Zinc in PDB 2cd9: Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form

All present enzymatic activity of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form:
1.1.1.47;

The structure of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form, PDB code: 2cd9 was solved by C.C.Milburn, H.J.Lamble, A.Theodossis, D.W.Hough, M.J.Danson, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	141.42 / 1.8
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.501, 90.310, 138.941, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 23

The binding sites of Zinc atom in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form (pdb code 2cd9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form, PDB code: 2cd9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1367 b:17.6 occ:0.70 ZN A:ZN1367 0.0 17.6 0.7 O A:HOH2315 0.3 16.8 0.9 OE2 A:GLU67 1.9 18.5 1.0 ZN A:ZN1367 1.9 14.7 0.1 O A:HOH2316 2.0 3.3 0.1 NE2 A:HIS66 2.1 17.2 1.0 SG A:CYS39 2.3 21.4 1.0 CE1 A:HIS66 2.9 18.8 1.0 CD A:GLU67 3.0 14.2 1.0 CD2 A:HIS66 3.1 17.7 1.0 CB A:CYS39 3.1 17.4 1.0 CG A:GLU67 3.4 13.6 1.0 NE2 A:GLN150 3.8 11.0 1.0 O A:HOH2314 3.9 23.6 1.0 ND1 A:HIS66 4.1 17.5 1.0 OE1 A:GLU67 4.1 15.4 1.0 CG A:HIS66 4.2 16.7 1.0 O A:HOH2042 4.2 43.8 1.0 CA A:CYS39 4.3 16.8 1.0 N A:CYS39 4.3 15.9 1.0 O A:HOH2044 4.4 13.2 1.0 O A:HOH2142 4.6 19.2 1.0 OD2 A:ASP42 4.6 14.4 1.0 O A:HOH2015 4.6 27.4 1.0 NZ A:LYS360 4.7 13.7 1.0 CD A:GLN150 4.7 15.0 1.0 O A:HOH2312 4.8 19.6 1.0 CB A:GLU67 4.9 12.8 1.0 OE1 A:GLN150 5.0 16.6 1.0 OG1 A:THR41 5.0 27.0 1.0

Zinc binding site 2 out of 6 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1367 b:14.7 occ:0.10 ZN A:ZN1367 0.0 14.7 0.1 O A:HOH2316 0.2 3.3 0.1 O A:HOH2315 1.9 16.8 0.9 ZN A:ZN1367 1.9 17.6 0.7 NE2 A:GLN150 2.4 11.0 1.0 OE2 A:GLU67 2.8 18.5 1.0 NE2 A:HIS66 2.9 17.2 1.0 O A:HOH2314 3.1 23.6 1.0 O A:HOH2142 3.1 19.2 1.0 CD A:GLN150 3.3 15.0 1.0 CD2 A:HIS66 3.3 17.7 1.0 OE1 A:GLN150 3.5 16.6 1.0 CD A:GLU67 3.6 14.2 1.0 SG A:CYS39 3.7 21.4 1.0 CG A:GLU67 3.8 13.6 1.0 O A:HOH2042 4.1 43.8 1.0 CE1 A:HIS66 4.2 18.8 1.0 CA A:PRO151 4.4 14.5 1.0 CB A:CYS39 4.5 17.4 1.0 CB A:PRO151 4.5 14.6 1.0 N A:PRO151 4.5 14.4 1.0 O A:HOH2015 4.6 27.4 1.0 O A:HOH2141 4.6 19.4 1.0 OE1 A:GLU67 4.6 15.4 1.0 CD A:PRO151 4.6 14.4 1.0 CG A:HIS66 4.7 16.7 1.0 CG A:GLN150 4.7 12.9 1.0 OD2 A:ASP154 4.7 18.4 1.0 O A:HOH2312 4.7 19.6 1.0 O A:HOH2090 4.8 35.1 1.0 C A:GLN150 5.0 13.4 1.0

Zinc binding site 3 out of 6 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1368 b:15.7 occ:1.00 SG A:CYS107 2.3 15.6 1.0 SG A:CYS99 2.3 14.7 1.0 SG A:CYS96 2.4 14.4 1.0 SG A:CYS93 2.4 17.1 1.0 CB A:CYS99 3.3 13.3 1.0 CB A:CYS107 3.3 13.7 1.0 CB A:CYS93 3.3 15.9 1.0 CB A:CYS96 3.5 14.0 1.0 CA A:CYS107 3.6 14.3 1.0 N A:CYS93 3.8 15.5 1.0 OG1 A:THR109 3.9 17.8 1.0 N A:GLU108 3.9 16.0 1.0 N A:CYS96 4.1 15.4 1.0 CA A:CYS93 4.2 16.5 1.0 C A:CYS107 4.2 15.3 1.0 N A:CYS99 4.3 12.6 1.0 CA A:CYS96 4.3 13.5 1.0 CA A:CYS99 4.4 14.1 1.0 N A:THR109 4.4 16.6 1.0 CG2 A:THR109 4.6 15.5 1.0 CB A:THR109 4.8 16.5 1.0 O A:CYS96 4.8 13.8 1.0 C A:CYS96 4.9 13.6 1.0 N A:CYS107 4.9 13.7 1.0 C A:CYS93 4.9 16.4 1.0

