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Calcium in PDB 1c9u: Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq

Enzymatic activity of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq

All present enzymatic activity of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq:
1.1.99.17;

Protein crystallography data

The structure of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq, PDB code: 1c9u 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 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.590, 158.720, 221.390, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 28.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq (pdb code 1c9u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq, PDB code: 1c9u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1c9u

Go back to Calcium Binding Sites List in 1c9u
Calcium binding site 1 out of 6 in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:23.1
occ:1.00
 O A:ALA269 2.3 17.6 1.0
O A:HOH1056 2.4 18.1 1.0
O A:TYR271 2.4 18.7 1.0
O A:HOH1020 2.6 19.9 1.0
OE2 A:GLU309 2.6 26.9 1.0
OD1 A:ASP273 2.6 19.0 1.0
OE1 A:GLU309 2.9 30.6 1.0
CD A:GLU309 3.1 26.5 1.0
C A:ALA269 3.5 15.9 1.0
CG A:ASP273 3.5 20.1 1.0
C A:TYR271 3.6 15.0 1.0
N A:TYR271 3.8 16.3 1.0
OD2 A:ASP273 3.9 19.0 1.0
OD2 A:ASP251 3.9 17.7 1.0
C A:GLY270 4.1 15.9 1.0
N A:ASP273 4.1 18.6 1.0
N A:ALA269 4.3 16.6 1.0
CA A:TYR271 4.3 11.9 1.0
CG A:ASP251 4.3 20.4 1.0
CA A:GLY270 4.3 15.5 1.0
N A:GLY270 4.3 16.3 1.0
OD1 A:ASP251 4.4 20.2 1.0
O A:SER275 4.4 25.8 1.0
CA A:ALA269 4.4 16.2 1.0
CG1 A:VAL268 4.5 12.8 1.0
N A:SER275 4.5 18.3 1.0
N A:ASP274 4.6 17.0 1.0
CG A:GLU309 4.6 25.8 1.0
N A:LYS272 4.7 16.7 1.0
O A:GLY270 4.7 17.0 1.0
CB A:ALA269 4.8 17.7 1.0
CB A:ASP273 4.8 16.8 1.0
CA A:LYS272 4.8 13.9 1.0
CA A:ASP273 4.9 15.3 1.0
CB A:TYR271 4.9 14.9 1.0

Calcium binding site 2 out of 6 in 1c9u

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Calcium binding site 2 out of 6 in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:15.8
occ:1.00
 O A:HOH1082 2.4 26.1 1.0
OE2 A:GLU253 2.5 21.1 1.0
O A:TYR263 2.5 16.4 1.0
O A:HOH1215 2.5 22.2 1.0
O A:HOH1042 2.6 20.4 1.0
OE1 A:GLU253 2.6 20.9 1.0
O A:HOH1018 2.7 17.1 1.0
CD A:GLU253 2.9 18.7 1.0
C A:TYR263 3.7 9.8 1.0
O A:VAL268 4.0 19.1 1.0
CB A:TYR263 4.2 7.7 1.0
N A:GLY270 4.2 16.3 1.0
CA A:TYR263 4.4 8.8 1.0
O A:GLY270 4.4 17.0 1.0
CG A:GLU253 4.4 19.4 1.0
O A:GLY226 4.5 21.9 1.0
O A:HOH1050 4.6 19.5 1.0
OD1 A:ASN255 4.7 13.2 1.0
OE2 A:GLU245 4.7 17.6 1.0
N A:GLY264 4.7 11.5 1.0
N A:TRP265 4.7 15.9 1.0
ND2 A:ASN255 4.7 15.8 1.0
CE1 A:PHE317 4.8 17.9 1.0
CA A:GLY270 4.8 15.5 1.0
O A:VAL318 4.9 18.1 1.0
CA A:GLY264 4.9 9.9 1.0
O A:HOH1067 5.0 32.3 1.0

