Sodium 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:

Calcium (Ca) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 10 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 7v0h

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Sodium binding site 1 out of 10 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 Sodium with other atoms in the Na 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:Na305

b:3.6
occ:0.58
 NA A:NA305 0.0 3.6 0.6
NA A:NA305 2.0 4.2 0.4
O A:HOH568 2.2 27.6 1.0
O C:HIS240 2.4 9.8 1.0
O C:HOH408 2.5 24.1 1.0
O C:HOH646 3.0 32.7 1.0
OE1 A:GLU239 3.0 16.2 1.0
C C:HIS240 3.5 5.7 1.0
O A:HIS240 4.1 9.8 1.0
CD A:GLU239 4.1 19.3 1.0
O A:HOH612 4.2 34.8 1.0
O C:HOH482 4.3 10.2 0.6
N C:HIS240 4.3 6.4 1.0
O A:HOH501 4.4 12.5 0.6
OE1 C:GLU239 4.4 16.1 1.0
CA C:HIS240 4.4 6.7 1.0
N C:LEU241 4.4 6.0 1.0
CA C:LEU241 4.4 5.4 1.0
O A:HOH401 4.5 26.2 1.0
CB C:HIS240 4.6 7.1 1.0
OE2 A:GLU239 4.6 19.4 1.0
N C:VAL242 4.7 6.6 1.0
O C:HOH605 4.7 11.9 0.5
CG2 C:VAL242 4.9 8.8 1.0

Sodium binding site 2 out of 10 in 7v0h

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Sodium binding site 2 out of 10 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 Sodium with other atoms in the Na 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
A:Na305

b:4.2
occ:0.43
 NA A:NA305 0.0 4.2 0.4
NA A:NA305 2.0 3.6 0.6
O A:HIS240 2.3 9.8 1.0
O A:HOH568 2.4 27.6 1.0
O C:HOH408 2.4 24.1 1.0
O A:HOH612 2.7 34.8 1.0
OE1 C:GLU239 3.2 16.1 1.0
C A:HIS240 3.5 6.6 1.0
O C:HIS240 4.1 9.8 1.0
OE1 A:GLU239 4.2 16.2 1.0
O A:HOH501 4.3 12.5 0.6
N A:HIS240 4.3 7.3 1.0
CD C:GLU239 4.3 13.2 1.0
O C:HOH646 4.3 32.7 1.0
CA A:HIS240 4.4 5.6 1.0
O C:HOH482 4.4 10.2 0.6
N A:LEU241 4.4 6.3 1.0
O C:HOH448 4.4 23.5 1.0
CA A:LEU241 4.5 7.2 1.0
CB A:HIS240 4.6 7.3 1.0
N A:VAL242 4.7 6.7 1.0
OE2 C:GLU239 4.8 14.7 1.0
O A:HOH625 4.8 22.7 1.0

Sodium binding site 3 out of 10 in 7v0h

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Sodium binding site 3 out of 10 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 Sodium with other atoms in the Na 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:Na304

b:4.2
occ:0.58
 NA B:NA304 0.0 4.2 0.6
NA B:NA304 1.9 4.7 0.4
O D:HOH659 2.4 11.9 0.3
O D:HIS240 2.4 9.6 1.0
O D:HOH534 2.4 26.8 1.0
O D:HOH404 2.5 18.6 1.0
OE1 B:GLU239 3.1 17.3 1.0
O D:HOH659 3.2 23.0 0.7
C D:HIS240 3.6 7.2 1.0
O B:HIS240 4.1 11.2 1.0
CD B:GLU239 4.2 16.2 1.0
O B:HOH633 4.3 31.9 1.0
O B:HOH483 4.3 15.9 1.0
OE1 D:GLU239 4.4 16.1 1.0
N D:HIS240 4.4 6.6 1.0
O D:HOH438 4.4 17.5 1.0
CA D:HIS240 4.4 5.3 1.0
N D:LEU241 4.5 5.8 1.0
CA D:LEU241 4.5 7.3 1.0
O B:HOH507 4.5 29.5 1.0
CB D:HIS240 4.6 6.1 1.0
O D:HOH651 4.6 21.8 1.0
N D:VAL242 4.7 6.2 1.0
OE2 B:GLU239 4.7 19.7 1.0
CG2 D:VAL242 5.0 7.9 1.0

