Atomistry » Sodium » PDB 3iwf-3k93 » 3iwk
Atomistry »
  Sodium »
    PDB 3iwf-3k93 »
      3iwk »

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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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

Go back to Sodium Binding Sites List in 3iwk
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: Sun Aug 17 15:51:50 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy