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

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

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

Protein crystallography data

The structure of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Xylose, PDB code: 2cdc 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 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.644, 91.032, 138.725, 90.00, 89.98, 90.00
R / Rfree (%) 20.4 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp and Xylose (pdb code 2cdc). 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 Xylose, PDB code: 2cdc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1371

b:10.2
occ:0.75
 O A:HOH2376 2.0 9.8 1.0
OE2 A:GLU67 2.0 14.2 1.0
NE2 A:HIS66 2.0 13.7 1.0
SG A:CYS39 2.3 14.4 1.0
CE1 A:HIS66 2.9 14.0 1.0
CB A:CYS39 3.0 12.9 1.0
CD A:GLU67 3.1 10.4 1.0
CD2 A:HIS66 3.1 13.1 1.0
O4A A:XYP1369 3.3 18.1 0.5
CG A:GLU67 3.5 9.7 1.0
OE1 A:GLN150 3.7 11.2 1.0
ND1 A:HIS66 4.0 13.4 1.0
O A:HOH2060 4.1 15.3 1.0
CG A:HIS66 4.1 12.4 1.0
O2 A:XYS1368 4.1 15.5 0.5
O2B A:XYP1369 4.1 15.5 0.5
OE1 A:GLU67 4.2 10.4 1.0
CA A:CYS39 4.3 12.2 1.0
N A:CYS39 4.4 11.6 1.0
O A:HOH2041 4.4 11.7 1.0
OD2 A:ASP42 4.5 13.7 1.0
C1 A:XYS1368 4.6 17.9 0.5
C1B A:XYP1369 4.6 17.9 0.5
C2 A:XYS1368 4.6 17.0 0.5
C2B A:XYP1369 4.6 17.0 0.5
CD A:GLN150 4.6 10.7 1.0
O A:HOH2039 4.6 30.8 1.0
NZ A:LYS360 4.7 11.0 1.0
O A:HOH2351 4.9 12.1 1.0
CB A:GLU67 5.0 10.7 1.0
NE2 A:GLN150 5.0 12.3 1.0

Zinc binding site 2 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1372

b:10.2
occ:1.00
 SG A:CYS99 2.3 11.0 1.0
SG A:CYS93 2.3 12.0 1.0
SG A:CYS96 2.4 11.1 1.0
SG A:CYS107 2.4 10.1 1.0
CB A:CYS99 3.3 10.3 1.0
CB A:CYS107 3.4 9.1 1.0
CB A:CYS93 3.4 12.8 1.0
CB A:CYS96 3.5 13.0 1.0
CA A:CYS107 3.6 9.8 1.0
OG1 A:THR109 3.9 15.1 1.0
N A:CYS93 3.9 12.4 1.0
N A:GLU108 3.9 11.6 1.0
N A:CYS96 4.1 13.5 1.0
CA A:CYS93 4.2 12.6 1.0
C A:CYS107 4.2 10.5 1.0
N A:CYS99 4.3 9.2 1.0
CA A:CYS96 4.3 11.7 1.0
CA A:CYS99 4.4 10.1 1.0
N A:THR109 4.4 13.8 1.0
CG2 A:THR109 4.7 15.7 1.0
O A:CYS96 4.7 11.8 1.0
CB A:THR109 4.8 13.8 1.0
C A:CYS96 4.8 11.9 1.0
C A:CYS93 4.9 12.8 1.0
N A:CYS107 4.9 9.1 1.0
N A:GLY94 5.0 13.7 1.0

