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Sodium in PDB 4npi: 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens

Protein crystallography data

The structure of 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens, PDB code: 4npi was solved by L.Huo, I.Davis, F.Liu, H.Iwaki, Y.Hasegawa, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 109.99 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.355, 141.747, 174.372, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.6

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens (pdb code 4npi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens, PDB code: 4npi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4npi

Go back to Sodium Binding Sites List in 4npi
Sodium binding site 1 out of 4 in the 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:27.7
occ:1.00
 O A:HOH779 2.4 29.0 1.0
OD1 A:ASN37 2.4 26.7 1.0
O A:GLU196 2.5 24.4 1.0
O A:ILE38 2.6 24.2 1.0
O A:HOH799 2.6 28.0 1.0
O A:ASP105 2.7 25.4 1.0
C A:GLU196 3.6 28.2 1.0
C A:ILE38 3.6 29.8 1.0
N A:ILE38 3.7 30.0 1.0
C A:ASP105 3.7 22.3 1.0
CG A:ASN37 3.7 25.3 1.0
CA A:ASP105 3.9 23.0 1.0
O A:HOH868 4.1 29.6 1.0
CA A:GLU196 4.2 24.9 1.0
CA A:ILE38 4.2 26.3 1.0
OE1 A:GLU196 4.4 30.5 1.0
CB A:ASP105 4.4 24.0 1.0
C A:ASN37 4.4 27.3 1.0
ND2 A:ASN37 4.5 24.9 1.0
CB A:GLU196 4.6 26.3 1.0
O A:HOH880 4.6 33.6 1.0
CA A:ASN37 4.6 28.4 1.0
CD A:PRO40 4.7 24.5 1.0
N A:ASN39 4.7 22.0 1.0
N A:SER197 4.7 23.9 1.0
CB A:ASN37 4.7 30.5 1.0
CG A:ASP105 4.8 26.7 1.0
O A:ILE345 4.8 23.5 1.0
O A:HOH741 4.8 26.9 1.0
CD1 A:ILE345 4.9 22.4 1.0
CB A:ILE38 4.9 30.5 1.0
N A:THR106 4.9 22.5 1.0
OD1 A:ASP105 5.0 25.3 1.0

Sodium binding site 2 out of 4 in 4npi

Go back to Sodium Binding Sites List in 4npi
Sodium binding site 2 out of 4 in the 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:27.9
occ:1.00
 OD1 B:ASN37 2.3 25.8 1.0
O B:HOH755 2.4 30.0 1.0
O B:GLU196 2.4 23.3 1.0
O B:HOH810 2.5 29.8 1.0
O B:ILE38 2.5 26.1 1.0
O B:ASP105 3.2 24.3 1.0
C B:GLU196 3.5 24.8 1.0
CG B:ASN37 3.6 25.0 1.0
N B:ILE38 3.6 26.2 1.0
C B:ILE38 3.6 27.4 1.0
CA B:GLU196 4.1 23.2 1.0
O B:HOH788 4.1 28.6 1.0
C B:ASP105 4.1 21.6 1.0
CA B:ILE38 4.2 27.0 1.0
CA B:ASP105 4.2 22.1 1.0
C B:ASN37 4.3 27.8 1.0
OE1 B:GLU196 4.3 26.2 1.0
ND2 B:ASN37 4.4 23.3 1.0
CA B:ASN37 4.5 25.4 1.0
CB B:GLU196 4.6 26.9 1.0
CB B:ASN37 4.6 26.0 1.0
CB B:ASP105 4.7 23.7 1.0
O B:HOH793 4.7 25.7 1.0
N B:ASN39 4.7 25.3 1.0
N B:SER197 4.7 22.5 1.0
CD B:PRO40 4.7 22.6 1.0
O B:HOH844 4.8 29.5 1.0
CB B:ILE38 4.8 28.0 1.0
O B:ILE345 4.8 23.2 1.0
CD1 B:ILE46 4.9 34.3 1.0
CG B:ASP105 5.0 27.9 1.0
OD1 B:ASP105 5.0 23.9 1.0
CA B:SER197 5.0 17.9 1.0