Calcium binding site 3 out of 6 in 1c9u

Go back to Calcium Binding Sites List in 1c9u
Calcium binding site 3 out of 6 in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:19.5
occ:1.00
 O7A A:PQQ1004 2.3 30.9 1.0
O A:GLY247 2.5 23.5 1.0
O A:PRO248 2.5 21.2 1.0
O A:HOH1049 2.5 13.9 1.0
O A:HOH1198 2.6 31.2 1.0
N6 A:PQQ1004 2.6 35.8 1.0
O5 A:PQQ1004 2.6 32.5 1.0
C7X A:PQQ1004 3.2 32.4 1.0
C7 A:PQQ1004 3.4 33.1 1.0
C5 A:PQQ1004 3.5 34.6 1.0
C A:PRO248 3.6 19.6 1.0
C6A A:PQQ1004 3.6 35.2 1.0
C A:GLY247 3.6 21.3 1.0
NH1 A:ARG228 4.0 15.1 1.0
NH2 A:ARG228 4.0 21.0 1.0
CA A:PRO248 4.1 19.3 1.0
CG2 A:THR348 4.2 19.8 1.0
CZ A:ARG228 4.2 21.4 1.0
N A:PRO248 4.3 19.0 1.0
OD1 A:ASP252 4.3 21.6 1.0
OG1 A:THR348 4.4 23.7 1.0
O7B A:PQQ1004 4.4 35.2 1.0
NE2 A:GLN246 4.5 18.1 1.0
O3 A:GOL1005 4.5 43.2 1.0
CB A:THR348 4.5 19.1 1.0
N A:GLY247 4.6 21.0 1.0
N A:ASN249 4.7 18.7 1.0
C8 A:PQQ1004 4.7 34.8 1.0
CA A:GLY247 4.8 22.5 1.0
C4 A:PQQ1004 4.8 33.7 1.0
CB A:GLN246 4.9 19.7 1.0
O A:HOH1144 4.9 33.0 1.0
C9A A:PQQ1004 4.9 34.2 1.0
CE3 A:TRP346 4.9 21.6 1.0
C A:GLN246 5.0 22.2 1.0

Calcium binding site 4 out of 6 in 1c9u

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Calcium binding site 4 out of 6 in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:12.8
occ:1.00
 O B:TYR271 2.4 14.7 1.0
O B:HOH1028 2.4 13.9 1.0
OD1 B:ASP273 2.5 17.2 1.0
O B:ALA269 2.5 17.3 1.0
O B:HOH1030 2.5 12.0 1.0
OE1 B:GLU309 2.6 22.9 1.0
OE2 B:GLU309 2.7 20.5 1.0
CD B:GLU309 3.0 22.5 1.0
CG B:ASP273 3.2 13.0 1.0
OD2 B:ASP273 3.5 18.7 1.0
C B:TYR271 3.6 11.9 1.0
C B:ALA269 3.7 16.2 1.0
N B:ASP273 3.9 15.3 1.0
N B:TYR271 4.0 15.0 1.0
OD2 B:ASP251 4.2 17.5 1.0
C B:GLY270 4.2 16.9 1.0
O B:SER275 4.3 19.4 1.0
N B:ALA269 4.3 18.3 1.0
N B:ASP274 4.3 17.9 1.0
CA B:TYR271 4.3 12.2 1.0
CG1 B:VAL268 4.4 11.3 1.0
CB B:ASP273 4.5 10.2 1.0
N B:SER275 4.5 15.3 1.0
CG B:GLU309 4.5 21.9 1.0
CA B:ALA269 4.5 17.4 1.0
N B:GLY270 4.6 12.6 1.0
N B:LYS272 4.6 13.1 1.0
CA B:GLY270 4.6 13.7 1.0
CA B:ASP273 4.6 17.9 1.0
CG B:ASP251 4.6 17.5 1.0
CA B:LYS272 4.7 13.4 1.0
O B:GLY270 4.7 20.9 1.0
OD1 B:ASP251 4.8 22.3 1.0
C B:ASP273 4.8 21.0 1.0
C B:LYS272 4.8 15.4 1.0
CB B:ALA269 4.9 23.3 1.0
CB B:TYR271 5.0 14.5 1.0

