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Sodium in PDB 3iwk: Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)

Enzymatic activity of Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)

All present enzymatic activity of Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1):
1.2.1.19;

Protein crystallography data

The structure of Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1), PDB code: 3iwk was solved by D.Kopecny, S.Morera, P.Briozzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.84 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.410, 216.870, 205.760, 90.00, 98.02, 90.00
R / Rfree (%) 20 / 24.4

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) (pdb code 3iwk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1), PDB code: 3iwk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 3iwk

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Sodium binding site 1 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:60.0
occ:1.00
 OD1 A:ASN27 2.4 47.1 1.0
O A:ASP99 2.4 37.8 1.0
O A:LEU189 2.4 33.8 1.0
OD1 A:ASP99 3.1 36.8 1.0
O A:ILE28 3.2 47.3 1.0
O A:HOH1778 3.4 27.5 1.0
CG A:ASN27 3.5 47.3 1.0
C A:ASP99 3.5 37.8 1.0
C A:LEU189 3.6 33.9 1.0
ND2 A:ASN27 3.9 48.0 1.0
CA A:ASP99 4.0 37.8 1.0
CG A:ASP99 4.1 37.3 1.0
C A:ILE28 4.3 47.4 1.0
N A:ILE28 4.4 47.2 1.0
CA A:LEU189 4.5 33.9 1.0
N A:ALA190 4.6 33.9 1.0
CB A:ASP99 4.6 37.6 1.0
N A:CYS100 4.6 37.9 1.0
CA A:ALA190 4.7 34.0 1.0
O A:ILE98 4.7 38.3 1.0
CB A:ASN27 4.8 47.1 1.0
C A:ASN27 4.9 47.1 1.0
CA A:ILE28 5.0 47.3 1.0
OD2 A:ASP99 5.0 36.3 1.0
CD A:PRO30 5.0 47.8 1.0
CA A:ASN27 5.0 47.1 1.0

Sodium binding site 2 out of 12 in 3iwk

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Sodium binding site 2 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:41.6
occ:1.00
 O B:LEU189 2.4 29.3 1.0
OD1 B:ASN27 2.5 42.9 1.0
O B:ASP99 2.5 41.3 1.0
OD1 B:ASP99 2.8 41.9 1.0
C B:LEU189 3.5 29.0 1.0
O B:ILE28 3.5 42.1 1.0
C B:ASP99 3.5 41.3 1.0
CG B:ASN27 3.6 41.8 1.0
O B:HOH1316 3.9 28.6 1.0
CA B:ASP99 3.9 41.1 1.0
CG B:ASP99 3.9 41.1 1.0
ND2 B:ASN27 4.0 43.1 1.0
O B:HOH876 4.2 31.2 1.0
CA B:LEU189 4.4 28.6 1.0
N B:ALA190 4.4 29.4 1.0
CA B:ALA190 4.5 29.8 1.0
CB B:ASP99 4.5 41.1 1.0
N B:ILE28 4.6 41.1 1.0
C B:ILE28 4.6 41.8 1.0
N B:CYS100 4.7 41.3 1.0
O B:ILE98 4.8 40.6 1.0
OD2 B:ASP99 4.8 40.9 1.0
CB B:ASN27 4.9 40.6 1.0
CB B:ALA190 5.0 29.8 1.0

Sodium binding site 3 out of 12 in 3iwk

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Sodium binding site 3 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na504

b:65.6
occ:1.00
 O C:ASP99 2.4 36.3 1.0
O C:LEU189 2.6 33.8 1.0
OD1 C:ASN27 2.6 45.6 1.0
O C:ILE28 3.2 42.7 1.0
O C:HOH1645 3.4 37.1 1.0
OD1 C:ASP99 3.4 37.1 1.0
CG C:ASN27 3.4 44.9 1.0
C C:ASP99 3.5 36.2 1.0
ND2 C:ASN27 3.6 45.2 1.0
C C:LEU189 3.8 33.7 1.0
CA C:ASP99 4.1 36.3 1.0
CG C:ASP99 4.3 36.2 1.0
C C:ILE28 4.3 42.6 1.0
N C:ILE28 4.5 43.2 1.0
CA C:LEU189 4.6 33.9 1.0
N C:CYS100 4.7 35.8 1.0
CD C:PRO30 4.7 42.0 1.0
N C:ALA190 4.8 33.4 1.0
CB C:ASN27 4.8 44.2 1.0
O C:ILE98 4.8 37.1 1.0
CB C:ASP99 4.8 36.4 1.0
CA C:ALA190 4.9 33.0 1.0
C C:ASN27 4.9 43.6 1.0
O C:VAL337 4.9 30.0 1.0
CA C:CYS100 5.0 35.3 1.0

