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Zinc in PDB 2cdb: Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose

Enzymatic activity of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose

All present enzymatic activity of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose:
1.1.1.47;

Protein crystallography data

The structure of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose, PDB code: 2cdb 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) 138.68 / 1.6
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.672, 91.394, 138.433, 90.00, 90.03, 90.00
R / Rfree (%) 19 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose (pdb code 2cdb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose, PDB code: 2cdb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2cdb

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Zinc binding site 1 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


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 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1370

b:6.9
occ:0.75
 NE2 A:HIS66 2.0 11.2 1.0
O A:HOH2320 2.0 5.8 1.0
OE2 A:GLU67 2.1 14.1 1.0
SG A:CYS39 2.3 12.1 1.0
CE1 A:HIS66 2.9 11.3 1.0
CB A:CYS39 3.0 10.0 1.0
CD2 A:HIS66 3.0 11.4 1.0
CD A:GLU67 3.1 10.1 1.0
CG A:GLU67 3.4 10.5 1.0
O1 A:BGC1368 3.7 15.9 0.9
OE1 A:GLN150 3.8 9.7 1.0
ND1 A:HIS66 4.0 10.7 1.0
O A:HOH2046 4.0 11.9 1.0
CG A:HIS66 4.1 9.2 1.0
O2 A:BGC1368 4.2 9.2 0.9
OE1 A:GLU67 4.2 10.2 1.0
CA A:CYS39 4.3 9.2 1.0
O A:HOH2028 4.4 10.5 1.0
N A:CYS39 4.4 8.5 1.0
O A:HOH2027 4.5 25.8 1.0
OD2 A:ASP42 4.5 11.0 1.0
CD A:GLN150 4.7 10.5 1.0
C2 A:BGC1368 4.8 11.6 0.9
NZ A:LYS360 4.8 9.1 1.0
C1 A:BGC1368 4.8 13.7 0.9
O A:HOH2299 4.9 15.9 1.0
CB A:GLU67 4.9 8.2 1.0

Zinc binding site 2 out of 8 in 2cdb

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Zinc binding site 2 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


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 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1371

b:9.2
occ:1.00
 SG A:CYS93 2.3 9.2 1.0
SG A:CYS99 2.4 7.4 1.0
SG A:CYS96 2.4 8.4 1.0
SG A:CYS107 2.4 8.1 1.0
CB A:CYS107 3.3 7.7 1.0
CB A:CYS93 3.3 9.1 1.0
CB A:CYS99 3.3 7.9 1.0
CB A:CYS96 3.5 8.9 1.0
CA A:CYS107 3.6 7.8 1.0
OG1 A:THR109 3.8 11.7 1.0
N A:GLU108 3.9 8.2 0.5
N A:CYS93 3.9 8.9 1.0
N A:CYS96 4.1 10.2 1.0
CA A:CYS93 4.2 8.4 1.0
C A:CYS107 4.2 7.6 1.0
N A:CYS99 4.3 7.2 1.0
CA A:CYS96 4.3 8.4 1.0
CA A:CYS99 4.4 7.5 1.0
N A:THR109 4.4 8.6 1.0
CG2 A:THR109 4.6 10.0 1.0
CB A:THR109 4.7 9.8 1.0
O A:CYS96 4.7 8.8 1.0
C A:CYS96 4.9 8.1 1.0
C A:CYS93 4.9 8.7 1.0
N A:CYS107 4.9 7.0 1.0
N A:GLY94 5.0 9.0 1.0

Zinc binding site 3 out of 8 in 2cdb

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Zinc binding site 3 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


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 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1370