Calcium binding site 5 out of 6 in 1c9u

Go back to Calcium Binding Sites List in 1c9u
Calcium binding site 5 out of 6 in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:21.5
occ:1.00
 O B:HOH1040 2.4 15.9 1.0
OE1 B:GLU253 2.5 15.4 1.0
OE2 B:GLU253 2.5 18.9 1.0
O B:TYR263 2.5 22.8 1.0
O B:HOH1027 2.6 6.2 1.0
O B:HOH1051 2.6 21.1 1.0
CD B:GLU253 2.8 17.6 1.0
C B:TYR263 3.6 20.1 1.0
CB B:TYR263 4.0 17.4 1.0
O B:VAL268 4.2 19.6 1.0
CA B:TYR263 4.2 18.7 1.0
CG B:GLU253 4.4 12.9 1.0
O B:GLY226 4.4 12.8 1.0
N B:GLY270 4.5 12.6 1.0
O B:HOH1134 4.5 20.7 1.0
OE2 B:GLU245 4.5 7.9 1.0
OD1 B:ASN255 4.6 15.5 1.0
ND2 B:ASN255 4.6 15.7 1.0
O B:GLY270 4.7 20.9 1.0
N B:TRP265 4.7 20.4 1.0
OE1 B:GLU245 4.7 14.9 1.0
N B:GLY264 4.8 15.4 1.0
O B:HOH1172 4.8 17.4 1.0
CD B:GLU245 4.9 6.0 1.0
CD2 B:TYR263 4.9 16.1 1.0
CG B:ASN255 5.0 10.4 1.0
CG B:TYR263 5.0 11.6 1.0

Calcium binding site 6 out of 6 in 1c9u

Go back to Calcium Binding Sites List in 1c9u
Calcium binding site 6 out of 6 in the Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Soluble Quinoprotein Glucose Dehydrogenase in Complex with Pqq within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:23.1
occ:1.00
 O B:HOH1066 2.4 17.0 1.0
O B:HOH1297 2.4 26.3 1.0
O7A B:PQQ1004 2.5 31.8 1.0
O5 B:PQQ1004 2.6 23.9 1.0
O B:GLY247 2.6 20.6 1.0
O B:PRO248 2.6 20.2 1.0
N6 B:PQQ1004 2.6 32.0 1.0
C7X B:PQQ1004 3.4 33.0 1.0
C5 B:PQQ1004 3.4 27.2 1.0
C7 B:PQQ1004 3.5 34.6 1.0
C6A B:PQQ1004 3.5 31.1 1.0
C B:PRO248 3.7 21.1 1.0
C B:GLY247 3.8 16.3 1.0
CG2 B:THR348 4.1 16.2 1.0
NH2 B:ARG228 4.1 14.6 1.0
CA B:PRO248 4.2 17.0 1.0
NE2 B:GLN246 4.3 12.5 1.0
OD1 B:ASP252 4.3 20.7 1.0
NH1 B:ARG228 4.3 21.2 1.0
O B:HOH1246 4.4 22.8 1.0
O B:HOH1093 4.4 23.4 1.0
CZ B:ARG228 4.4 15.3 1.0
N B:PRO248 4.4 17.1 1.0
OG1 B:THR348 4.5 23.2 1.0
CB B:THR348 4.5 22.1 1.0
O7B B:PQQ1004 4.6 35.4 1.0
N B:GLY247 4.6 14.0 1.0
C4 B:PQQ1004 4.7 28.9 1.0
C8 B:PQQ1004 4.8 32.3 1.0
N B:ASN249 4.8 21.1 1.0
CA B:GLY247 4.8 15.2 1.0
C9A B:PQQ1004 4.9 30.6 1.0
CB B:GLN246 5.0 12.8 1.0

Reference:

A.Oubrie, H.J.Rozeboom, K.H.Kalk, A.J.Olsthoorn, J.A.Duine, B.W.Dijkstra. Structure and Mechanism of Soluble Quinoprotein Glucose Dehydrogenase. Embo J. V. 18 5187 1999.
ISSN: ISSN 0261-4189
PubMed: 10508152
DOI: 10.1093/EMBOJ/18.19.5187
Page generated: Thu Jul 11 06:53:52 2024

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