Zinc binding site 4 out of 6 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1367 b:16.1 occ:0.70 ZN B:ZN1367 0.0 16.1 0.7 O B:HOH2351 0.3 74.7 0.1 O B:HOH2352 2.0 24.5 0.9 OE2 B:GLU67 2.0 17.9 1.0 NE2 B:HIS66 2.0 17.1 1.0 ZN B:ZN1367 2.0 5.9 0.1 SG B:CYS39 2.4 19.2 1.0 CE1 B:HIS66 2.9 17.0 1.0 CD2 B:HIS66 3.0 16.2 1.0 CD B:GLU67 3.0 15.8 1.0 CB B:CYS39 3.1 16.9 1.0 CG B:GLU67 3.5 11.0 1.0 NE2 B:GLN150 3.7 11.1 1.0 O B:HOH2353 3.8 24.0 1.0 ND1 B:HIS66 4.0 16.0 1.0 CG B:HIS66 4.1 14.9 1.0 OE1 B:GLU67 4.1 15.0 1.0 CA B:CYS39 4.3 16.7 1.0 N B:CYS39 4.3 14.9 1.0 O B:HOH2050 4.3 39.9 1.0 O B:HOH2051 4.4 15.4 1.0 O B:HOH2178 4.5 22.4 1.0 O B:HOH2018 4.5 37.4 1.0 OD2 B:ASP42 4.6 13.5 1.0 CD B:GLN150 4.7 14.6 1.0 O B:HOH2347 4.8 17.0 1.0 NZ B:LYS360 4.8 16.1 1.0 CB B:GLU67 4.9 13.2 1.0 OE1 B:GLN150 5.0 18.0 1.0

Zinc binding site 5 out of 6 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1367 b:5.9 occ:0.10 ZN B:ZN1367 0.0 5.9 0.1 O B:HOH2352 0.6 24.5 0.9 O B:HOH2351 1.8 74.7 0.1 ZN B:ZN1367 2.0 16.1 0.7 O B:HOH2353 2.3 24.0 1.0 NE2 B:GLN150 2.7 11.1 1.0 OE2 B:GLU67 2.9 17.9 1.0 O B:HOH2178 3.2 22.4 1.0 NE2 B:HIS66 3.4 17.1 1.0 SG B:CYS39 3.6 19.2 1.0 CD B:GLN150 3.7 14.6 1.0 CD B:GLU67 3.8 15.8 1.0 CD2 B:HIS66 3.9 16.2 1.0 OE1 B:GLN150 3.9 18.0 1.0 O B:HOH2018 4.0 37.4 1.0 O B:HOH2175 4.1 19.3 1.0 CB B:PRO151 4.1 15.7 1.0 CB B:CYS39 4.1 16.9 1.0 CA B:PRO151 4.2 15.0 1.0 O B:HOH2347 4.2 17.0 1.0 CG B:GLU67 4.2 11.0 1.0 O B:HOH2050 4.2 39.9 1.0 OD2 B:ASP154 4.4 16.9 1.0 N B:PRO151 4.5 14.6 1.0 CE1 B:HIS66 4.6 17.0 1.0 CD B:PRO151 4.6 15.8 1.0 CG B:PRO151 4.8 15.8 1.0 OE1 B:GLU67 4.8 15.0 1.0

Zinc binding site 6 out of 6 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1368 b:15.8 occ:1.00 SG B:CYS99 2.3 14.1 1.0 SG B:CYS107 2.3 14.3 1.0 SG B:CYS96 2.4 12.7 1.0 SG B:CYS93 2.4 15.3 1.0 CB B:CYS107 3.3 13.2 1.0 CB B:CYS93 3.3 17.8 1.0 CB B:CYS99 3.3 13.6 1.0 CB B:CYS96 3.5 14.9 1.0 CA B:CYS107 3.6 13.6 1.0 OG1 B:THR109 3.8 16.7 1.0 N B:CYS93 3.9 15.8 1.0 N B:GLU108 3.9 15.0 1.0 N B:CYS96 4.1 16.7 1.0 C B:CYS107 4.2 14.6 1.0 CA B:CYS93 4.2 16.9 1.0 N B:CYS99 4.3 13.1 1.0 CA B:CYS96 4.3 14.2 1.0 CA B:CYS99 4.4 14.6 1.0 N B:THR109 4.4 16.3 1.0 CB B:THR109 4.8 16.7 1.0 O B:CYS96 4.8 11.4 1.0 CG2 B:THR109 4.8 16.9 1.0 C B:CYS96 4.8 13.5 1.0 C B:CYS93 4.9 17.5 1.0 N B:CYS107 4.9 12.9 1.0

C.C.Milburn, H.J.Lamble, A.Theodossis, S.D.Bull, D.W.Hough, M.J.Danson, G.L.Taylor. The Structural Basis of Substrate Promiscuity in Glucose Dehydrogenase From the Hyperthermophilic Archaeon Sulfolobus Solfataricus. J.Biol.Chem. V. 281 14796 2006.
ISSN: ISSN 0021-9258
PubMed: 16556607
DOI: 10.1074/JBC.M601334200