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

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

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

Protein crystallography data

The structure of Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp, PDB code: 2cda 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 / 2.28
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.620, 92.296, 138.264, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 2cda

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1368

b:35.1
occ:0.70
O A:HOH2075 1.8 2.9 1.0
NE2 A:HIS66 2.2 23.1 1.0
OE2 A:GLU67 2.2 19.2 1.0
SG A:CYS39 2.4 27.1 1.0
CE1 A:HIS66 2.9 22.4 1.0
CD2 A:HIS66 3.1 20.6 1.0
CB A:CYS39 3.2 20.2 1.0
CD A:GLU67 3.2 12.4 1.0
CG A:GLU67 3.6 11.1 1.0
OE1 A:GLN150 3.6 12.7 1.0
O A:HOH2014 3.8 23.5 1.0
ND1 A:HIS66 4.0 20.9 1.0
CG A:HIS66 4.1 19.1 1.0
OE1 A:GLU67 4.2 9.6 1.0
O A:HOH2029 4.3 9.6 1.0
CA A:CYS39 4.4 19.5 1.0
O A:HOH2008 4.5 18.7 1.0
N A:CYS39 4.5 17.6 1.0
CD A:GLN150 4.5 8.1 1.0
O A:HOH2010 4.6 27.1 1.0
O A:HOH2069 4.8 11.7 1.0
NZ A:LYS360 4.8 4.3 1.0
OD2 A:ASP42 4.9 14.4 1.0
NE2 A:GLN150 5.0 4.8 1.0

Zinc binding site 2 out of 4 in 2cda

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Zinc binding site 2 out of 4 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1369

b:21.3
occ:1.00
SG A:CYS107 2.3 17.0 1.0
SG A:CYS99 2.3 22.4 1.0
SG A:CYS96 2.4 19.6 1.0
SG A:CYS93 2.5 23.6 1.0
CB A:CYS93 3.3 21.4 1.0
CB A:CYS99 3.3 19.0 1.0
CB A:CYS107 3.4 17.5 1.0
CA A:CYS107 3.6 17.3 1.0
CB A:CYS96 3.6 20.7 1.0
N A:CYS93 3.8 19.5 1.0
N A:GLU108 3.9 20.3 1.0
OG1 A:THR109 3.9 21.1 1.0
N A:CYS96 4.1 21.8 1.0
CA A:CYS93 4.1 22.0 1.0
C A:CYS107 4.2 18.9 1.0
CA A:CYS96 4.4 21.1 1.0
N A:THR109 4.4 23.2 1.0
N A:CYS99 4.4 18.3 1.0
CA A:CYS99 4.4 19.9 1.0
CG2 A:THR109 4.6 21.8 1.0
CB A:THR109 4.8 22.3 1.0
C A:CYS93 4.8 22.5 1.0
O A:CYS96 4.9 21.7 1.0
N A:CYS107 4.9 15.9 1.0
C A:CYS96 5.0 20.8 1.0
C A:GLY92 5.0 18.5 1.0

Zinc binding site 3 out of 4 in 2cda

Go back to Zinc Binding Sites List in 2cda
Zinc binding site 3 out of 4 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1368

b:30.6
occ:0.70
O B:HOH2081 1.7 9.6 1.0
OE2 B:GLU67 1.9 20.5 1.0
NE2 B:HIS66 2.2 19.6 1.0
SG B:CYS39 2.5 23.5 1.0
CD B:GLU67 2.9 14.8 1.0
CD2 B:HIS66 3.0 17.3 1.0
OE1 B:GLN150 3.2 8.1 1.0
CG B:GLU67 3.2 11.6 1.0
CE1 B:HIS66 3.2 21.4 1.0
O B:HOH2080 3.5 17.6 1.0
CB B:CYS39 3.6 19.2 1.0
O B:HOH2031 3.6 26.6 1.0
OE1 B:GLU67 4.0 16.6 1.0
CD B:GLN150 4.1 6.1 1.0
CG B:HIS66 4.2 16.6 1.0
ND1 B:HIS66 4.2 20.9 1.0
NE2 B:GLN150 4.4 2.6 1.0
O B:HOH2010 4.6 15.1 1.0
O B:HOH2074 4.7 20.7 1.0
NZ B:LYS360 4.7 12.3 1.0
CB B:GLU67 4.8 12.9 1.0
CA B:CYS39 4.8 19.8 1.0
N B:CYS39 4.8 17.1 1.0

Zinc binding site 4 out of 4 in 2cda

Go back to Zinc Binding Sites List in 2cda
Zinc binding site 4 out of 4 in the Sulfolobus Solfataricus Glucose Dehydrogenase 1 in Complex with Nadp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1369

b:19.9
occ:1.00
SG B:CYS99 2.3 18.4 1.0
SG B:CYS107 2.3 15.5 1.0
SG B:CYS93 2.4 22.7 1.0
SG B:CYS96 2.5 18.0 1.0
CB B:CYS107 3.2 15.4 1.0
CB B:CYS93 3.3 19.9 1.0
CB B:CYS99 3.4 19.1 1.0
CA B:CYS107 3.6 16.4 1.0
CB B:CYS96 3.8 18.1 1.0
N B:CYS93 3.8 17.9 1.0
OG1 B:THR109 3.9 22.5 1.0
N B:GLU108 4.0 19.4 1.0
CA B:CYS93 4.1 20.6 1.0
N B:CYS96 4.2 20.6 1.0
C B:CYS107 4.2 17.9 1.0
N B:CYS99 4.4 18.0 1.0
N B:THR109 4.4 23.0 1.0
CA B:CYS96 4.5 18.9 1.0
CA B:CYS99 4.5 19.7 1.0
CG2 B:THR109 4.7 22.8 1.0
CB B:THR109 4.8 23.7 1.0
N B:CYS107 4.9 16.1 1.0
C B:CYS93 4.9 20.5 1.0
O B:CYS96 4.9 18.0 1.0
N B:GLY94 4.9 20.6 1.0
C B:CYS96 5.0 18.7 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 Dec 16 03:19:10 2020

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