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Calcium in PDB 4ywe: Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia

Protein crystallography data

The structure of Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia, PDB code: 4ywe was solved by Seattle Structural 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) 19.95 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 85.320, 93.070, 139.430, 89.12, 78.55, 89.85
R / Rfree (%) 19.8 / 24.3

Other elements in 4ywe:

The structure of Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia (pdb code 4ywe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia, PDB code: 4ywe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 4ywe

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Calcium binding site 1 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:57.2
occ:1.00
 O A:HOH829 2.4 18.1 1.0
OD1 A:ASP91 2.5 30.2 1.0
O A:VAL24 2.5 26.1 1.0
O A:ASP91 2.5 25.9 1.0
O A:HOH814 2.5 25.3 1.0
O A:ASP177 2.6 19.9 1.0
C A:ASP91 3.5 24.6 1.0
C A:VAL24 3.6 29.9 1.0
CG A:ASP91 3.6 30.5 1.0
C A:ASP177 3.8 21.4 1.0
CA A:ASP91 3.8 24.4 1.0
N A:VAL24 3.8 28.9 1.0
O A:HOH750 3.8 34.8 1.0
CA A:VAL24 4.2 30.1 1.0
CD A:PRO26 4.3 26.7 1.0
CB A:ASP91 4.3 25.1 1.0
CG1 A:VAL23 4.3 30.7 1.0
CA A:ALA178 4.5 17.2 1.0
O A:HOH618 4.5 30.5 1.0
OD2 A:ASP91 4.5 32.1 1.0
CB A:ALA178 4.6 16.2 1.0
N A:ALA178 4.6 16.5 1.0
O A:HOH673 4.6 24.2 1.0
CD1 A:ILE324 4.6 26.2 1.0
N A:ASP25 4.6 25.9 1.0
N A:THR92 4.7 23.3 1.0
CA A:ASP177 4.7 22.0 1.0
CB A:VAL24 4.7 31.1 1.0
C A:VAL23 4.8 30.4 1.0
CA A:ASP25 5.0 23.5 1.0
O A:ARG90 5.0 27.9 1.0

Calcium binding site 2 out of 11 in 4ywe

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Calcium binding site 2 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:46.4
occ:1.00
 O B:ASP91 2.5 22.9 1.0
O B:ASP177 2.5 20.4 1.0
OD1 B:ASP91 2.5 32.0 1.0
O B:VAL24 2.5 22.1 1.0
O B:HOH756 2.6 14.2 1.0
O B:HOH735 2.7 34.3 1.0
C B:ASP91 3.4 20.3 1.0
CG B:ASP91 3.6 28.0 1.0
C B:VAL24 3.6 27.6 1.0
C B:ASP177 3.6 18.4 1.0
CA B:ASP91 3.8 21.0 1.0
N B:VAL24 3.9 29.1 1.0
O B:HOH726 4.2 27.4 1.0
CD B:PRO26 4.2 25.8 1.0
CA B:VAL24 4.3 29.4 1.0
CB B:ASP91 4.3 20.6 1.0
CG1 B:VAL23 4.3 22.2 1.0
CA B:ALA178 4.4 21.1 1.0
O B:HOH813 4.4 17.1 1.0
N B:ALA178 4.4 18.0 1.0
OD2 B:ASP91 4.5 24.0 1.0
CB B:ALA178 4.5 23.1 1.0
CA B:ASP177 4.6 21.8 1.0
CD1 B:ILE324 4.6 18.0 1.0
N B:THR92 4.7 20.0 1.0
N B:ASP25 4.7 26.6 1.0
O B:HOH661 4.8 33.0 1.0
CB B:VAL24 4.8 30.7 1.0
C B:VAL23 4.9 29.3 1.0
O B:HOH650 4.9 33.5 1.0
O B:ARG90 5.0 27.7 1.0
CA B:ASP25 5.0 27.8 1.0

