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Calcium in PDB 1qbi: Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus

Enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus

All present enzymatic activity of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus:
1.1.99.17;

Protein crystallography data

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

Resolution Low / High (Å) 20.00 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.148, 92.100, 84.910, 90.00, 105.17, 90.00
R / Rfree (%) 16.5 / 20.8

Other elements in 1qbi:

The structure of Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus also contains other interesting chemical elements:

Platinum (Pt) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus (pdb code 1qbi). 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, PDB code: 1qbi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1qbi

Go back to Calcium Binding Sites List in 1qbi
Calcium binding site 1 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca465

b:8.4
occ:1.00
O A:TYR271 2.3 8.2 1.0
OD1 A:ASP273 2.3 6.1 1.0
O A:ALA269 2.3 7.5 1.0
O A:HOH486 2.3 5.3 1.0
O A:HOH875 2.5 7.7 1.0
OE1 A:GLU309 2.5 11.7 1.0
OE2 A:GLU309 2.5 7.8 1.0
CD A:GLU309 2.9 11.9 1.0
CG A:ASP273 3.3 8.9 1.0
C A:TYR271 3.5 8.8 1.0
C A:ALA269 3.5 8.3 1.0
OD2 A:ASP273 3.7 7.9 1.0
N A:TYR271 3.8 8.7 1.0
N A:ASP273 3.9 7.8 1.0
C A:GLY270 4.1 7.0 1.0
CA A:TYR271 4.2 7.6 1.0
N A:ALA269 4.2 8.7 1.0
O A:SER275 4.3 7.5 1.0
CG A:GLU309 4.4 10.2 1.0
OD2 A:ASP251 4.4 7.1 1.0
CA A:ALA269 4.4 6.9 1.0
OD1 A:ASP251 4.4 9.3 1.0
CA A:GLY270 4.4 8.6 1.0
N A:GLY270 4.4 7.2 1.0
CB A:ASP273 4.5 6.7 1.0
CG A:ASP251 4.5 10.4 1.0
N A:LYS272 4.5 8.2 1.0
N A:ASP274 4.5 8.7 1.0
CG1 A:VAL268 4.5 7.8 1.0
N A:SER275 4.6 7.9 1.0
CA A:ASP273 4.6 9.0 1.0
CB A:ALA269 4.7 8.8 1.0
O A:GLY270 4.7 9.9 1.0
CA A:LYS272 4.7 10.2 1.0
CB A:TYR271 4.7 8.0 1.0
C A:LYS272 4.8 10.7 1.0
C A:ASP273 4.9 9.6 1.0
CB A:TYR277 4.9 9.6 1.0

Calcium binding site 2 out of 6 in 1qbi

Go back to Calcium Binding Sites List in 1qbi
Calcium binding site 2 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca466

b:7.3
occ:1.00
O A:TYR263 2.3 8.9 1.0
O A:HOH504 2.3 7.5 1.0
O A:HOH521 2.3 7.8 1.0
OE2 A:GLU253 2.4 8.8 1.0
O A:HOH487 2.4 8.7 1.0
O A:HOH500 2.4 9.1 1.0
OE1 A:GLU253 2.5 10.3 1.0
CD A:GLU253 2.8 11.0 1.0
C A:TYR263 3.5 8.6 1.0
CB A:TYR263 4.0 7.3 1.0
CA A:TYR263 4.1 8.2 1.0
O A:VAL268 4.2 10.1 1.0
N A:GLY270 4.3 7.2 1.0
CG A:GLU253 4.3 11.0 1.0
O A:GLY226 4.4 7.9 1.0
O A:HOH928 4.4 23.7 1.0
O A:GLY270 4.4 9.9 1.0
OE2 A:GLU245 4.5 11.9 1.0
O A:HOH499 4.5 11.2 1.0
N A:GLY264 4.5 7.8 1.0
OD1 A:ASN255 4.6 8.0 1.0
ND2 A:ASN255 4.6 7.7 1.0
N A:TRP265 4.7 7.4 1.0
O A:VAL318 4.8 9.1 1.0
CA A:GLY270 4.9 8.6 1.0
CD A:PRO320 4.9 6.5 1.0
CA A:GLY264 4.9 7.5 1.0
CE1 A:PHE317 4.9 6.6 1.0