Sodium binding site 4 out of 12 in 3iwk

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Sodium binding site 4 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na504

b:43.3
occ:1.00
 OD1 D:ASN27 2.4 41.9 1.0
O D:LEU189 2.5 34.3 1.0
O D:ASP99 2.5 43.5 1.0
OD1 D:ASP99 2.6 44.1 1.0
O D:HOH989 3.3 38.1 1.0
CG D:ASN27 3.3 42.7 1.0
C D:ASP99 3.5 43.5 1.0
ND2 D:ASN27 3.6 43.4 1.0
C D:LEU189 3.7 34.0 1.0
CG D:ASP99 3.7 44.0 1.0
O D:ILE28 3.7 44.1 1.0
CA D:ASP99 3.8 43.6 1.0
O D:HOH516 4.1 38.3 1.0
CB D:ASP99 4.3 43.5 1.0
CA D:ALA190 4.5 34.2 1.0
N D:ALA190 4.5 34.1 1.0
CA D:LEU189 4.6 33.6 1.0
OD2 D:ASP99 4.6 44.5 1.0
N D:ILE28 4.6 43.1 1.0
CB D:ASN27 4.7 42.2 1.0
N D:CYS100 4.7 43.5 1.0
C D:ILE28 4.7 44.0 1.0
O D:ILE98 4.7 43.7 1.0
CB D:ALA190 4.9 34.2 1.0

Sodium binding site 5 out of 12 in 3iwk

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Sodium binding site 5 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na504

b:47.5
occ:1.00
 O E:ASP99 2.5 37.7 1.0
OD1 E:ASN27 2.5 45.5 1.0
O E:LEU189 2.8 33.5 1.0
CG E:ASN27 3.2 45.4 1.0
OD1 E:ASP99 3.2 39.7 1.0
O E:ILE28 3.2 44.5 1.0
ND2 E:ASN27 3.3 46.5 1.0
C E:ASP99 3.5 37.7 1.0
O E:HOH1408 3.9 38.2 1.0
CA E:ASP99 3.9 38.0 1.0
C E:LEU189 4.0 33.5 1.0
CG E:ASP99 4.2 38.5 1.0
C E:ILE28 4.3 44.7 1.0
N E:ILE28 4.3 44.8 1.0
CB E:ASN27 4.6 45.1 1.0
O E:ILE98 4.6 38.6 1.0
CB E:ASP99 4.7 38.1 1.0
N E:CYS100 4.7 37.3 1.0
CD E:PRO30 4.8 44.7 1.0
CA E:LEU189 4.8 33.6 1.0
C E:ASN27 4.8 44.8 1.0
N E:ALA190 4.9 33.4 1.0
CA E:ASN27 4.9 44.9 1.0
CA E:ILE28 4.9 44.7 1.0
CA E:ALA190 4.9 33.5 1.0

Sodium binding site 6 out of 12 in 3iwk

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Sodium binding site 6 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na504

b:34.3
occ:1.00
 O F:ASP99 2.4 34.9 1.0
OD1 F:ASN27 2.5 37.9 1.0
O F:LEU189 2.5 28.9 1.0
OD1 F:ASP99 2.8 36.2 1.0
C F:ASP99 3.5 34.9 1.0
CG F:ASN27 3.6 37.4 1.0
C F:LEU189 3.6 28.7 1.0
O F:ILE28 3.8 37.8 1.0
CG F:ASP99 3.8 35.5 1.0
CA F:ASP99 3.9 34.9 1.0
ND2 F:ASN27 4.0 38.5 1.0
O F:HOH1637 4.0 24.9 1.0
O F:HOH520 4.1 27.7 1.0
CA F:ALA190 4.4 28.7 1.0
N F:ALA190 4.5 28.6 1.0
CB F:ASP99 4.5 35.0 1.0
CA F:LEU189 4.6 28.5 1.0
N F:CYS100 4.7 34.5 1.0
OD2 F:ASP99 4.7 35.3 1.0
CB F:ALA190 4.8 28.6 1.0
O F:ILE98 4.8 35.4 1.0
C F:ILE28 4.8 37.8 1.0
N F:ILE28 4.8 37.4 1.0
CB F:ASN27 4.9 37.0 1.0

Sodium binding site 7 out of 12 in 3iwk

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Sodium binding site 7 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na504

b:43.8
occ:1.00
 OD1 G:ASN27 2.2 43.3 1.0
O G:LEU189 2.5 32.2 1.0
O G:ASP99 2.6 37.3 1.0
OD1 G:ASP99 2.8 36.7 1.0
CG G:ASN27 3.2 42.7 1.0
C G:ASP99 3.6 37.3 1.0
O G:HOH1303 3.6 34.1 1.0
ND2 G:ASN27 3.6 43.6 1.0
O G:ILE28 3.6 40.4 1.0
C G:LEU189 3.6 32.0 1.0
CG G:ASP99 3.9 37.4 1.0
CA G:ASP99 3.9 37.4 1.0
CB G:ASP99 4.5 37.5 1.0
N G:ALA190 4.5 32.2 1.0
N G:ILE28 4.5 41.2 1.0
CA G:ALA190 4.5 32.3 1.0
CA G:LEU189 4.5 31.8 1.0
CB G:ASN27 4.5 41.9 1.0
C G:ILE28 4.6 40.8 1.0
N G:CYS100 4.8 36.9 1.0
OD2 G:ASP99 4.8 36.8 1.0
O G:ILE98 4.8 38.0 1.0
CB G:ALA190 5.0 32.0 1.0
CA G:ASN27 5.0 41.9 1.0

