1 A:HIS270 3.8 28.5 1.0 O1 A:RNS1462 3.9 27.8 0.6 OD1 A:ASP267 4.1 33.6 1.0 OD2 A:ASP334 4.1 24.7 1.0 OD2 A:ASP267 4.1 26.7 1.0 O A:HOH1517 4.2 22.1 1.0 C1 A:RNS1462 4.2 19.6 0.6 CB A:ASP302 4.3 22.0 1.0 CG A:ASP267 4.3 18.9 1.0 CG A:ASP334 4.3 25.2 1.0 OD1 A:ASP334 4.5 34.5 1.0 CG A:HIS270 4.6 25.4 1.0 CZ A:PHE336 4.6 80.3 1.0 OG A:SER296 4.6 23.8 1.0 C3 A:RNS1462 4.7 17.3 0.6 ZN A:ZN450 4.7 36.9 1.0 O A:ASP302 4.7 31.7 1.0 O A:ASP334 4.8 34.8 1.0 ND1 A:HIS270 4.8 35.3 1.0 NZ A:LYS236 4.8 36.4 1.0 C4 A:RNS1462 4.8 10.0 0.6 CE A:LYS236 4.9 21.9 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn451 b:53.5 occ:1.00 OD1 B:ASP302 2.0 37.3 1.0 OD1 B:ASP304 2.4 50.4 1.0 OD2 B:ASP302 2.6 44.6 1.0 CG B:ASP302 2.6 33.4 1.0 OD2 B:ASP304 2.9 26.4 1.0 NE2 B:HIS270 3.0 22.2 1.0 CG B:ASP304 3.0 31.4 1.0 O1 B:RNS2462 3.1 39.9 0.5 CD2 B:HIS270 3.4 18.4 1.0 O2 B:RNS2462 3.5 40.8 0.5 O B:HOH2533 4.0 21.2 1.0 CB B:ASP302 4.1 22.7 1.0 O4 B:RNS2462 4.1 56.0 0.5 C1 B:RNS2462 4.1 29.0 0.5 CE1 B:HIS270 4.2 25.7 1.0 OD2 B:ASP267 4.3 22.6 1.0 O B:ASP302 4.4 31.6 1.0 C2 B:RNS2462 4.4 22.4 0.5 OG B:SER296 4.4 24.4 1.0 OD1 B:ASP267 4.5 32.1 1.0 CB B:ASP304 4.5 20.7 1.0 CG B:ASP267 4.6 16.4 1.0 CZ B:PHE336 4.7 79.2 1.0 OD2 B:ASP334 4.7 21.5 1.0 C B:ASP302 4.8 27.6 1.0 O B:ASP334 4.8 29.9 1.0 CG B:HIS270 4.8 26.8 1.0 CG B:ASP334 4.8 25.0 1.0 CA B:ASP302 4.8 26.2 1.0 N B:ASP304 4.9 26.4 1.0 NZ B:LYS236 4.9 36.3 1.0 O B:HOH2505 4.9 41.4 1.0 OD1 B:ASP334 4.9 28.5 1.0 CA B:ASP304 4.9 19.6 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn451 b:51.4 occ:1.00 OD1 C:ASP302 2.2 38.0 1.0 OD2 C:ASP302 2.4 42.8 1.0 CG C:ASP302 2.7 31.1 1.0 NE2 C:HIS270 2.7 25.3 1.0 OD1 C:ASP304 2.9 51.2 1.0 O2 C:RNS3462 3.1 38.6 0.5 O1 C:RNS3462 3.1 26.9 0.5 OD2 C:ASP304 3.2 29.0 1.0 CD2 C:HIS270 3.3 17.7 1.0 CG C:ASP304 3.4 31.7 1.0 CE1 C:HIS270 3.9 27.0 1.0 C1 C:RNS3462 3.9 14.0 0.5 O4 C:RNS3462 3.9 45.7 0.5 C2 C:RNS3462 4.1 21.6 0.5 OD2 C:ASP267 4.1 22.1 1.0 CB C:ASP302 4.2 24.6 1.0 OD2 C:ASP334 4.3 23.6 1.0 OD1 C:ASP267 4.3 35.5 1.0 O C:HOH3532 4.3 22.0 1.0 CG C:ASP267 4.5 17.2 1.0 CZ C:PHE336 4.6 78.5 1.0 CG C:HIS270 4.6 25.6 1.0 CG C:ASP334 4.6 23.5 1.0 OG C:SER296 4.7 21.6 1.0 O C:ASP302 4.7 33.2 1.0 O C:ASP334 4.7 32.1 1.0 OD1 C:ASP334 4.8 31.4 1.0 NZ C:LYS236 4.8 36.8 1.0 CE C:LYS236 4.9 20.1 1.0 ND1 C:HIS270 4.9 36.1 1.0 CB C:ASP304 4.9 18.2 1.0 ZN C:ZN450 4.9 36.6 1.0

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of L-Rhamnose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn451 b:61.0 occ:1.00 OD1 D:ASP302 2.4 40.7 1.0 OD2 D:ASP302 2.4 45.5 1.0 CG D:ASP302 2.7 37.0 1.0 NE2 D:HIS270 2.8 24.6 1.0 O2 D:RNS4462 2.9 29.2 0.5 O1 D:RNS4462 3.0 30.8 0.5 OD1 D:ASP304 3.0 54.9 1.0 OD2 D:ASP304 3.2 31.1 1.0 CD2 D:HIS270 3.4 22.1 1.0 CG D:ASP304 3.5 35.9 1.0 O4 D:RNS4462 3.6 37.6 0.5 C1 D:RNS4462 3.7 23.2 0.5 C2 D:RNS4462 3.9 20.7 0.5 CE1 D:HIS270 4.0 29.9 1.0 OD2 D:ASP334 4.2 29.0 1.0 OD2 D:ASP267 4.2 25.2 1.0 CB D:ASP302 4.3 26.4 1.0 OD1 D:ASP267 4.3 36.1 1.0 O D:HOH4546 4.4 21.0 1.0 CG D:ASP267 4.4 19.5 1.0 CG D:ASP334 4.5 27.5 1.0 OD1 D:ASP334 4.6 34.7 1.0 O D:ASP302 4.6 34.8 1.0 CZ D:PHE336 4.6 82.2 1.0 CG D:HIS270 4.7 28.4 1.0 OG D:SER296 4.7 26.8 1.0 ZN D:ZN450 4.7 41.8 1.0 CE D:LYS236 4.8 25.2 1.0 C4 D:RNS4462 4.8 18.3 0.5 NZ D:LYS236 4.8 40.4 1.0 C3 D:RNS4462 4.9 19.3 0.5 ND1 D:HIS270 5.0 37.5 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