Calcium binding site 3 out of 6 in 1qbi

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Calcium binding site 3 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca468

b:18.4
occ:1.00
O A:HOH664 2.3 14.5 1.0
O A:GLY247 2.4 9.0 1.0
O A:PRO248 2.4 7.4 1.0
O A:HOH672 2.4 17.7 1.0
O A:HOH520 2.4 10.0 1.0
O A:HOH870 2.6 26.1 1.0
C A:PRO248 3.4 7.9 1.0
C A:GLY247 3.5 8.9 1.0
CA A:PRO248 3.8 8.6 1.0
N A:PRO248 4.0 8.8 1.0
NH1 A:ARG228 4.1 10.9 1.0
CG2 A:THR348 4.2 11.7 1.0
NH2 A:ARG228 4.2 9.6 1.0
O A:HOH746 4.3 28.0 1.0
NE2 A:GLN246 4.3 11.2 1.0
OD1 A:ASP252 4.3 9.3 1.0
O A:HOH759 4.3 33.7 1.0
CZ A:ARG228 4.4 9.7 1.0
O A:HOH659 4.5 25.4 1.0
OG1 A:THR348 4.5 16.2 1.0
N A:GLY247 4.5 8.5 1.0
N A:ASN249 4.6 8.4 1.0
CB A:THR348 4.6 11.9 1.0
CA A:GLY247 4.7 8.2 1.0
O A:HOH709 4.7 22.4 1.0
CB A:GLN246 4.8 5.8 1.0
CE3 A:TRP346 4.9 19.6 1.0
CA A:ASN249 5.0 8.2 1.0

Calcium binding site 4 out of 6 in 1qbi

Go back to Calcium Binding Sites List in 1qbi
Calcium binding site 4 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca463

b:8.0
occ:1.00
O B:TYR263 2.2 6.1 1.0
O B:HOH470 2.3 6.4 1.0
O B:HOH473 2.3 6.0 1.0
O B:HOH493 2.4 4.7 1.0
O B:HOH483 2.4 6.0 1.0
OE2 B:GLU253 2.4 9.5 1.0
OE1 B:GLU253 2.5 8.1 1.0
CD B:GLU253 2.9 8.8 1.0
C B:TYR263 3.4 4.3 1.0
CB B:TYR263 4.0 5.4 1.0
CA B:TYR263 4.1 6.7 1.0
O B:VAL268 4.3 9.4 1.0
N B:GLY270 4.3 6.8 1.0
CG B:GLU253 4.4 5.3 1.0
O B:GLY226 4.4 7.5 1.0
O B:GLY270 4.4 7.5 1.0
N B:GLY264 4.5 6.1 1.0
O B:HOH600 4.5 19.9 1.0
OE2 B:GLU245 4.6 10.9 1.0
O B:HOH590 4.6 9.4 1.0
OD1 B:ASN255 4.6 7.8 1.0
N B:TRP265 4.6 6.6 1.0
ND2 B:ASN255 4.7 9.2 1.0
O B:VAL318 4.8 7.0 1.0
CA B:GLY264 4.8 6.7 1.0
CE1 B:PHE317 4.8 6.6 1.0
CA B:GLY270 4.9 5.3 1.0
CD2 B:TYR263 5.0 5.7 1.0
CD B:PRO320 5.0 6.8 1.0

