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Sodium in PDB 4i25: 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens

Protein crystallography data

The structure of 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens, PDB code: 4i25 was solved by L.Huo, I.Davis, L.Chen, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.22 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.253, 142.932, 175.125, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.8

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens (pdb code 4i25). 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 Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens, PDB code: 4i25:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4i25

Go back to Sodium Binding Sites List in 4i25
Sodium binding site 1 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 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 Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:29.3
occ:1.00
 O A:HOH1029 2.3 35.4 1.0
O A:GLU196 2.6 27.6 1.0
OD1 A:ASN37 2.6 27.7 1.0
O A:ILE38 2.7 23.4 1.0
O A:HOH746 2.7 33.4 1.0
O A:ASP105 2.8 25.9 1.0
C A:GLU196 3.6 29.2 1.0
C A:ASP105 3.7 23.9 1.0
C A:ILE38 3.7 25.4 1.0
N A:ILE38 3.8 23.1 1.0
CG A:ASN37 3.8 25.5 1.0
CA A:ASP105 3.9 26.1 1.0
O A:HOH777 4.2 27.8 1.0
CA A:GLU196 4.2 27.2 1.0
CB A:ASP105 4.3 31.1 1.0
CA A:ILE38 4.3 23.7 1.0
OE1 A:GLU196 4.5 36.0 1.0
ND2 A:ASN37 4.5 26.1 1.0
C A:ASN37 4.5 25.7 1.0
CD A:PRO40 4.6 27.0 1.0
CA A:ASN37 4.7 26.1 1.0
O A:ILE345 4.7 21.6 1.0
N A:SER197 4.7 26.2 1.0
CG A:ASP105 4.7 31.8 1.0
CB A:GLU196 4.8 29.5 1.0
N A:ASN39 4.8 27.4 1.0
O A:HOH761 4.8 28.9 1.0
CD1 A:ILE46 4.8 34.2 1.0
CB A:ASN37 4.8 27.5 1.0
OD1 A:ASP105 4.9 31.9 1.0
CD1 A:ILE345 4.9 24.5 1.0
N A:THR106 5.0 26.2 1.0
CB A:ILE38 5.0 28.0 1.0
CA A:SER197 5.0 24.9 1.0

Sodium binding site 2 out of 4 in 4i25

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Sodium binding site 2 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 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 Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:32.5
occ:1.00
 O B:HOH789 2.1 39.6 1.0
O B:GLU196 2.5 29.5 1.0
OD1 B:ASN37 2.5 26.1 1.0
O B:HOH741 2.7 33.0 1.0
O B:ILE38 2.7 25.3 1.0
O B:ASP105 3.2 26.4 1.0
C B:GLU196 3.6 28.5 1.0
N B:ILE38 3.7 28.6 1.0
C B:ILE38 3.7 26.9 1.0
CG B:ASN37 3.7 25.4 1.0
O B:HOH746 4.1 26.5 1.0
C B:ASP105 4.1 26.1 1.0
CA B:GLU196 4.1 26.8 1.0
CA B:ASP105 4.1 26.6 1.0
CA B:ILE38 4.3 27.7 1.0
C B:ASN37 4.4 26.4 1.0
ND2 B:ASN37 4.4 24.8 1.0
CB B:ASP105 4.5 29.1 1.0
OE1 B:GLU196 4.6 39.0 1.0
CA B:ASN37 4.6 26.7 1.0
O B:HOH777 4.6 30.8 1.0
CD1 B:ILE46 4.7 33.5 1.0
CB B:GLU196 4.7 27.0 1.0
O B:ILE345 4.7 23.4 1.0
N B:SER197 4.7 24.1 1.0
N B:ASN39 4.8 22.1 1.0
CB B:ASN37 4.8 25.1 1.0
CD B:PRO40 4.8 24.5 1.0
O B:HOH993 4.8 42.8 1.0
CG B:ASP105 4.9 35.8 1.0
CB B:ILE38 5.0 29.2 1.0
CD1 B:ILE345 5.0 25.8 1.0