Sodium binding site 4 out of 10 in 7v0h

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Sodium binding site 4 out of 10 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 Sodium with other atoms in the Na 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
B:Na304

b:4.7
occ:0.42
 NA B:NA304 0.0 4.7 0.4
NA B:NA304 1.9 4.2 0.6
O D:HOH534 2.2 26.8 1.0
O B:HIS240 2.4 11.2 1.0
O D:HOH404 2.4 18.6 1.0
O B:HOH633 2.8 31.9 1.0
OE1 D:GLU239 3.3 16.1 1.0
C B:HIS240 3.5 7.0 1.0
O D:HOH659 3.7 11.9 0.3
O D:HIS240 4.1 9.6 1.0
OE1 B:GLU239 4.2 17.3 1.0
O B:HOH483 4.2 15.9 1.0
N B:HIS240 4.3 6.6 1.0
CD D:GLU239 4.4 14.3 1.0
CA B:HIS240 4.4 5.5 1.0
N B:LEU241 4.4 5.7 1.0
O D:HOH413 4.4 24.2 1.0
CA B:LEU241 4.5 6.8 1.0
O D:HOH438 4.6 17.5 1.0
O D:HOH659 4.6 23.0 0.7
CB B:HIS240 4.6 6.3 1.0
N B:VAL242 4.7 6.1 1.0
O B:HOH636 4.7 23.5 1.0
OE2 D:GLU239 4.9 14.4 1.0

Sodium binding site 5 out of 10 in 7v0h

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Sodium binding site 5 out of 10 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 Sodium with other atoms in the Na 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
B:Na305

b:20.6
occ:1.00
 O B:HOH409 2.2 36.1 1.0
O B:HOH572 2.6 36.1 1.0
OE1 B:GLU106 4.3 32.2 1.0
OE2 B:GLU106 4.5 41.8 1.0
CD B:GLU106 4.8 29.3 1.0

Sodium binding site 6 out of 10 in 7v0h

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Sodium binding site 6 out of 10 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 Sodium with other atoms in the Na 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:Na306

b:4.3
occ:0.66
 NA E:NA306 0.0 4.3 0.7
NA E:NA306 2.0 4.0 0.3
O E:HOH483 2.3 27.6 1.0
O G:HIS240 2.4 9.5 1.0
O G:HOH406 2.5 21.5 1.0
OE2 E:GLU239 2.6 8.2 0.5
O E:HOH615 2.6 31.1 1.0
OE1 E:GLU239 2.8 11.1 0.5
CD E:GLU239 3.1 10.9 0.5
OE1 E:GLU239 3.3 11.5 0.5
C G:HIS240 3.5 7.2 1.0
O E:HIS240 4.1 11.3 1.0
O G:HOH445 4.3 16.9 1.0
O E:HOH613 4.3 32.5 1.0
N G:HIS240 4.3 8.8 1.0
OE1 G:GLU239 4.3 15.3 1.0
CA G:HIS240 4.4 6.4 1.0
CD E:GLU239 4.4 11.1 0.5
N G:LEU241 4.4 6.6 1.0
O E:HOH454 4.4 15.3 1.0
CA G:LEU241 4.5 6.0 1.0
CG E:GLU239 4.6 10.5 0.5
O E:HOH403 4.6 25.7 1.0
CB G:HIS240 4.6 6.6 1.0
N G:VAL242 4.7 6.1 1.0
O G:HOH636 4.7 24.2 1.0
OE2 E:GLU239 4.9 12.3 0.5
CG2 G:VAL242 5.0 9.8 1.0

Sodium binding site 7 out of 10 in 7v0h

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Sodium binding site 7 out of 10 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 Sodium with other atoms in the Na 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
E:Na306

b:4.0
occ:0.34
 NA E:NA306 0.0 4.0 0.3
NA E:NA306 2.0 4.3 0.7
O E:HOH483 2.2 27.6 1.0
O G:HOH406 2.4 21.5 1.0
O E:HIS240 2.4 11.3 1.0
O E:HOH613 2.7 32.5 1.0
OE1 E:GLU239 3.0 11.1 0.5
OE1 G:GLU239 3.2 15.3 1.0
C E:HIS240 3.6 7.9 1.0
CD E:GLU239 3.8 10.9 0.5
OE2 E:GLU239 3.9 8.2 0.5
O E:HOH615 4.0 31.1 1.0
O G:HIS240 4.1 9.5 1.0
O G:HOH447 4.1 21.6 1.0
O E:HOH454 4.3 15.3 1.0
CD G:GLU239 4.3 13.6 1.0
N E:HIS240 4.4 8.1 1.0
O G:HOH445 4.4 16.9 1.0
CA E:HIS240 4.4 6.8 1.0
N E:LEU241 4.5 6.0 1.0
OE1 E:GLU239 4.5 11.5 0.5
CA E:LEU241 4.5 8.1 1.0
CB E:HIS240 4.6 9.2 1.0
O E:HOH634 4.7 21.8 1.0
N E:VAL242 4.7 6.5 1.0
OE2 G:GLU239 4.8 17.2 1.0

