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Sodium in PDB 4k3i: Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group

Enzymatic activity of Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group

All present enzymatic activity of Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group:
1.4.9.1; 1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group, PDB code: 4k3i was solved by E.Y.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.06 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 346.356, 55.558, 112.548, 90.00, 106.55, 90.00
R / Rfree (%) 14.4 / 19

Other elements in 4k3i:

The structure of Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group 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 Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group (pdb code 4k3i). 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 Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group, PDB code: 4k3i:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4k3i

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Sodium binding site 1 out of 4 in the Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group


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 Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:24.0
occ:1.00
 O A:HOH850 2.3 28.6 1.0
OD1 A:ASN231 2.4 24.5 1.0
O A:HOH826 2.4 26.6 1.0
OG1 A:THR233 2.4 25.2 1.0
O A:HOH821 2.4 28.0 1.0
O A:HOH816 2.5 25.8 1.0
CG A:ASN231 3.2 22.7 1.0
ND2 A:ASN231 3.4 21.1 1.0
CB A:THR233 3.6 25.5 1.0
O A:HOH609 3.8 28.3 1.0
N A:THR233 3.9 24.3 1.0
CG2 A:THR233 4.0 27.9 1.0
O A:HOH677 4.1 39.7 1.0
CA A:THR233 4.2 24.6 1.0
O A:HOH619 4.4 24.4 1.0
O A:HOH849 4.5 33.7 1.0
N A:ALA234 4.5 24.2 1.0
CB A:ASN231 4.5 22.9 1.0
N A:GLU232 4.6 24.1 1.0
C A:ASN231 4.7 22.9 1.0
O A:HOH842 4.7 32.2 1.0
CA A:ASN231 4.8 23.4 1.0
O A:HOH644 4.8 28.3 1.0
C A:THR233 4.8 24.2 1.0

Sodium binding site 2 out of 4 in 4k3i

Go back to Sodium Binding Sites List in 4k3i
Sodium binding site 2 out of 4 in the Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group


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 Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:29.0
occ:1.00
 O A:ARG252 2.3 26.1 0.5
O A:HOH866 2.3 41.9 1.0
O A:HOH820 2.3 29.3 1.0
O A:ILE255 2.3 27.4 1.0
O A:LEU250 2.4 26.3 1.0
O A:HOH774 2.6 41.7 1.0
O A:ARG252 2.7 23.1 0.5
C A:ARG252 3.4 27.0 0.5
C A:ILE255 3.5 27.3 1.0
C A:ARG252 3.5 24.3 0.5
C A:LEU250 3.5 25.1 1.0
C A:ALA251 3.9 26.4 1.0
N A:ILE255 3.9 26.2 1.0
N A:ARG252 4.0 23.9 0.5
N A:ARG252 4.0 26.2 0.5
CA A:ILE255 4.1 25.8 1.0
CA A:PRO253 4.1 29.8 1.0
O A:ALA251 4.1 27.0 1.0
N A:PRO253 4.2 28.2 1.0
CB A:ILE255 4.2 26.0 1.0
N A:GLY254 4.2 31.6 1.0
CA A:ALA251 4.2 25.6 1.0
OE2 A:GLU256 4.3 57.5 1.0
CD1 A:LEU250 4.3 27.1 1.0
CA A:ARG252 4.3 26.0 0.5
N A:ALA251 4.4 26.4 1.0
CA A:ARG252 4.4 22.1 0.5
C A:PRO253 4.4 29.8 1.0
CA A:LEU250 4.5 23.7 1.0
N A:GLU256 4.6 27.5 1.0
CD A:GLU256 4.7 49.9 1.0
CG A:LEU250 4.8 25.0 1.0
CA A:GLU256 4.8 30.5 1.0
C A:GLY254 4.9 31.2 1.0
O A:LEU249 5.0 20.5 1.0

Sodium binding site 3 out of 4 in 4k3i

Go back to Sodium Binding Sites List in 4k3i
Sodium binding site 3 out of 4 in the Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group


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 Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:37.5
occ:1.00
 O B:HOH745 2.1 38.0 1.0
O B:HOH770 2.2 39.5 1.0
O B:HOH775 2.2 40.3 1.0
O B:HOH738 2.4 37.6 1.0
OG1 B:THR233 2.4 37.5 1.0
OD1 B:ASN231 2.4 32.0 1.0
CG B:ASN231 3.2 34.3 1.0
ND2 B:ASN231 3.4 33.7 1.0
CB B:THR233 3.7 39.0 1.0
O B:HOH717 4.0 47.5 1.0
N B:THR233 4.1 37.2 1.0
CG2 B:THR233 4.1 38.8 1.0
O B:HOH773 4.2 31.6 1.0
CA B:THR233 4.4 35.1 1.0
CB B:ASN231 4.6 31.6 1.0
N B:ALA234 4.6 32.5 1.0
O B:HOH763 4.7 55.5 1.0
O B:HOH637 4.7 39.5 1.0
N B:GLU232 4.8 35.8 1.0
C B:ASN231 4.9 35.6 1.0
CA B:ASN231 4.9 34.7 1.0
C B:THR233 5.0 34.3 1.0

Sodium binding site 4 out of 4 in 4k3i

Go back to Sodium Binding Sites List in 4k3i
Sodium binding site 4 out of 4 in the Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group


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 Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug, C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:32.4
occ:1.00
 O B:HOH744 2.0 46.2 1.0
O B:HOH743 2.1 34.4 1.0
O B:ILE255 2.3 36.0 1.0
O B:ARG252 2.4 30.9 1.0
O B:LEU250 2.4 36.5 1.0
O B:HOH700 2.5 47.0 1.0
C B:ILE255 3.4 32.6 1.0
C B:ARG252 3.4 30.3 1.0
C B:LEU250 3.6 33.9 1.0
N B:ILE255 3.8 33.6 1.0
C B:ALA251 3.9 34.6 1.0
CA B:ILE255 4.0 33.6 1.0
N B:ARG252 4.0 34.0 1.0
CA B:PRO253 4.0 39.2 1.0
O B:ALA251 4.1 36.6 1.0
N B:GLY254 4.2 40.2 1.0
N B:PRO253 4.2 33.8 1.0
CB B:ILE255 4.2 33.5 1.0
CA B:ALA251 4.3 34.1 1.0
OE1 B:GLU256 4.3 63.0 1.0
C B:PRO253 4.4 35.1 1.0
CA B:ARG252 4.4 31.0 1.0
N B:ALA251 4.4 32.4 1.0
N B:GLU256 4.5 37.1 1.0
CD1 B:LEU250 4.6 33.7 1.0
CA B:LEU250 4.6 30.1 1.0
CD B:GLU256 4.7 54.3 1.0
C B:GLY254 4.8 38.0 1.0
OE2 B:GLU256 4.8 64.4 1.0
CA B:GLU256 4.8 39.1 1.0
CG B:LEU250 4.8 33.4 1.0

Reference:

E.T.Yukl, L.M.Jensen, V.L.Davidson, C.M.Wilmot. Structures of Maug in Complex with Quinol and Quinone Madh. Acta Crystallogr.,Sect.F V. 69 738 2013.
ISSN: ESSN 1744-3091
PubMed: 23832199
DOI: 10.1107/S1744309113016539
Page generated: Mon Oct 7 16:24:35 2024

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