b:6.9
occ:0.75
 OE2 B:GLU67 1.9 9.7 1.0
NE2 B:HIS66 2.0 10.5 1.0
O B:HOH2291 2.0 7.0 1.0
SG B:CYS39 2.3 11.1 1.0
CE1 B:HIS66 2.9 8.9 1.0
CD B:GLU67 3.0 6.9 1.0
CD2 B:HIS66 3.1 11.1 1.0
CB B:CYS39 3.1 9.9 1.0
CG B:GLU67 3.4 8.4 1.0
O1 B:BGC1368 3.5 16.0 0.9
OE1 B:GLN150 3.7 9.0 1.0
O B:HOH2045 4.0 10.5 1.0
ND1 B:HIS66 4.0 8.9 1.0
OE1 B:GLU67 4.1 7.4 1.0
CG B:HIS66 4.1 9.7 1.0
O2 B:BGC1368 4.3 10.7 0.9
O B:HOH2282 4.3 26.1 1.0
CA B:CYS39 4.3 9.4 1.0
N B:CYS39 4.3 8.0 1.0
O B:HOH2035 4.5 9.3 1.0
OD2 B:ASP42 4.6 10.6 1.0
CD B:GLN150 4.6 9.9 1.0
NZ B:LYS360 4.7 7.5 1.0
C2 B:BGC1368 4.7 12.2 0.9
C1 B:BGC1368 4.7 13.8 0.9
CB B:ALA41 4.8 11.7 1.0
O B:HOH2274 4.9 14.3 1.0
CB B:GLU67 4.9 7.8 1.0
NE2 B:GLN150 5.0 11.5 1.0

Zinc binding site 4 out of 8 in 2cdb

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Zinc binding site 4 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


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 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1371

b:9.5
occ:1.00
 SG B:CYS93 2.3 10.5 1.0
SG B:CYS99 2.4 8.8 1.0
SG B:CYS96 2.4 9.4 1.0
SG B:CYS107 2.4 9.8 1.0
CB B:CYS99 3.3 9.0 1.0
CB B:CYS107 3.3 9.1 1.0
CB B:CYS93 3.3 11.5 1.0
CB B:CYS96 3.5 11.8 1.0
CA B:CYS107 3.6 8.0 1.0
OG1 B:THR109 3.8 13.5 1.0
N B:CYS93 3.9 11.3 1.0
N B:GLU108 3.9 9.7 1.0
N B:CYS96 4.1 13.1 1.0
CA B:CYS93 4.2 12.1 1.0
C B:CYS107 4.2 9.1 1.0
N B:CYS99 4.3 8.9 1.0
CA B:CYS96 4.3 11.2 1.0
CA B:CYS99 4.4 8.1 1.0
N B:THR109 4.4 12.1 1.0
CG2 B:THR109 4.7 12.4 1.0
O B:CYS96 4.8 10.5 1.0
CB B:THR109 4.8 12.9 1.0
C B:CYS96 4.8 10.3 1.0
C B:CYS93 4.9 12.3 1.0
N B:GLY94 4.9 12.6 1.0
N B:CYS107 4.9 8.1 1.0

Zinc binding site 5 out of 8 in 2cdb

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Zinc binding site 5 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


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 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1370

b:6.9
occ:0.75
 OE2 C:GLU67 2.0 11.5 1.0
NE2 C:HIS66 2.0 10.3 1.0
O C:HOH2323 2.0 7.9 1.0
SG C:CYS39 2.3 12.2 1.0
CE1 C:HIS66 2.9 9.6 1.0
CD2 C:HIS66 3.0 8.3 1.0
CD C:GLU67 3.0 7.6 1.0
CB C:CYS39 3.1 10.4 1.0
CG C:GLU67 3.4 8.2 1.0
O1 C:BGC1368 3.7 17.4 0.9
OE1 C:GLN150 3.8 8.1 1.0
O C:HOH2040 4.1 13.9 1.0
ND1 C:HIS66 4.1 8.8 1.0
CG C:HIS66 4.1 8.6 1.0
OE1 C:GLU67 4.2 9.8 1.0
O2 C:BGC1368 4.3 9.8 0.9
CA C:CYS39 4.3 9.2 1.0
O C:HOH2310 4.3 30.6 1.0
O C:HOH2028 4.4 10.0 1.0
N C:CYS39 4.4 8.6 1.0
OD2 C:ASP42 4.5 9.7 1.0
CD C:GLN150 4.7 7.8 1.0
C2 C:BGC1368 4.7 12.8 0.9
NZ C:LYS360 4.8 8.0 1.0
O C:HOH2306 4.8 12.1 1.0
C1 C:BGC1368 4.8 15.4 0.9
CB C:GLU67 4.9 8.6 1.0

Zinc binding site 6 out of 8 in 2cdb

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Zinc binding site 6 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


