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Sodium in PDB 4oe2: 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens

Protein crystallography data

The structure of 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens, PDB code: 4oe2 was solved by L.Huo, I.Davis, F.Liu, S.Esaki, 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) 41.74 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.534, 141.977, 173.798, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.7

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens (pdb code 4oe2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens, PDB code: 4oe2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4oe2

Go back to Sodium Binding Sites List in 4oe2
Sodium binding site 1 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- 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 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:30.8
occ:1.00
 O A:HOH740 2.3 31.4 1.0
OD1 A:ASN37 2.4 27.1 1.0
O A:GLU196 2.5 26.6 1.0
O A:ASP105 2.6 28.8 1.0
O A:ILE38 2.6 30.2 1.0
O A:HOH707 2.8 29.9 1.0
C A:ASP105 3.5 26.3 1.0
CG A:ASN37 3.6 29.2 1.0
C A:GLU196 3.7 30.9 1.0
C A:ILE38 3.7 33.9 1.0
N A:ILE38 3.7 32.2 1.0
CA A:ASP105 3.8 26.4 1.0
ND2 A:ASN37 4.2 30.4 1.0
CB A:ASP105 4.3 28.0 1.0
CA A:ILE38 4.3 33.0 1.0
CA A:GLU196 4.4 27.8 1.0
O A:HOH850 4.4 31.8 1.0
C A:ASN37 4.5 33.0 1.0
OE1 A:GLU196 4.6 36.1 1.0
CD A:PRO40 4.6 31.6 1.0
CD1 A:ILE46 4.7 32.8 1.0
CG A:ASP105 4.7 29.3 1.0
CA A:ASN37 4.7 30.5 1.0
CB A:ASN37 4.7 32.4 1.0
N A:ASN39 4.7 31.2 1.0
N A:SER197 4.8 27.8 1.0
N A:THR106 4.8 28.1 1.0
CD1 A:ILE345 4.8 29.2 1.0
O A:ILE345 4.8 26.3 1.0
CB A:GLU196 4.8 29.1 1.0
OD1 A:ASP105 4.9 31.8 1.0
CA A:SER197 5.0 23.4 1.0

Sodium binding site 2 out of 4 in 4oe2

Go back to Sodium Binding Sites List in 4oe2
Sodium binding site 2 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- 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 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:31.9
occ:1.00
 OD1 B:ASN37 2.3 28.6 1.0
O B:HOH712 2.4 32.0 1.0
O B:HOH705 2.4 32.5 1.0
O B:GLU196 2.5 27.2 1.0
O B:ILE38 2.6 30.7 1.0
O B:ASP105 3.3 27.3 1.0
CG B:ASN37 3.5 29.8 1.0
N B:ILE38 3.6 32.5 1.0
C B:ILE38 3.6 35.9 1.0
C B:GLU196 3.6 30.0 1.0
CA B:ASP105 4.1 25.6 1.0
C B:ASP105 4.1 28.2 1.0
CA B:ILE38 4.1 34.2 1.0
ND2 B:ASN37 4.2 30.0 1.0
O B:HOH746 4.2 30.6 1.0
C B:ASN37 4.2 32.5 1.0
CA B:GLU196 4.3 30.7 1.0
CA B:ASN37 4.5 33.0 1.0
CB B:ASP105 4.5 27.8 1.0
CD1 B:ILE46 4.5 30.6 1.0
CB B:ASN37 4.5 29.6 1.0
OE1 B:GLU196 4.6 32.1 1.0
N B:ASN39 4.7 30.3 1.0
N B:SER197 4.7 22.7 1.0
CB B:GLU196 4.8 28.2 1.0
CD B:PRO40 4.9 27.9 1.0
CG B:ASP105 4.9 34.5 1.0
O B:HOH857 4.9 32.1 1.0
CB B:ILE38 4.9 31.9 1.0
O B:HOH832 4.9 34.9 1.0
O B:ILE345 4.9 23.2 1.0
CA B:SER197 5.0 24.3 1.0

Sodium binding site 3 out of 4 in 4oe2

Go back to Sodium Binding Sites List in 4oe2
Sodium binding site 3 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- 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 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:42.7
occ:1.00
 OD1 C:ASN37 2.4 41.2 1.0
O C:GLU196 2.6 38.0 1.0
O C:ILE38 2.7 43.0 1.0
O C:HOH906 3.0 40.3 1.0
O C:ASP105 3.1 43.0 1.0
CG C:ASN37 3.6 45.2 1.0
C C:GLU196 3.7 42.1 1.0
C C:ILE38 3.7 47.9 1.0
N C:ILE38 3.8 42.2 1.0
C C:ASP105 3.9 36.6 1.0
CA C:ASP105 4.0 40.3 1.0
CA C:GLU196 4.2 40.5 1.0
CA C:ILE38 4.3 45.6 1.0
C C:ASN37 4.3 46.7 1.0
OE1 C:GLU196 4.3 40.7 1.0
O C:HOH866 4.4 46.8 1.0
CB C:ASP105 4.4 40.5 1.0
ND2 C:ASN37 4.4 43.6 1.0
CA C:ASN37 4.5 40.4 1.0
O C:HOH837 4.6 43.5 1.0
CB C:ASN37 4.7 43.0 1.0
N C:ASN39 4.7 41.5 1.0
CB C:GLU196 4.8 35.2 1.0
N C:SER197 4.8 38.3 1.0
OD1 C:ASP105 4.8 46.0 1.0
CG C:ASP105 4.9 45.7 1.0
CD1 C:ILE46 4.9 47.5 1.0
CB C:ILE38 5.0 48.2 1.0
O C:ILE345 5.0 35.4 1.0

Sodium binding site 4 out of 4 in 4oe2

Go back to Sodium Binding Sites List in 4oe2
Sodium binding site 4 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- 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 2.00 Angstroms X-Ray Crystal Structure of E268A 2-Aminomuconate 6- Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:30.5
occ:1.00
 OD1 D:ASN37 2.4 30.4 1.0
O D:GLU196 2.5 25.7 1.0
O D:ILE38 2.6 28.8 1.0
O D:HOH707 2.7 37.0 1.0
O D:HOH730 2.8 33.6 1.0
O D:ASP105 3.0 31.9 1.0
C D:GLU196 3.6 31.0 1.0
CG D:ASN37 3.6 32.0 1.0
C D:ILE38 3.6 34.7 1.0
N D:ILE38 3.6 31.4 1.0
C D:ASP105 3.9 29.1 1.0
CA D:ASP105 4.0 28.3 1.0
CA D:GLU196 4.1 29.5 1.0
CA D:ILE38 4.2 31.2 1.0
O D:HOH767 4.3 31.2 1.0
C D:ASN37 4.3 32.1 1.0
ND2 D:ASN37 4.4 31.4 1.0
CB D:ASP105 4.4 30.7 1.0
OE1 D:GLU196 4.5 34.4 1.0
CD1 D:ILE46 4.5 33.8 1.0
CA D:ASN37 4.5 33.8 1.0
CB D:GLU196 4.6 26.3 1.0
CB D:ASN37 4.6 33.2 1.0
N D:ASN39 4.7 26.9 1.0
N D:SER197 4.7 29.8 1.0
CG D:ASP105 4.7 34.2 1.0
CD D:PRO40 4.8 29.5 1.0
O D:HOH827 4.8 32.2 1.0
OD1 D:ASP105 4.8 29.0 1.0
O D:ILE345 4.9 25.5 1.0
CB D:ILE38 5.0 30.8 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 17:26:56 2024

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