Calcium binding site 3 out of 11 in 4ywe

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Calcium binding site 3 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:54.9
occ:1.00
 O C:VAL24 2.5 29.3 1.0
O C:ASP177 2.5 25.2 1.0
OD1 C:ASP91 2.5 32.3 1.0
O C:ASP91 2.5 25.8 1.0
O C:HOH755 2.5 17.4 1.0
O C:HOH854 2.6 34.6 1.0
C C:ASP91 3.5 25.8 1.0
C C:VAL24 3.6 31.2 1.0
CG C:ASP91 3.6 37.5 1.0
C C:ASP177 3.7 29.5 1.0
CA C:ASP91 3.8 31.9 1.0
N C:VAL24 3.8 35.9 1.0
CA C:VAL24 4.2 32.4 1.0
CD C:PRO26 4.3 29.1 1.0
CB C:ASP91 4.3 25.8 1.0
CG1 C:VAL23 4.4 37.7 1.0
CA C:ALA178 4.5 29.9 1.0
OD2 C:ASP91 4.5 36.9 1.0
O C:HOH624 4.5 45.9 1.0
N C:ALA178 4.5 30.3 1.0
CA C:ASP177 4.6 30.7 1.0
CB C:ALA178 4.6 28.7 1.0
N C:ASP25 4.6 29.9 1.0
CD1 C:ILE324 4.7 27.7 1.0
O C:HOH845 4.7 17.3 1.0
N C:THR92 4.7 25.5 1.0
CB C:VAL24 4.7 32.1 1.0
C C:VAL23 4.8 37.5 1.0
O C:ARG90 4.9 33.6 1.0
O C:HOH634 5.0 38.5 1.0
CA C:ASP25 5.0 29.7 1.0

Calcium binding site 4 out of 11 in 4ywe

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Calcium binding site 4 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:36.2
occ:1.00
 OD1 D:ASP338 2.5 35.0 1.0
OD2 D:ASP342 2.6 28.9 1.0
O D:HOH619 2.7 17.7 1.0
OD1 D:ASP342 3.3 24.9 1.0
CG D:ASP342 3.3 26.2 1.0
CG D:ASP338 3.4 29.0 1.0
OD2 D:ASP338 3.6 27.1 1.0
O D:HOH620 4.0 28.4 1.0
O D:ASP338 4.2 19.4 1.0
O D:HOH891 4.4 21.0 1.0
NE2 D:HIS375 4.6 22.2 1.0
CB D:ASP338 4.7 23.8 1.0
CB D:ASP342 4.8 22.5 1.0
C D:ASP338 4.9 19.0 1.0
O D:HOH919 4.9 35.5 1.0
CA D:ASP338 5.0 22.0 1.0

Calcium binding site 5 out of 11 in 4ywe

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Calcium binding site 5 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:44.2
occ:1.00
 O D:ASP91 2.4 22.5 1.0
O D:VAL24 2.5 25.7 1.0
O D:HOH744 2.5 18.8 1.0
O D:ASP177 2.6 19.2 1.0
OD1 D:ASP91 2.6 19.9 1.0
O D:HOH826 2.8 21.2 1.0
C D:ASP91 3.4 20.6 1.0
CG D:ASP91 3.6 22.6 1.0
C D:VAL24 3.6 34.0 1.0
C D:ASP177 3.7 23.9 1.0
CA D:ASP91 3.8 22.8 1.0
N D:VAL24 3.9 37.0 1.0
O D:HOH825 4.0 26.0 1.0
CD D:PRO26 4.2 29.7 1.0
CA D:VAL24 4.3 34.1 1.0
CB D:ASP91 4.3 22.5 1.0
CG1 D:VAL23 4.4 33.8 1.0
OD2 D:ASP91 4.4 26.1 1.0
O D:HOH801 4.5 19.9 1.0
CA D:ALA178 4.5 22.3 1.0
N D:ALA178 4.5 23.2 1.0
CD1 D:ILE324 4.6 18.6 1.0
O D:HOH609 4.6 38.0 1.0
CA D:ASP177 4.6 23.8 1.0
N D:THR92 4.6 18.0 1.0
CB D:ALA178 4.7 18.8 1.0
N D:ASP25 4.7 31.7 1.0
CB D:VAL24 4.7 32.7 1.0
C D:VAL23 4.8 36.0 1.0
O D:ARG90 5.0 27.6 1.0

