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

Enzymatic activity of Sulfolobus Solfataricus Glucose Dehydrogenase 1 - Apo Form

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

Protein crystallography data

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

Zinc Binding Sites:

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 2cd9

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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 2cd9

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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 2cd9

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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 2cd9

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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 2cd9

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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 2cd9

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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

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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