Sodium binding site 8 out of 12 in 3iwk

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Sodium binding site 8 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na504

b:30.3
occ:1.00
 O H:LEU189 2.3 29.4 1.0
OD1 H:ASN27 2.4 37.6 1.0
O H:ASP99 2.4 36.0 1.0
O H:HOH1206 2.6 34.9 1.0
OD1 H:ASP99 2.8 37.0 1.0
CG H:ASN27 3.4 37.6 1.0
C H:LEU189 3.5 29.1 1.0
C H:ASP99 3.5 36.1 1.0
ND2 H:ASN27 3.7 39.0 1.0
CG H:ASP99 3.8 36.3 1.0
O H:HOH890 3.9 39.3 1.0
O H:ILE28 3.9 36.8 1.0
CA H:ASP99 4.0 36.1 1.0
N H:ALA190 4.4 29.1 1.0
CA H:ALA190 4.4 29.2 1.0
CA H:LEU189 4.4 28.7 1.0
CB H:ASP99 4.5 36.2 1.0
OD2 H:ASP99 4.6 36.1 1.0
N H:CYS100 4.7 36.0 1.0
CB H:ASN27 4.7 37.0 1.0
N H:ILE28 4.8 37.0 1.0
CB H:ALA190 4.9 29.2 1.0
C H:ILE28 4.9 37.0 1.0

Sodium binding site 9 out of 12 in 3iwk

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Sodium binding site 9 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na504

b:61.7
occ:1.00
 O I:ASP99 2.6 35.7 1.0
O I:LEU189 2.9 31.9 1.0
O I:ILE28 3.0 42.4 1.0
O I:HOH1476 3.0 31.7 1.0
OD1 I:ASN27 3.1 42.5 1.0
C I:ASP99 3.8 35.9 1.0
CG I:ASN27 4.0 42.2 1.0
C I:LEU189 4.0 31.9 1.0
OD1 I:ASP99 4.0 37.2 1.0
O I:VAL337 4.1 28.9 1.0
C I:ILE28 4.1 42.4 1.0
ND2 I:ASN27 4.3 43.0 1.0
CD I:PRO30 4.3 42.4 1.0
N I:ILE28 4.4 42.1 1.0
CA I:ASP99 4.5 36.2 1.0
CA I:LEU189 4.6 31.7 1.0
CG2 I:VAL337 4.6 27.5 1.0
N I:CYS100 4.8 35.6 1.0
CA I:ILE28 4.8 42.3 1.0
CB I:LEU189 4.8 31.6 1.0
CG I:ASP99 4.9 36.9 1.0
O I:ILE98 5.0 36.7 1.0
CG I:PRO30 5.0 42.2 1.0
CA I:CYS100 5.0 35.4 1.0

Sodium binding site 10 out of 12 in 3iwk

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Sodium binding site 10 out of 12 in the Crystal Structure of Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1)


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 Aminoaldehyde Dehydrogenase 1 From Pisum Sativum (PSAMADH1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na504

b:42.0
occ:1.00
 OD1 J:ASN27 2.5 51.5 1.0
O J:LEU189 2.5 35.3 1.0
O J:ASP99 2.6 40.5 1.0
OD1 J:ASP99 2.7 41.2 1.0
CG J:ASN27 3.5 50.6 1.0
C J:ASP99 3.6 40.6 1.0
C J:LEU189 3.7 35.4 1.0
O J:ILE28 3.8 49.0 1.0
CG J:ASP99 3.8 41.3 1.0
ND2 J:ASN27 3.9 51.5 1.0
CA J:ASP99 4.0 40.8 1.0
O J:HOH1569 4.2 31.6 1.0
O J:HOH896 4.2 38.7 1.0
CA J:ALA190 4.5 35.7 1.0
N J:ILE28 4.5 49.3 1.0
N J:ALA190 4.5 35.6 1.0
CB J:ASP99 4.5 40.8 1.0
CA J:LEU189 4.6 35.1 1.0
C J:ILE28 4.7 49.0 1.0
OD2 J:ASP99 4.7 42.0 1.0
N J:CYS100 4.8 40.5 1.0
CB J:ASN27 4.8 49.9 1.0

Reference:

M.Tylichova, D.Kopecny, S.Morera, P.Briozzo, R.Lenobel, J.Snegaroff, M.Sebela. Structural and Functional Characterization of Plant Aminoaldehyde Dehydrogenase From Pisum Sativum with A Broad Specificity For Natural and Synthetic Aminoaldehydes. J.Mol.Biol. V. 396 870 2010.
ISSN: ISSN 0022-2836
PubMed: 20026072
DOI: 10.1016/J.JMB.2009.12.015
Page generated: Mon Oct 7 11:04:18 2024

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