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Sodium in PDB 4l3g: Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days

Enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days

All present enzymatic activity of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days, PDB code: 4l3g was solved by E.T.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.62 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.530, 83.520, 107.780, 109.94, 91.54, 105.78
R / Rfree (%) 15.8 / 21

Other elements in 4l3g:

The structure of Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days (pdb code 4l3g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days, PDB code: 4l3g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4l3g

Go back to Sodium Binding Sites List in 4l3g
Sodium binding site 1 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:47.0
occ:1.00
 O A:HOH638 2.3 46.7 1.0
O A:HOH609 2.3 43.4 1.0
O A:HOH512 2.4 41.0 1.0
OG1 A:THR233 2.4 41.6 1.0
OD1 A:ASN231 2.7 39.8 1.0
CG A:ASN231 3.3 43.0 1.0
ND2 A:ASN231 3.5 42.2 1.0
CB A:THR233 3.6 42.5 1.0
N A:THR233 3.7 43.5 1.0
CG2 A:THR233 3.9 45.0 1.0
CA A:THR233 4.2 41.9 1.0
O A:HOH619 4.3 46.7 1.0
N A:GLU232 4.4 42.7 1.0
N A:ALA234 4.5 41.9 1.0
O A:HOH614 4.6 41.7 1.0
CB A:ASN231 4.7 42.2 1.0
C A:ASN231 4.7 43.0 1.0
C A:THR233 4.8 41.3 1.0
C A:GLU232 4.8 42.8 1.0
CA A:ASN231 4.9 43.2 1.0

Sodium binding site 2 out of 4 in 4l3g

Go back to Sodium Binding Sites List in 4l3g
Sodium binding site 2 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:30.0
occ:1.00
 O A:LEU250 2.3 37.0 1.0
O A:HOH573 2.4 51.7 1.0
O A:ILE255 2.5 43.6 1.0
O A:HOH562 2.6 44.3 1.0
O A:ARG252 2.6 32.6 1.0
C A:ARG252 3.4 32.2 1.0
C A:LEU250 3.5 38.8 1.0
C A:ILE255 3.7 41.7 1.0
C A:ALA251 3.8 33.2 1.0
CA A:PRO253 3.9 36.4 1.0
N A:ARG252 4.0 32.2 1.0
N A:ILE255 4.0 37.6 1.0
N A:PRO253 4.0 34.6 1.0
N A:GLY254 4.1 41.5 1.0
O A:ALA251 4.1 35.0 1.0
CA A:ALA251 4.1 35.1 1.0
CB A:ILE255 4.2 37.4 1.0
CA A:ILE255 4.2 38.7 1.0
N A:ALA251 4.2 36.0 1.0
C A:PRO253 4.2 37.0 1.0
CD1 A:LEU250 4.3 43.4 1.0
CA A:ARG252 4.3 34.2 1.0
OE2 A:GLU256 4.4 60.3 1.0
CA A:LEU250 4.5 38.9 1.0
C A:GLY254 4.8 40.3 1.0
CG A:LEU250 4.8 43.5 1.0
N A:GLU256 4.8 43.7 1.0
O A:LEU249 4.9 37.2 1.0
CD A:GLU256 4.9 60.7 1.0
OE1 A:GLU256 5.0 67.8 1.0

Sodium binding site 3 out of 4 in 4l3g

Go back to Sodium Binding Sites List in 4l3g
Sodium binding site 3 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:42.2
occ:1.00
 OD1 B:ASN231 2.3 33.7 1.0
O B:HOH714 2.3 41.6 1.0
O B:HOH705 2.3 37.4 1.0
O B:HOH616 2.4 39.0 1.0
OG1 B:THR233 2.6 44.1 1.0
CG B:ASN231 3.0 33.6 1.0
ND2 B:ASN231 3.2 33.4 1.0
O B:HOH711 3.8 42.0 1.0
CB B:THR233 3.8 39.4 1.0
CG2 B:THR233 4.0 39.2 1.0
N B:THR233 4.1 37.0 1.0
CB B:ASN231 4.4 32.6 1.0
CA B:THR233 4.4 38.0 1.0
N B:ALA234 4.5 34.0 1.0
CA B:ASN231 4.8 31.8 1.0
C B:ASN231 4.8 33.3 1.0
N B:GLU232 4.8 35.5 1.0
C B:THR233 5.0 36.8 1.0

Sodium binding site 4 out of 4 in 4l3g

Go back to Sodium Binding Sites List in 4l3g
Sodium binding site 4 out of 4 in the Crystal Structure of the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days


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 the E113Q-Maug/Pre-Methylamine Dehydrogenase Complex Aged 120 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:30.0
occ:1.00
 O B:HOH702 2.2 46.8 1.0
O B:ILE255 2.2 32.5 1.0
O B:LEU250 2.3 30.0 1.0
O B:HOH674 2.5 40.1 1.0
O B:HOH596 2.6 41.9 1.0
O B:ARG252 2.7 32.0 1.0
C B:ILE255 3.3 32.0 1.0
C B:LEU250 3.5 32.1 1.0
C B:ARG252 3.7 32.4 1.0
N B:ILE255 3.8 33.2 1.0
CA B:ILE255 4.0 31.4 1.0
C B:ALA251 4.0 31.0 1.0
N B:ARG252 4.2 30.5 1.0
N B:GLY254 4.2 37.3 1.0
CD1 B:LEU250 4.2 32.0 1.0
CA B:PRO253 4.2 36.4 1.0
CB B:ILE255 4.2 32.3 1.0
CA B:ALA251 4.3 30.8 1.0
N B:ALA251 4.3 30.8 1.0
N B:PRO253 4.4 34.0 1.0
O B:ALA251 4.4 31.0 1.0
OE2 B:GLU256 4.4 55.4 1.0
N B:GLU256 4.4 32.3 1.0
CA B:LEU250 4.5 31.0 1.0
C B:PRO253 4.5 35.8 1.0
CA B:ARG252 4.6 32.5 0.5
CA B:ARG252 4.6 29.8 0.5
C B:GLY254 4.7 39.3 1.0
CG B:LEU250 4.7 31.8 1.0
CD B:GLU256 4.7 46.0 1.0
OE1 B:GLU256 4.7 51.9 1.0
CA B:GLU256 4.8 34.9 1.0

Reference:

N.Abu Tarboush, E.T.Yukl, S.Shin, M.Feng, C.M.Wilmot, V.L.Davidson. Carboxyl Group of GLU113 Is Required For Stabilization of the Diferrous and Bis-Fe(IV) States of Maug. Biochemistry V. 52 6358 2013.
ISSN: ISSN 0006-2960
PubMed: 23952537
DOI: 10.1021/BI400905S
Page generated: Mon Oct 7 16:41:00 2024

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