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 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1371

b:8.4
occ:1.00
 SG C:CYS99 2.3 7.7 1.0
SG C:CYS93 2.4 9.3 1.0
SG C:CYS96 2.4 9.0 1.0
SG C:CYS107 2.4 8.5 1.0
CB C:CYS99 3.2 7.7 1.0
CB C:CYS107 3.2 6.5 1.0
CB C:CYS93 3.4 10.5 1.0
CB C:CYS96 3.6 10.0 1.0
CA C:CYS107 3.6 7.8 1.0
OG1 C:THR109 3.9 10.1 1.0
N C:CYS93 3.9 9.9 1.0
N C:GLU108 4.0 8.9 1.0
N C:CYS96 4.1 9.7 1.0
CA C:CYS93 4.2 10.2 1.0
C C:CYS107 4.2 8.3 1.0
N C:CYS99 4.3 6.9 1.0
CA C:CYS99 4.3 7.5 1.0
CA C:CYS96 4.3 9.0 1.0
N C:THR109 4.4 9.8 1.0
CG2 C:THR109 4.6 10.6 1.0
O C:CYS96 4.7 8.5 1.0
CB C:THR109 4.7 9.5 1.0
C C:CYS96 4.8 8.8 1.0
N C:CYS107 4.9 7.0 1.0
C C:CYS93 4.9 10.9 1.0
N C:GLY94 4.9 11.1 1.0

Zinc binding site 7 out of 8 in 2cdb

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Zinc binding site 7 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1370

b:7.0
occ:0.75
 NE2 D:HIS66 2.0 10.3 1.0
OE2 D:GLU67 2.0 10.7 1.0
O D:HOH2342 2.1 8.7 1.0
SG D:CYS39 2.2 12.1 1.0
CE1 D:HIS66 2.9 10.7 1.0
CD2 D:HIS66 3.0 10.9 1.0
CD D:GLU67 3.0 7.8 1.0
CB D:CYS39 3.2 10.5 1.0
CG D:GLU67 3.4 7.5 1.0
O1 D:BGC1368 3.6 14.8 0.9
OE1 D:GLN150 3.8 9.7 1.0
ND1 D:HIS66 4.0 10.5 1.0
O D:HOH2060 4.0 11.8 1.0
CG D:HIS66 4.1 8.8 1.0
OE1 D:GLU67 4.2 8.0 1.0
O2 D:BGC1368 4.3 8.8 0.9
CA D:CYS39 4.3 10.2 1.0
N D:CYS39 4.3 9.1 1.0
O D:HOH2042 4.5 9.0 1.0
OD2 D:ASP42 4.5 9.3 1.0
CD D:GLN150 4.6 8.3 1.0
NZ D:LYS360 4.7 6.9 1.0
O D:HOH2046 4.7 39.3 1.0
C2 D:BGC1368 4.7 11.7 0.9
C1 D:BGC1368 4.8 13.2 0.9
O D:HOH2331 4.8 27.2 1.0
O D:HOH2328 4.8 12.8 1.0
CB D:GLU67 4.9 7.7 1.0
CB D:ALA41 4.9 11.7 1.0

Zinc binding site 8 out of 8 in 2cdb

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Zinc binding site 8 out of 8 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1371

b:10.0
occ:1.00
 SG D:CYS93 2.3 9.3 1.0
SG D:CYS96 2.3 7.6 1.0
SG D:CYS99 2.4 7.9 1.0
SG D:CYS107 2.4 8.2 1.0
CB D:CYS107 3.2 8.0 1.0
CB D:CYS99 3.2 7.9 1.0
CB D:CYS93 3.3 10.4 1.0
CB D:CYS96 3.5 10.1 1.0
CA D:CYS107 3.6 8.2 1.0
N D:CYS93 3.8 9.3 1.0
OG1 D:THR109 3.9 9.6 1.0
N D:GLU108 4.0 8.5 1.0
N D:CYS96 4.1 10.8 1.0
CA D:CYS93 4.2 10.1 1.0
C D:CYS107 4.2 8.8 1.0
N D:CYS99 4.3 7.0 1.0
CA D:CYS96 4.3 8.8 1.0
CA D:CYS99 4.3 7.5 1.0
N D:THR109 4.5 10.0 1.0
CG2 D:THR109 4.7 9.1 1.0
O D:CYS96 4.7 8.1 1.0
CB D:THR109 4.8 10.9 1.0
C D:CYS96 4.8 8.6 1.0
C D:CYS93 4.8 10.4 1.0
N D:CYS107 4.9 7.4 1.0
N D:GLY94 4.9 11.0 1.0
C D:GLY92 5.0 9.7 1.0

Reference:

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
Page generated: Wed Oct 16 22:17:40 2024

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