Calcium binding site 6 out of 11 in 4ywe

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Calcium binding site 6 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca502

b:46.6
occ:1.00
 OD1 E:ASP91 2.4 25.8 1.0
O E:HOH672 2.4 16.6 1.0
O E:ASP177 2.5 30.4 1.0
O E:VAL24 2.5 34.9 1.0
O E:ASP91 2.5 25.5 1.0
O E:HOH836 2.5 21.2 1.0
C E:ASP91 3.5 25.5 1.0
CG E:ASP91 3.5 29.1 1.0
C E:VAL24 3.6 38.5 1.0
C E:ASP177 3.6 28.9 1.0
CA E:ASP91 3.8 28.1 1.0
N E:VAL24 3.9 36.7 1.0
CA E:VAL24 4.2 37.2 1.0
CD E:PRO26 4.3 34.8 1.0
CB E:ASP91 4.3 25.5 1.0
CG1 E:VAL23 4.3 37.3 1.0
OD2 E:ASP91 4.4 33.0 1.0
O E:HOH790 4.4 21.4 1.0
CA E:ALA178 4.5 32.2 1.0
N E:ALA178 4.5 31.4 1.0
CA E:ASP177 4.6 27.0 1.0
CD1 E:ILE324 4.6 30.9 1.0
CB E:ALA178 4.7 33.5 1.0
N E:ASP25 4.7 36.6 1.0
CB E:VAL24 4.7 39.9 1.0
O E:HOH634 4.7 29.7 1.0
N E:THR92 4.7 26.4 1.0
C E:VAL23 4.8 33.3 1.0
CA E:ASP25 5.0 37.0 1.0

Calcium binding site 7 out of 11 in 4ywe

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Calcium binding site 7 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca504

b:40.6
occ:1.00
 OD1 F:ASP338 2.4 38.1 1.0
O F:HOH613 2.6 50.4 1.0
OD2 F:ASP342 2.6 33.1 1.0
O F:HOH627 3.0 24.2 1.0
OD1 F:ASP342 3.1 34.3 1.0
O F:HOH602 3.2 36.3 1.0
CG F:ASP342 3.2 31.8 1.0
CG F:ASP338 3.4 35.6 1.0
OD2 F:ASP338 3.7 37.2 1.0
O F:ASP338 4.3 23.2 1.0
NE2 F:HIS375 4.7 21.6 1.0
CB F:ASP338 4.7 30.6 1.0
CB F:ASP342 4.7 29.9 1.0
O F:HOH824 4.8 15.2 1.0
C F:ASP338 4.9 22.6 1.0
CA F:ASP338 5.0 27.4 1.0

Calcium binding site 8 out of 11 in 4ywe

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Calcium binding site 8 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


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 A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca505

b:61.9
occ:1.00
 O F:VAL24 2.5 36.1 1.0
O F:ASP177 2.5 25.2 1.0
OD1 F:ASP91 2.5 26.8 1.0
O F:ASP91 2.6 21.4 1.0
O F:HOH819 2.7 36.6 1.0
O F:HOH778 2.8 39.3 1.0
C F:VAL24 3.6 39.3 1.0
C F:ASP177 3.6 22.9 1.0
C F:ASP91 3.6 20.9 1.0
CG F:ASP91 3.6 28.0 1.0
N F:VAL24 3.7 41.2 1.0
CA F:ASP91 3.9 30.8 1.0
CA F:VAL24 4.1 39.9 1.0
CG1 F:VAL23 4.1 30.8 1.0
O F:HOH842 4.4 24.6 1.0
CA F:ALA178 4.4 25.7 1.0
CD F:PRO26 4.4 28.3 1.0
O F:HOH706 4.4 23.8 1.0
CB F:ASP91 4.4 21.3 1.0
N F:ALA178 4.4 25.4 1.0
OD2 F:ASP91 4.5 30.6 1.0
CA F:ASP177 4.6 23.3 1.0
C F:VAL23 4.6 37.9 1.0
O F:HOH608 4.6 33.3 1.0
CB F:ALA178 4.6 23.4 1.0
CG F:PRO26 4.7 28.4 1.0
N F:ASP25 4.7 39.6 1.0
CB F:VAL24 4.7 40.6 1.0
CD1 F:ILE324 4.8 27.1 1.0
N F:THR92 4.8 20.1 1.0
CA F:VAL23 4.9 34.3 1.0