Sodium binding site 3 out of 4 in 4i25

Go back to Sodium Binding Sites List in 4i25
Sodium binding site 3 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 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 Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na602

b:36.7
occ:1.00
 O C:HOH797 2.2 36.5 1.0
O C:HOH765 2.5 38.1 1.0
OD1 C:ASN37 2.5 30.0 1.0
O C:ILE38 2.6 33.2 1.0
O C:GLU196 2.7 30.9 1.0
O C:ASP105 3.3 31.9 1.0
C C:ILE38 3.6 33.4 1.0
N C:ILE38 3.7 35.0 1.0
CG C:ASN37 3.7 31.1 1.0
C C:GLU196 3.7 29.1 1.0
C C:ASP105 4.1 28.7 1.0
O C:HOH813 4.2 33.3 1.0
CA C:ILE38 4.2 34.5 1.0
CA C:GLU196 4.2 28.9 1.0
CA C:ASP105 4.2 32.7 1.0
C C:ASN37 4.3 32.5 1.0
CA C:ASN37 4.5 30.5 1.0
ND2 C:ASN37 4.5 31.6 1.0
OE1 C:GLU196 4.6 39.9 1.0
CB C:ASP105 4.7 33.4 1.0
N C:ASN39 4.7 30.2 1.0
CB C:ASN37 4.7 31.8 1.0
CD1 C:ILE46 4.7 39.6 1.0
CB C:GLU196 4.8 26.4 1.0
CD C:PRO40 4.8 33.0 1.0
O C:ILE345 4.9 26.9 1.0
N C:SER197 4.9 26.8 1.0
OD1 C:ASP105 4.9 35.1 1.0
CB C:ILE38 4.9 39.0 1.0
CG C:ASP105 4.9 40.7 1.0

Sodium binding site 4 out of 4 in 4i25

Go back to Sodium Binding Sites List in 4i25
Sodium binding site 4 out of 4 in the 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 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 Nad- and Substrate-Bound 2- Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na602

b:30.7
occ:1.00
 O D:HOH794 2.2 30.9 1.0
OD1 D:ASN37 2.5 26.1 1.0
O D:GLU196 2.6 25.1 1.0
O D:HOH757 2.6 27.5 1.0
O D:ILE38 2.7 23.9 1.0
O D:ASP105 3.1 27.2 1.0
C D:GLU196 3.7 24.7 1.0
CG D:ASN37 3.7 23.8 1.0
C D:ILE38 3.7 26.1 1.0
N D:ILE38 3.8 22.8 1.0
C D:ASP105 4.0 25.9 1.0
CA D:ASP105 4.1 27.0 1.0
O D:HOH782 4.2 28.1 1.0
CA D:GLU196 4.2 25.6 1.0
OE1 D:GLU196 4.3 36.8 1.0
CA D:ILE38 4.3 23.6 1.0
C D:ASN37 4.4 23.6 1.0
ND2 D:ASN37 4.5 25.1 1.0
CB D:ASP105 4.5 29.2 1.0
CA D:ASN37 4.6 26.1 1.0
CD D:PRO40 4.7 24.2 1.0
CB D:GLU196 4.7 26.3 1.0
CD1 D:ILE46 4.7 33.6 1.0
O D:ILE345 4.7 21.1 1.0
CB D:ASN37 4.7 25.3 1.0
O D:HOH776 4.8 25.4 1.0
N D:ASN39 4.8 23.0 1.0
N D:SER197 4.8 24.6 1.0
O D:HOH992 4.8 43.4 1.0
CG D:ASP105 4.8 31.4 1.0
CB D:ILE38 4.9 24.1 1.0
OD1 D:ASP105 4.9 27.3 1.0

Reference:

L.Huo, I.Davis, L.Chen, A.Liu. 2.00 Angstroms X-Ray Crystal Structure of Nad- and Substrate-Bound 2-Aminomuconate 6-Semialdehyde Dehydrogenase From Pseudomonas Fluorescens To Be Published.
Page generated: Sun Aug 17 19:45:34 2025

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