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Calcium in PDB 1cru: Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine

Enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine

All present enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine:
1.1.99.17;

Protein crystallography data

The structure of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine, PDB code: 1cru was solved by A.Oubrie, H.J.Rozeboom, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.579, 92.658, 85.727, 90.00, 105.37, 90.00
R / Rfree (%) 17.4 / 19.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine (pdb code 1cru). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine, PDB code: 1cru:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1cru

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Calcium binding site 1 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:8.9
occ:1.00
 O A:ALA269 2.3 9.5 1.0
OD1 A:ASP273 2.3 9.0 1.0
O A:TYR271 2.3 10.1 1.0
O A:HOH663 2.4 10.3 1.0
OE2 A:GLU309 2.5 11.0 1.0
OE1 A:GLU309 2.5 9.9 1.0
O A:HOH632 2.6 10.4 1.0
CD A:GLU309 2.9 8.8 1.0
CG A:ASP273 3.3 9.0 1.0
C A:ALA269 3.5 8.8 1.0
C A:TYR271 3.5 9.0 1.0
OD2 A:ASP273 3.7 11.0 1.0
N A:TYR271 3.9 8.0 1.0
N A:ASP273 4.0 10.3 1.0
C A:GLY270 4.2 8.5 1.0
N A:ALA269 4.2 8.4 1.0
CA A:TYR271 4.3 8.0 1.0
OD2 A:ASP251 4.3 10.0 1.0
CA A:ALA269 4.4 8.8 1.0
O A:SER275 4.4 10.2 1.0
N A:GLY270 4.4 9.4 1.0
CG A:GLU309 4.4 9.4 1.0
CA A:GLY270 4.4 10.1 1.0
CB A:ASP273 4.5 10.2 1.0
OD1 A:ASP251 4.5 8.6 1.0
CG1 A:VAL268 4.5 9.7 1.0
N A:LYS272 4.6 8.9 1.0
CG A:ASP251 4.6 10.5 1.0
N A:ASP274 4.6 10.0 1.0
N A:SER275 4.6 10.5 1.0
CB A:ALA269 4.7 11.7 1.0
CA A:ASP273 4.7 12.0 1.0
CA A:LYS272 4.7 9.4 1.0
O A:GLY270 4.8 9.0 1.0
CB A:TYR271 4.8 7.5 1.0
C A:LYS272 4.9 11.8 1.0
CB A:TYR277 4.9 10.8 1.0
C A:ASP273 5.0 10.6 1.0

Calcium binding site 2 out of 6 in 1cru

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Calcium binding site 2 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:8.2
occ:1.00
 O A:HOH650 2.3 7.8 1.0
O A:HOH605 2.4 9.2 1.0
O A:TYR263 2.4 8.3 1.0
OE2 A:GLU253 2.4 11.4 1.0
O A:HOH640 2.4 12.0 1.0
O A:HOH601 2.5 8.7 1.0
OE1 A:GLU253 2.5 8.3 1.0
CD A:GLU253 2.8 8.1 1.0
C A:TYR263 3.5 7.7 1.0
CB A:TYR263 4.1 9.0 1.0
CA A:TYR263 4.2 8.7 1.0
O A:VAL268 4.3 10.4 1.0
CG A:GLU253 4.3 5.8 1.0
O A:HOH853 4.4 22.3 1.0
N A:GLY270 4.4 9.4 1.0
O A:GLY270 4.5 9.0 1.0
O A:GLY226 4.5 9.2 1.0
O A:HOH693 4.5 13.1 1.0
OE2 A:GLU245 4.6 11.1 1.0
OD1 A:ASN255 4.6 10.2 1.0
N A:GLY264 4.6 8.1 1.0
ND2 A:ASN255 4.6 10.3 1.0
N A:TRP265 4.7 10.4 1.0
CA A:GLY264 4.9 9.7 1.0
O A:VAL318 4.9 9.4 1.0
CA A:GLY270 4.9 10.1 1.0
CE1 A:PHE317 5.0 8.6 1.0

