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Calcium in PDB 7v0h: Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product

Enzymatic activity of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product

All present enzymatic activity of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product:
1.1.1.47;

Protein crystallography data

The structure of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product, PDB code: 7v0h was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.08 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.72, 116.66, 180.62, 90, 90, 90
R / Rfree (%) 13.9 / 15.9

Other elements in 7v0h:

The structure of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product also contains other interesting chemical elements:

Sodium (Na) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product (pdb code 7v0h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product, PDB code: 7v0h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 7v0h

Go back to Calcium Binding Sites List in 7v0h
Calcium binding site 1 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:14.8
occ:0.69
 OD1 A:ASN248 2.3 17.3 1.0
O D:HOH458 2.3 21.6 1.0
O D:SER145 2.3 11.0 1.0
O D:HOH564 2.4 23.6 1.0
O A:HOH589 2.5 29.3 1.0
O D:HOH619 2.6 26.9 1.0
O A:HOH436 2.8 28.0 1.0
CG A:ASN248 3.5 16.8 1.0
C D:SER145 3.6 10.3 1.0
O A:HOH418 4.1 27.0 1.0
ND2 A:ASN248 4.2 13.8 1.0
O A:ASN248 4.2 12.6 1.0
O C:HOH442 4.3 14.7 1.0
C A:ASN248 4.3 13.9 1.0
CA D:ILE146 4.3 7.5 1.0
OXT A:ASN248 4.4 15.4 1.0
N D:ILE146 4.4 8.4 1.0
CA D:SER145 4.5 9.8 1.0
O D:HOH526 4.6 27.0 1.0
CB A:ASN248 4.6 13.7 1.0
OXT D:ASN248 4.7 16.5 1.0
O A:HOH586 4.8 23.0 1.0
C D:ILE146 4.9 9.2 1.0
OG1 D:THR147 4.9 8.7 1.0

Calcium binding site 2 out of 8 in 7v0h

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Calcium binding site 2 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:12.4
occ:0.65
 O C:SER145 2.3 11.6 1.0
O B:HOH615 2.3 25.5 1.0
O C:HOH455 2.3 22.2 1.0
OD1 B:ASN248 2.4 18.6 1.0
O C:HOH600 2.4 25.9 1.0
O C:HOH560 2.4 18.4 1.0
O B:HOH556 2.7 23.3 1.0
C C:SER145 3.6 7.8 1.0
CG B:ASN248 3.6 16.8 1.0
O B:HOH432 4.1 20.1 1.0
ND2 B:ASN248 4.2 14.2 1.0
O D:HOH459 4.3 11.3 1.0
O B:ASN248 4.3 13.6 1.0
OXT B:ASN248 4.3 16.0 1.0
C B:ASN248 4.3 14.2 1.0
CA C:ILE146 4.4 7.6 1.0
N C:ILE146 4.4 8.3 1.0
CA C:SER145 4.5 7.7 1.0
OXT C:ASN248 4.7 20.5 1.0
O C:HOH432 4.7 26.0 1.0
CB B:ASN248 4.7 13.4 1.0
C C:ILE146 4.9 9.1 1.0
OG1 C:THR147 4.9 9.7 1.0

Calcium binding site 3 out of 8 in 7v0h

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Calcium binding site 3 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:15.3
occ:0.62
 O B:HOH527 2.3 25.1 1.0
OD1 C:ASN248 2.3 21.9 1.0
O B:HOH449 2.4 20.9 1.0
O B:SER145 2.4 10.6 1.0
O C:HOH610 2.4 33.6 1.0
O B:HOH616 2.5 29.1 1.0
O C:HOH525 2.9 30.5 1.0
CG C:ASN248 3.5 21.9 1.0
C B:SER145 3.6 9.0 1.0
O B:HOH583 3.8 31.7 1.0
O C:HOH432 4.1 26.0 1.0
ND2 C:ASN248 4.2 17.0 1.0
O C:ASN248 4.3 17.3 1.0
O A:HOH427 4.3 13.2 1.0
OXT C:ASN248 4.4 20.5 1.0
CA B:ILE146 4.4 9.6 1.0
C C:ASN248 4.4 18.7 1.0
N B:ILE146 4.5 7.2 1.0
CA B:SER145 4.6 8.8 1.0
CB C:ASN248 4.7 17.3 1.0
OXT B:ASN248 4.7 16.0 1.0
OG1 B:THR147 4.9 10.2 1.0
C B:ILE146 4.9 9.5 1.0
O B:HOH412 4.9 37.4 1.0

Calcium binding site 4 out of 8 in 7v0h

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Calcium binding site 4 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:14.4
occ:0.66
 O A:HOH544 2.3 20.6 1.0
OD1 D:ASN248 2.3 19.7 1.0
O A:SER145 2.3 13.6 1.0
O A:HOH515 2.3 22.8 1.0
O A:HOH588 2.4 30.1 1.0
O D:HOH625 2.6 29.7 1.0
O D:HOH503 2.7 20.6 0.6
CG D:ASN248 3.5 17.5 1.0
C A:SER145 3.6 10.2 1.0
O D:HOH503 4.0 14.4 0.4
ND2 D:ASN248 4.2 15.7 1.0
O D:HOH469 4.2 27.4 1.0
O D:ASN248 4.2 12.6 1.0
O B:HOH463 4.2 14.8 1.0
C D:ASN248 4.3 11.7 1.0
CA A:ILE146 4.3 7.7 1.0
N A:ILE146 4.4 8.0 1.0
OXT D:ASN248 4.4 16.5 1.0
CA A:SER145 4.5 9.5 1.0
CB D:ASN248 4.7 13.8 1.0
O D:HOH604 4.7 18.5 1.0
OXT A:ASN248 4.8 15.4 1.0
OG1 A:THR147 4.9 10.1 1.0
C A:ILE146 4.9 9.5 1.0
O A:HOH418 5.0 27.0 1.0