Sodium binding site 3 out of 4 in 4npi

Go back to Sodium Binding Sites List in 4npi
Sodium binding site 3 out of 4 in the 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:40.3
occ:1.00
 O C:HOH996 2.3 41.4 1.0
O C:GLU196 2.5 33.6 1.0
OD1 C:ASN37 2.6 40.1 1.0
O C:ILE38 2.7 42.8 1.0
O C:ASP105 3.1 35.7 1.0
C C:GLU196 3.5 37.4 1.0
N C:ILE38 3.7 43.8 1.0
C C:ILE38 3.7 44.8 1.0
CG C:ASN37 3.8 41.5 1.0
O C:HOH807 4.0 34.7 1.0
CA C:GLU196 4.0 33.6 1.0
C C:ASP105 4.1 31.2 1.0
CA C:ILE38 4.2 43.0 1.0
CA C:ASP105 4.3 37.1 1.0
OE1 C:GLU196 4.3 36.8 1.0
C C:ASN37 4.4 42.6 1.0
CB C:GLU196 4.5 30.3 1.0
CD1 C:ILE46 4.6 43.2 1.0
CA C:ASN37 4.6 40.2 1.0
ND2 C:ASN37 4.6 41.0 1.0
CB C:ASP105 4.7 36.2 1.0
O C:ILE345 4.7 35.6 1.0
N C:SER197 4.7 32.8 1.0
CD1 C:ILE345 4.7 33.4 1.0
N C:ASN39 4.8 35.1 1.0
O C:HOH920 4.8 43.5 1.0
CB C:ASN37 4.8 42.9 1.0
CB C:ILE38 4.8 44.0 1.0
CD C:PRO40 4.9 39.6 1.0

Sodium binding site 4 out of 4 in 4npi

Go back to Sodium Binding Sites List in 4npi
Sodium binding site 4 out of 4 in the 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.94 Angstroms X-Ray Crystal Structure of Nad- and Intermediate- Bound Alpha-Aminomuconate-Epsilon-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:26.7
occ:1.00
 O D:HOH1005 2.3 33.5 1.0
O D:GLU196 2.5 22.0 1.0
OD1 D:ASN37 2.6 26.8 1.0
O D:HOH783 2.6 27.1 1.0
O D:ILE38 2.7 24.7 1.0
O D:ASP105 2.7 28.4 1.0
C D:GLU196 3.5 26.9 1.0
C D:ASP105 3.7 25.7 1.0
C D:ILE38 3.7 30.6 1.0
N D:ILE38 3.7 30.4 1.0
CG D:ASN37 3.8 30.1 1.0
CA D:ASP105 3.9 27.9 1.0
CA D:GLU196 4.1 27.4 1.0
O D:HOH780 4.3 34.0 1.0
CB D:ASP105 4.3 29.0 1.0
CA D:ILE38 4.3 25.8 1.0
OE1 D:GLU196 4.4 33.1 1.0
C D:ASN37 4.4 26.9 1.0
CB D:GLU196 4.5 24.0 1.0
ND2 D:ASN37 4.6 26.8 1.0
CA D:ASN37 4.6 31.3 1.0
N D:SER197 4.7 26.8 1.0
CD D:PRO40 4.7 27.0 1.0
CG D:ASP105 4.7 30.7 1.0
N D:ASN39 4.8 26.6 1.0
O D:HOH840 4.8 27.3 1.0
O D:ILE345 4.8 24.7 1.0
CB D:ASN37 4.8 31.5 1.0
OD1 D:ASP105 4.9 28.7 1.0
CD1 D:ILE345 4.9 19.3 1.0
N D:THR106 4.9 23.8 1.0
CB D:ILE38 5.0 27.9 1.0
O D:HOH935 5.0 34.6 1.0
CA D:SER197 5.0 24.6 1.0
CD1 D:ILE46 5.0 31.0 1.0

Reference:

L.Huo, I.Davis, F.Liu, H.Iwaki, Y.Hasegawa, A.Liu. Crystallographic and Spectroscopic Snapshots Reveal A Dehydrogenase in Action Nat Commun 2014.
ISSN: ESSN 2041-1723
DOI: 10.1038/NCOMMS6935
Page generated: Mon Oct 7 17:16:18 2024

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