Sodium binding site 8 out of 10 in 7v0h

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Sodium binding site 8 out of 10 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 Sodium with other atoms in the Na 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
F:Na305

b:3.5
occ:0.53
 NA F:NA305 0.0 3.5 0.5
NA F:NA305 2.0 5.1 0.5
O F:HOH486 2.1 26.5 1.0
O H:HIS240 2.4 11.0 1.0
O H:HOH406 2.5 18.9 1.0
OE2 F:GLU239 2.6 9.2 0.4
OE1 F:GLU239 2.7 9.4 0.4
O H:HOH639 3.0 31.9 1.0
CD F:GLU239 3.0 10.4 0.4
OE1 F:GLU239 3.3 10.8 0.6
C H:HIS240 3.5 8.1 1.0
O F:HIS240 4.1 9.6 1.0
OE1 H:GLU239 4.3 14.4 1.0
N H:HIS240 4.4 7.0 1.0
O F:HOH483 4.4 17.3 1.0
O F:HOH407 4.4 30.3 1.0
O F:HOH626 4.4 32.8 1.0
O H:HOH439 4.4 17.1 1.0
CA H:HIS240 4.4 7.1 1.0
CD F:GLU239 4.4 7.9 0.6
N H:LEU241 4.4 7.1 1.0
CA H:LEU241 4.5 6.9 1.0
CG F:GLU239 4.5 9.0 0.4
CB H:HIS240 4.6 6.4 1.0
N H:VAL242 4.6 7.7 1.0
O H:HOH647 4.7 25.0 1.0
OE2 F:GLU239 4.9 9.6 0.6
CG2 H:VAL242 5.0 8.4 1.0

Sodium binding site 9 out of 10 in 7v0h

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Sodium binding site 9 out of 10 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 Sodium with other atoms in the Na binding site number 9 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:Na305

b:5.1
occ:0.47
 NA F:NA305 0.0 5.1 0.5
NA F:NA305 2.0 3.5 0.5
O F:HOH486 2.2 26.5 1.0
O H:HOH406 2.4 18.9 1.0
O F:HIS240 2.4 9.6 1.0
O F:HOH626 2.7 32.8 1.0
OE1 F:GLU239 2.9 9.4 0.4
OE1 H:GLU239 3.2 14.4 1.0
C F:HIS240 3.6 7.6 1.0
CD F:GLU239 3.9 10.4 0.4
OE2 F:GLU239 4.0 9.2 0.4
O H:HIS240 4.1 11.0 1.0
O F:HOH483 4.2 17.3 1.0
CD H:GLU239 4.3 14.8 1.0
O H:HOH639 4.3 31.9 1.0
N F:HIS240 4.4 8.0 1.0
O H:HOH429 4.4 22.5 1.0
CA F:HIS240 4.4 5.8 1.0
O H:HOH439 4.5 17.1 1.0
N F:LEU241 4.5 5.8 1.0
CA F:LEU241 4.5 5.8 0.6
CA F:LEU241 4.5 5.8 0.4
OE1 F:GLU239 4.6 10.8 0.6
CB F:HIS240 4.6 6.3 1.0
O F:HOH633 4.7 21.7 1.0
N F:VAL242 4.7 6.6 1.0
OE2 H:GLU239 4.8 18.0 1.0
CD2 F:LEU241 5.0 8.8 0.4
CG2 F:VAL242 5.0 8.0 1.0

Sodium binding site 10 out of 10 in 7v0h

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Sodium binding site 10 out of 10 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 Sodium with other atoms in the Na binding site number 10 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:Na306

b:20.3
occ:1.00
 O F:HOH415 2.3 27.4 1.0
O F:HOH506 2.6 34.4 1.0
OE2 F:GLU106 4.4 28.6 1.0
OE1 F:GLU106 4.5 23.7 1.0
CD F:GLU106 4.9 21.8 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 Apr 7 16:41:29 2023

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