Calcium binding site 3 out of 6 in 1cru

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Calcium binding site 3 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:10.8
occ:1.00
 O A:HOH675 2.4 16.4 1.0
O7A A:PQQ504 2.4 9.4 1.0
O A:PRO248 2.4 10.7 1.0
O A:GLY247 2.4 10.4 1.0
O A:HOH615 2.4 10.5 1.0
N6 A:PQQ504 2.5 9.2 1.0
O5 A:PQQ504 2.5 9.8 1.0
C7X A:PQQ504 3.2 9.9 1.0
C7 A:PQQ504 3.3 8.9 1.0
C A:PRO248 3.4 9.7 1.0
C5 A:PQQ504 3.4 12.5 1.0
C6A A:PQQ504 3.4 11.6 1.0
C A:GLY247 3.5 11.3 1.0
CA A:PRO248 3.8 10.9 1.0
N2 A:HDN505 3.9 22.6 0.3
N1 A:HDN505 4.0 19.4 0.3
N A:PRO248 4.1 10.1 1.0
C1 A:HDN505 4.2 23.2 0.3
CG2 A:THR348 4.2 11.5 1.0
N1 A:HDN505 4.3 30.7 0.4
N1 A:HDN505 4.3 31.2 0.4
NH1 A:ARG228 4.3 12.6 1.0
NE2 A:GLN246 4.4 9.1 1.0
NH2 A:ARG228 4.4 13.4 1.0
O7B A:PQQ504 4.4 10.0 1.0
OD1 A:ASP252 4.5 11.5 1.0
OG1 A:THR348 4.5 12.1 1.0
O A:HOH685 4.6 17.5 1.0
CB A:THR348 4.6 9.8 1.0
N A:ASN249 4.6 10.5 1.0
CZ A:ARG228 4.6 12.1 1.0
C8 A:PQQ504 4.6 10.5 1.0
N A:GLY247 4.7 9.2 1.0
C4 A:PQQ504 4.7 11.8 1.0
CA A:GLY247 4.7 9.8 1.0
C9A A:PQQ504 4.8 10.2 1.0
N2 A:HDN505 4.8 31.9 0.4
CE3 A:TRP346 4.8 15.8 1.0
CZ3 A:TRP346 4.9 18.2 1.0
CA A:ASN249 5.0 10.0 1.0

Calcium binding site 4 out of 6 in 1cru

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Calcium binding site 4 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3002

b:7.9
occ:1.00
 O B:HOH3102 2.3 7.8 1.0
O B:HOH3140 2.4 11.7 1.0
O B:HOH3105 2.4 9.7 1.0
O B:TYR263 2.4 8.2 1.0
O B:HOH3124 2.4 8.5 1.0
OE2 B:GLU253 2.5 9.3 1.0
OE1 B:GLU253 2.5 6.9 1.0
CD B:GLU253 2.9 5.9 1.0
C B:TYR263 3.5 7.1 1.0
CB B:TYR263 4.0 7.5 1.0
CA B:TYR263 4.2 8.1 1.0
O B:VAL268 4.3 9.4 1.0
N B:GLY270 4.4 8.4 1.0
CG B:GLU253 4.4 5.9 1.0
O B:GLY270 4.5 8.1 1.0
O B:HOH3174 4.5 12.2 1.0
O B:GLY226 4.5 7.0 1.0
OD1 B:ASN255 4.6 10.2 1.0
N B:GLY264 4.6 7.1 1.0
OE2 B:GLU245 4.6 9.6 1.0
ND2 B:ASN255 4.7 9.9 1.0
N B:TRP265 4.7 8.1 1.0
O B:HOH3305 4.8 24.2 1.0
CA B:GLY264 4.8 7.9 1.0
CA B:GLY270 4.9 9.4 1.0
O B:VAL318 4.9 8.9 1.0
CE1 B:PHE317 4.9 8.4 1.0