Calcium binding site 5 out of 8 in 7v0h

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Calcium binding site 5 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca303

b:15.0
occ:0.73
 O H:SER145 2.3 11.9 1.0
O H:HOH513 2.3 23.5 1.0
OD1 E:ASN248 2.3 18.6 1.0
O H:HOH547 2.4 23.1 1.0
O E:HOH596 2.5 26.6 1.0
O E:HOH540 2.6 27.8 1.0
O H:HOH607 2.6 29.5 1.0
CG E:ASN248 3.5 16.4 1.0
C H:SER145 3.5 10.8 1.0
O E:HOH467 4.1 27.9 1.0
ND2 E:ASN248 4.2 11.6 1.0
O G:HOH451 4.3 14.9 1.0
O E:ASN248 4.3 14.5 1.0
CA H:ILE146 4.3 6.2 1.0
C E:ASN248 4.4 13.8 1.0
N H:ILE146 4.4 6.5 1.0
OXT E:ASN248 4.4 16.6 1.0
CA H:SER145 4.5 7.1 1.0
CB E:ASN248 4.7 13.1 1.0
OXT H:ASN248 4.8 16.4 1.0
C H:ILE146 4.8 7.8 1.0
OG1 H:THR147 4.9 9.2 1.0
O E:HOH587 4.9 22.1 1.0
O H:HOH456 5.0 26.4 1.0

Calcium binding site 6 out of 8 in 7v0h

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Calcium binding site 6 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


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 Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca307

b:14.7
occ:0.61
 OD1 H:ASN248 2.3 18.6 1.0
O E:HOH510 2.3 24.7 1.0
O E:SER145 2.3 11.6 1.0
O E:HOH590 2.4 28.3 1.0
O H:HOH612 2.4 26.2 1.0
O E:HOH473 2.5 25.9 1.0
O H:HOH524 2.7 29.5 1.0
CG H:ASN248 3.5 19.2 1.0
C E:SER145 3.6 10.1 1.0
ND2 H:ASN248 4.2 16.2 1.0
O F:HOH445 4.3 14.6 1.0
O H:ASN248 4.3 15.7 1.0
O H:HOH494 4.3 28.2 1.0
CA E:ILE146 4.3 6.7 1.0
C H:ASN248 4.3 14.4 1.0
OXT H:ASN248 4.4 16.4 1.0
N E:ILE146 4.4 8.5 1.0
CA E:SER145 4.5 8.7 1.0
O E:HOH522 4.6 30.6 1.0
CB H:ASN248 4.7 14.0 1.0
O H:HOH591 4.8 20.6 1.0
OXT E:ASN248 4.8 16.6 1.0
OG1 E:THR147 4.8 11.0 1.0
C E:ILE146 4.8 9.6 1.0

Calcium binding site 7 out of 8 in 7v0h

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Calcium binding site 7 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:12.6
occ:0.63
 O G:HOH586 2.2 24.3 1.0
O G:HOH528 2.3 24.8 1.0
O F:HOH615 2.3 28.0 1.0
O G:SER145 2.3 11.2 1.0
OD1 F:ASN248 2.4 18.7 1.0
O G:HOH560 2.4 23.3 1.0
O F:HOH509 2.7 25.0 1.0
CG F:ASN248 3.6 16.1 1.0
C G:SER145 3.6 8.8 1.0
O F:HOH484 4.1 22.6 1.0
ND2 F:ASN248 4.2 16.6 1.0
O H:HOH445 4.2 13.7 1.0
O F:ASN248 4.3 13.3 1.0
C F:ASN248 4.4 13.0 1.0
OXT F:ASN248 4.4 15.6 1.0
CA G:ILE146 4.4 9.4 1.0
N G:ILE146 4.5 8.6 1.0
CA G:SER145 4.5 7.8 1.0
CB F:ASN248 4.7 14.0 1.0
OXT G:ASN248 4.8 21.4 1.0
OG1 G:THR147 4.9 8.6 1.0
C G:ILE146 4.9 8.7 1.0

Calcium binding site 8 out of 8 in 7v0h

Go back to Calcium Binding Sites List in 7v0h
Calcium binding site 8 out of 8 in the Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca303

b:15.7
occ:0.58
 O F:HOH518 2.3 26.6 1.0
O F:HOH536 2.3 21.5 1.0
OD1 G:ASN248 2.3 23.1 1.0
O F:SER145 2.4 10.5 1.0
O F:HOH608 2.5 28.1 1.0
O G:HOH610 2.6 33.4 1.0
O G:HOH537 2.7 34.4 1.0
CG G:ASN248 3.5 21.6 1.0
C F:SER145 3.6 6.8 1.0
ND2 G:ASN248 4.1 21.1 1.0
O G:ASN248 4.3 18.8 1.0
O E:HOH452 4.3 15.3 1.0
CA F:ILE146 4.3 7.6 1.0
OXT G:ASN248 4.4 21.4 1.0
C G:ASN248 4.4 20.7 1.0
N F:ILE146 4.4 8.0 1.0
CA F:SER145 4.6 8.4 1.0
CB G:ASN248 4.7 20.2 1.0
OXT F:ASN248 4.8 15.6 1.0
C F:ILE146 4.9 8.7 1.0
OG1 F:THR147 4.9 10.1 1.0

Reference:

J.Abendroth, N.D.Debouwer, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Putative Glucose 1-Dehydrogenase From Burkholderia Cenocepacia in Complex with Nadp and A Potential Reaction Product To Be Published.
Page generated: Fri Jul 19 05:13:30 2024

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