Calcium binding site 9 out of 11 in 4ywe

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Calcium binding site 9 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca506

b:39.5
occ:1.00
 O G:ASP177 2.4 24.6 1.0
O G:ASP91 2.4 18.9 1.0
O G:HOH796 2.5 27.1 1.0
OD1 G:ASP91 2.5 28.4 1.0
O G:VAL24 2.6 32.5 1.0
O G:HOH749 2.7 18.3 1.0
C G:ASP91 3.4 22.7 1.0
C G:ASP177 3.6 22.2 1.0
CG G:ASP91 3.6 26.7 1.0
C G:VAL24 3.7 30.4 1.0
CA G:ASP91 3.8 23.2 1.0
N G:VAL24 4.0 21.3 1.0
CD G:PRO26 4.2 20.6 1.0
CB G:ASP91 4.3 23.1 1.0
CB G:ALA178 4.3 20.2 1.0
CA G:ALA178 4.3 23.9 1.0
CA G:VAL24 4.4 29.7 1.0
CD1 G:ILE324 4.4 27.8 1.0
N G:ALA178 4.4 16.1 1.0
CG1 G:VAL23 4.5 27.1 1.0
OD2 G:ASP91 4.6 29.0 1.0
CA G:ASP177 4.6 16.6 1.0
N G:THR92 4.6 22.6 1.0
N G:ASP25 4.8 30.8 1.0
O G:HOH731 4.9 20.8 1.0
CB G:VAL24 4.9 31.1 1.0
O G:HOH622 4.9 25.1 1.0
CG G:PRO26 5.0 21.1 1.0
C G:VAL23 5.0 28.3 1.0
O G:ARG90 5.0 28.1 1.0

Calcium binding site 10 out of 11 in 4ywe

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Calcium binding site 10 out of 11 in the Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca507

b:70.7
occ:1.00
 O G:HIS242 2.4 10.3 1.0
O H:HOH919 2.4 10.4 1.0
O H:GLY452 2.5 19.8 1.0
O G:HOH760 2.8 22.8 1.0
O H:GLY455 2.9 20.3 1.0
N H:GLY452 3.3 19.4 1.0
C H:GLY452 3.3 19.5 1.0
CA H:GLY452 3.5 19.7 1.0
C G:HIS242 3.5 13.6 1.0
C H:GLY455 3.6 20.7 1.0
CB G:HIS242 3.9 17.3 1.0
O H:HOH932 3.9 62.9 1.0
C H:VAL451 4.0 16.1 1.0
CB H:HIS456 4.2 12.7 1.0
CA H:GLY455 4.2 13.4 1.0
CD G:PRO244 4.3 9.4 1.0
CA G:HIS242 4.4 13.8 1.0
CD2 H:HIS456 4.4 14.2 1.0
N H:GLY455 4.4 19.3 1.0
N H:HIS456 4.4 12.4 1.0
CA H:VAL451 4.5 14.7 1.0
N G:VAL243 4.5 14.3 1.0
O G:ASN241 4.5 20.9 1.0
O H:HOH913 4.6 29.8 1.0
N H:HIS453 4.6 23.1 1.0
CA G:VAL243 4.6 14.4 1.0
CG H:HIS456 4.7 13.2 1.0
CA H:HIS456 4.7 14.6 1.0
O H:VAL451 4.7 17.4 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), D.M.Dranow, D.Lorimer, T.E.Edwards. Crystal Structure of A Putative Aldehyde Dehydrogenase From Burkholderia Cenocepacia To Be Published.
Page generated: Sun Jul 14 15:16:15 2024

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