Calcium binding site 5 out of 6 in 1cru

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Calcium binding site 5 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3003

b:8.3
occ:1.00
 O B:ALA269 2.3 7.9 1.0
O B:TYR271 2.3 9.5 1.0
O B:HOH3144 2.3 9.6 1.0
OD1 B:ASP273 2.4 7.9 1.0
OE2 B:GLU309 2.5 8.7 1.0
OE1 B:GLU309 2.5 7.9 1.0
O B:HOH3101 2.6 9.0 1.0
CD B:GLU309 2.9 7.8 1.0
CG B:ASP273 3.3 10.2 1.0
C B:ALA269 3.5 7.6 1.0
C B:TYR271 3.5 8.5 1.0
OD2 B:ASP273 3.8 10.7 1.0
N B:TYR271 3.8 7.1 1.0
N B:ASP273 4.0 9.1 1.0
C B:GLY270 4.1 6.5 1.0
CA B:TYR271 4.2 8.1 1.0
N B:ALA269 4.2 7.5 1.0
O B:SER275 4.3 10.2 1.0
CA B:ALA269 4.4 6.2 1.0
OD2 B:ASP251 4.4 9.5 1.0
N B:GLY270 4.4 8.4 1.0
CG B:GLU309 4.4 7.1 1.0
CA B:GLY270 4.4 9.4 1.0
CB B:ASP273 4.5 10.0 1.0
OD1 B:ASP251 4.5 8.8 1.0
N B:LYS272 4.5 9.1 1.0
CG1 B:VAL268 4.5 8.2 1.0
CG B:ASP251 4.6 10.5 1.0
N B:ASP274 4.6 9.5 1.0
N B:SER275 4.6 9.6 1.0
CB B:ALA269 4.7 10.2 1.0
CA B:ASP273 4.7 10.2 1.0
CA B:LYS272 4.7 8.1 1.0
O B:GLY270 4.7 8.1 1.0
CB B:TYR271 4.8 8.4 1.0
C B:LYS272 4.9 9.9 1.0
CB B:TYR277 4.9 8.9 1.0
C B:ASP273 5.0 10.2 1.0

Calcium binding site 6 out of 6 in 1cru

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Calcium binding site 6 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus in Complex with Pqq and Methylhydrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3004

b:10.2
occ:1.00
 O B:HOH3167 2.3 17.2 1.0
O B:PRO248 2.4 10.6 1.0
O7A B:PQQ3005 2.4 11.0 1.0
O B:GLY247 2.4 10.3 1.0
O B:HOH3108 2.4 10.1 1.0
N6 B:PQQ3005 2.5 11.0 1.0
O5 B:PQQ3005 2.5 13.7 1.0
C7X B:PQQ3005 3.2 11.3 1.0
C7 B:PQQ3005 3.3 10.7 1.0
C5 B:PQQ3005 3.4 13.6 1.0
C B:PRO248 3.4 9.5 1.0
C6A B:PQQ3005 3.5 11.7 1.0
C B:GLY247 3.5 10.2 1.0
N1 B:HDN3001 3.8 19.6 0.7
CA B:PRO248 3.8 9.6 1.0
N B:PRO248 4.1 8.8 1.0
N2 B:HDN3001 4.1 23.3 0.7
NH1 B:ARG228 4.3 11.5 1.0
CG2 B:THR348 4.3 10.8 1.0
C1 B:HDN3001 4.3 22.1 0.7
NE2 B:GLN246 4.3 8.3 1.0
NH2 B:ARG228 4.4 11.6 1.0
O7B B:PQQ3005 4.4 11.0 1.0
OD1 B:ASP252 4.5 11.1 1.0
OG1 B:THR348 4.5 11.4 1.0
CZ B:ARG228 4.6 10.4 1.0
CB B:THR348 4.6 9.2 1.0
C8 B:PQQ3005 4.6 11.8 1.0
N B:ASN249 4.6 9.1 1.0
O B:HOH3137 4.7 14.4 1.0
N B:GLY247 4.7 8.0 1.0
C4 B:PQQ3005 4.7 12.9 1.0
CA B:GLY247 4.8 7.8 1.0
C9A B:PQQ3005 4.8 11.0 1.0
CE3 B:TRP346 4.9 12.8 1.0
CA B:ASN249 5.0 9.3 1.0
CZ3 B:TRP346 5.0 14.3 1.0

Reference:

A.Oubrie, H.J.Rozeboom, B.W.Dijkstra. Active-Site Structure of the Soluble Quinoprotein Glucose Dehydrogenase Complexed with Methylhydrazine: A Covalent Cofactor-Inhibitor Complex. Proc.Natl.Acad.Sci.Usa V. 96 11787 1999.
ISSN: ISSN 0027-8424
PubMed: 10518528
DOI: 10.1073/PNAS.96.21.11787
Page generated: Sat Dec 12 02:52:00 2020

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