Zinc binding site 3 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1371

b:10.9
occ:0.75
 O B:HOH2401 2.0 9.0 1.0
NE2 B:HIS66 2.0 14.6 1.0
OE2 B:GLU67 2.0 14.2 1.0
SG B:CYS39 2.2 15.6 1.0
CE1 B:HIS66 2.9 14.2 1.0
CD2 B:HIS66 3.0 13.8 1.0
CD B:GLU67 3.1 10.0 1.0
CB B:CYS39 3.1 14.0 1.0
CG B:GLU67 3.5 12.0 1.0
O4A B:XYP1369 3.5 24.8 1.0
OE1 B:GLN150 3.7 11.5 1.0
O B:HOH2100 4.0 14.3 1.0
ND1 B:HIS66 4.0 13.9 1.0
CG B:HIS66 4.1 12.0 1.0
OE1 B:GLU67 4.2 10.1 1.0
O2B B:XYP1369 4.2 18.1 1.0
CA B:CYS39 4.3 12.6 1.0
N B:CYS39 4.3 11.4 1.0
O B:HOH2077 4.5 12.6 1.0
OD2 B:ASP42 4.6 14.0 1.0
CD B:GLN150 4.6 11.0 1.0
NZ B:LYS360 4.7 12.5 1.0
C2B B:XYP1369 4.7 21.0 1.0
C1B B:XYP1369 4.7 21.7 1.0
O B:HOH2378 4.9 17.1 1.0
NE2 B:GLN150 5.0 11.5 1.0
CB B:GLU67 5.0 10.6 1.0

Zinc binding site 4 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1372

b:12.0
occ:1.00
 SG B:CYS93 2.3 13.3 1.0
SG B:CYS96 2.3 12.0 1.0
SG B:CYS99 2.4 11.4 1.0
SG B:CYS107 2.4 11.4 1.0
CB B:CYS99 3.3 11.9 1.0
CB B:CYS93 3.3 14.6 1.0
CB B:CYS107 3.3 10.3 1.0
CB B:CYS96 3.6 13.0 1.0
CA B:CYS107 3.6 10.6 1.0
N B:CYS93 3.9 13.7 1.0
OG1 B:THR109 3.9 15.5 1.0
N B:GLU108 4.0 12.4 1.0
N B:CYS96 4.1 15.2 1.0
CA B:CYS93 4.2 14.6 1.0
C B:CYS107 4.2 11.5 1.0
N B:CYS99 4.3 10.2 1.0
CA B:CYS96 4.3 13.2 1.0
CA B:CYS99 4.4 10.8 1.0
N B:THR109 4.4 14.4 1.0
CG2 B:THR109 4.6 15.7 1.0
CB B:THR109 4.8 15.0 1.0
O B:CYS96 4.8 12.7 1.0
C B:CYS93 4.8 15.0 1.0
C B:CYS96 4.8 12.7 1.0
N B:GLY94 4.9 15.8 1.0
N B:CYS107 4.9 9.6 1.0

Zinc binding site 5 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1371

b:10.9
occ:0.75
 O C:HOH2411 2.0 9.0 1.0
OE2 C:GLU67 2.0 14.1 1.0
NE2 C:HIS66 2.1 14.7 1.0
SG C:CYS39 2.2 14.8 1.0
CE1 C:HIS66 2.9 15.8 1.0
CD C:GLU67 3.0 10.6 1.0
CD2 C:HIS66 3.1 13.4 1.0
CB C:CYS39 3.1 12.8 1.0
CG C:GLU67 3.4 9.9 1.0
O4A C:XYP1369 3.5 18.4 1.0
OE1 C:GLN150 3.8 10.3 1.0
O C:HOH2089 4.0 12.3 1.0
ND1 C:HIS66 4.1 14.3 1.0
CG C:HIS66 4.1 13.4 1.0
OE1 C:GLU67 4.2 10.0 1.0
O2B C:XYP1369 4.2 16.1 1.0
CA C:CYS39 4.3 11.6 1.0
N C:CYS39 4.4 10.4 1.0
O C:HOH2060 4.4 13.7 1.0
OD2 C:ASP42 4.6 11.9 1.0
NZ C:LYS360 4.6 11.8 1.0
C1B C:XYP1369 4.7 20.0 1.0
C2B C:XYP1369 4.7 19.2 1.0
CD C:GLN150 4.7 10.1 1.0
CB C:GLU67 4.9 10.2 1.0
O C:HOH2389 4.9 17.8 1.0