Calcium binding site 5 out of 6 in 1qbi

Go back to Calcium Binding Sites List in 1qbi
Calcium binding site 5 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca464

b:7.9
occ:1.00
O B:ALA269 2.3 5.4 1.0
O B:HOH999 2.3 6.2 1.0
O B:TYR271 2.3 8.5 1.0
OD1 B:ASP273 2.3 4.8 1.0
OE2 B:GLU309 2.5 6.6 1.0
OE1 B:GLU309 2.5 9.4 1.0
O B:HOH480 2.5 5.4 1.0
CD B:GLU309 2.8 9.7 1.0
CG B:ASP273 3.3 10.4 1.0
C B:ALA269 3.5 8.2 1.0
C B:TYR271 3.5 6.8 1.0
OD2 B:ASP273 3.7 7.5 1.0
N B:TYR271 3.9 7.0 1.0
N B:ASP273 4.0 8.4 1.0
C B:GLY270 4.2 5.3 1.0
N B:ALA269 4.2 7.0 1.0
CA B:TYR271 4.3 6.3 1.0
O B:SER275 4.3 9.2 1.0
CG B:GLU309 4.3 6.7 1.0
CA B:ALA269 4.3 7.3 1.0
OD2 B:ASP251 4.3 7.0 1.0
N B:GLY270 4.4 6.8 1.0
CA B:GLY270 4.4 5.3 1.0
CB B:ASP273 4.5 9.3 1.0
N B:ASP274 4.5 8.0 1.0
CG1 B:VAL268 4.5 10.2 1.0
CG B:ASP251 4.6 8.0 1.0
N B:SER275 4.6 6.9 1.0
OD1 B:ASP251 4.6 7.4 1.0
N B:LYS272 4.6 6.8 1.0
CB B:ALA269 4.6 6.3 1.0
CA B:ASP273 4.7 9.2 1.0
O B:GLY270 4.7 7.5 1.0
CA B:LYS272 4.7 8.0 1.0
CB B:TYR271 4.8 8.1 1.0
CB B:TYR277 4.9 10.1 1.0
C B:LYS272 4.9 9.0 1.0
C B:ASP273 5.0 10.4 1.0

Calcium binding site 6 out of 6 in 1qbi

Go back to Calcium Binding Sites List in 1qbi
Calcium binding site 6 out of 6 in the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca467

b:17.5
occ:1.00
O B:HOH592 2.3 12.6 1.0
O B:PRO248 2.3 7.0 1.0
O B:GLY247 2.3 8.5 1.0
O B:HOH572 2.4 13.2 1.0
O B:HOH533 2.4 10.2 1.0
C B:PRO248 3.3 5.4 1.0
C B:GLY247 3.5 7.6 1.0
CA B:PRO248 3.7 6.0 1.0
O B:HOH634 3.9 28.1 1.0
O B:HOH567 3.9 31.0 1.0
N B:PRO248 4.0 7.1 1.0
NH1 B:ARG228 4.1 8.5 1.0
O B:HOH729 4.1 32.5 1.0
NH2 B:ARG228 4.1 8.6 1.0
CG2 B:THR348 4.2 11.9 1.0
NE2 B:GLN246 4.3 9.1 1.0
OD1 B:ASP252 4.4 7.0 1.0
CZ B:ARG228 4.4 8.7 1.0
OG1 B:THR348 4.5 14.8 1.0
N B:ASN249 4.5 6.4 1.0
CB B:THR348 4.6 10.4 1.0
N B:GLY247 4.6 7.2 1.0
O B:HOH539 4.6 14.6 1.0
CA B:GLY247 4.7 7.2 1.0
O B:HOH608 4.8 18.0 1.0
CB B:GLN246 4.8 7.8 1.0
CA B:ASN249 4.9 6.5 1.0

Reference:

A.Oubrie, H.J.Rozeboom, K.H.Kalk, J.A.Duine, B.W.Dijkstra. The 1.7 A Crystal Structure of the Apo Form of the Soluble Quinoprotein Glucose Dehydrogenase From Acinetobacter Calcoaceticus Reveals A Novel Internal Conserved Sequence Repeat. J.Mol.Biol. V. 289 319 1999.
ISSN: ISSN 0022-2836
PubMed: 10366508
DOI: 10.1006/JMBI.1999.2766
Page generated: Wed Oct 28 07:21:54 2020

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