Zinc binding site 6 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1372

b:10.8
occ:1.00
 SG C:CYS93 2.3 11.4 1.0
SG C:CYS99 2.4 9.5 1.0
SG C:CYS107 2.4 9.5 1.0
SG C:CYS96 2.4 10.2 1.0
CB C:CYS107 3.3 9.1 1.0
CB C:CYS99 3.3 9.9 1.0
CB C:CYS93 3.4 12.0 1.0
CB C:CYS96 3.6 11.4 1.0
CA C:CYS107 3.6 9.5 1.0
OG1 C:THR109 3.8 14.6 1.0
N C:CYS93 3.9 11.8 1.0
N C:GLU108 4.0 10.4 1.0
N C:CYS96 4.1 12.4 1.0
CA C:CYS93 4.2 12.2 1.0
C C:CYS107 4.2 9.6 1.0
N C:CYS99 4.3 9.7 1.0
CA C:CYS96 4.3 10.7 1.0
CA C:CYS99 4.4 9.7 1.0
N C:THR109 4.4 12.4 1.0
O C:CYS96 4.7 11.1 1.0
CG2 C:THR109 4.7 14.9 1.0
CB C:THR109 4.8 13.3 1.0
C C:CYS96 4.8 10.1 1.0
N C:CYS107 4.9 8.0 1.0
C C:CYS93 4.9 13.1 1.0
N C:GLY94 4.9 13.6 1.0
C C:GLY92 5.0 12.0 1.0

Zinc binding site 7 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1372

b:11.1
occ:0.75
 OE2 D:GLU67 2.0 13.7 1.0
O D:HOH2392 2.0 10.3 1.0
NE2 D:HIS66 2.0 13.4 1.0
SG D:CYS39 2.2 14.0 1.0
CE1 D:HIS66 2.9 12.5 1.0
CD D:GLU67 3.0 11.3 1.0
CD2 D:HIS66 3.0 12.7 1.0
CB D:CYS39 3.1 14.0 1.0
CG D:GLU67 3.5 9.6 1.0
O4A D:XYP1370 3.5 22.7 0.5
OE1 D:GLN150 3.7 9.8 1.0
O D:HOH2070 4.0 15.7 1.0
ND1 D:HIS66 4.0 12.2 1.0
CG D:HIS66 4.1 10.4 1.0
OE1 D:GLU67 4.1 11.8 1.0
O2 D:XYS1369 4.2 19.3 0.5
O2B D:XYP1370 4.2 19.3 0.5
CA D:CYS39 4.3 12.9 1.0
N D:CYS39 4.3 11.6 1.0
O D:HOH2043 4.5 12.3 1.0
OD2 D:ASP42 4.5 12.5 1.0
O D:HOH2388 4.6 31.5 1.0
NZ D:LYS360 4.7 11.1 1.0
C2 D:XYS1369 4.7 21.6 0.5
C2B D:XYP1370 4.7 21.6 0.5
CD D:GLN150 4.7 10.7 1.0
C1 D:XYS1369 4.7 22.3 0.5
C1B D:XYP1370 4.7 22.3 0.5
O D:HOH2372 4.8 15.4 1.0
CB D:GLU67 4.9 10.1 1.0
CB D:ALA41 4.9 13.4 1.0
C D:ILE38 5.0 10.6 1.0

Zinc binding site 8 out of 8 in 2cdc

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


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 Xylose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1373

b:11.6
occ:1.00
 SG D:CYS93 2.3 12.6 1.0
SG D:CYS99 2.3 11.0 1.0
SG D:CYS107 2.4 10.1 1.0
SG D:CYS96 2.4 10.4 1.0
CB D:CYS107 3.2 9.1 1.0
CB D:CYS99 3.3 9.4 1.0
CB D:CYS93 3.4 13.8 1.0
CB D:CYS96 3.6 13.2 1.0
CA D:CYS107 3.6 9.4 1.0
OG1 D:THR109 3.8 12.8 1.0
N D:CYS93 3.9 13.3 1.0
N D:GLU108 4.0 10.3 1.0
N D:CYS96 4.1 14.3 1.0
CA D:CYS93 4.2 13.8 1.0
C D:CYS107 4.3 9.9 1.0
N D:CYS99 4.3 9.5 1.0
CA D:CYS96 4.4 12.3 1.0
CA D:CYS99 4.4 9.3 1.0
N D:THR109 4.4 13.2 1.0
CG2 D:THR109 4.5 14.1 1.0
CB D:THR109 4.7 13.8 1.0
O D:CYS96 4.8 10.7 1.0
C D:CYS93 4.9 14.2 1.0
C D:CYS96 4.9 11.8 1.0
N D:CYS107 4.9 9.3 1.0
N D:GLY94 4.9 15.0 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 22:18:05 2024

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