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Sodium in PDB 3sxt: Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug

Enzymatic activity of Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug

All present enzymatic activity of Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug:
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, PDB code: 3sxt was solved by L.M.R.Jensen, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.01 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.639, 135.664, 111.557, 90.00, 97.37, 90.00
R / Rfree (%) 14.5 / 18.7

Other elements in 3sxt:

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

Sodium binding site 1 out of 4 in 3sxt

Go back to Sodium Binding Sites List in 3sxt
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:34.8
occ:1.00
 OD1 A:ASN231 2.3 27.9 1.0
O A:HOH650 2.4 23.9 1.0
O A:HOH665 2.4 26.8 1.0
O A:HOH593 2.4 23.3 1.0
OG1 A:THR233 2.5 30.8 1.0
O A:HOH508 2.6 22.9 1.0
CG A:ASN231 3.2 27.0 1.0
ND2 A:ASN231 3.5 26.4 1.0
CB A:THR233 3.7 31.6 1.0
N A:THR233 3.9 32.4 1.0
CG2 A:THR233 4.0 31.8 1.0
O A:HOH681 4.0 31.2 1.0
O A:HOH654 4.1 30.0 1.0
CA A:THR233 4.3 31.5 1.0
CB A:ASN231 4.5 27.2 1.0
N A:ALA234 4.5 29.9 1.0
O A:HOH575 4.6 26.0 1.0
O A:HOH671 4.6 30.8 1.0
O A:HOH789 4.6 32.3 1.0
N A:GLU232 4.7 30.1 1.0
C A:ASN231 4.7 28.9 1.0
CA A:ASN231 4.8 27.4 1.0
C A:THR233 4.8 30.8 1.0
O A:HOH781 4.9 17.6 0.5

Sodium binding site 2 out of 4 in 3sxt

Go back to Sodium Binding Sites List in 3sxt
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:40.4
occ:1.00
 O A:HOH757 2.1 39.6 1.0
O A:ARG252 2.3 34.7 1.0
O A:ILE255 2.4 39.6 1.0
O A:HOH666 2.4 31.6 1.0
O A:LEU250 2.4 35.1 1.0
O A:HOH640 2.9 44.7 1.0
C A:ARG252 3.4 36.6 1.0
C A:ILE255 3.5 38.8 1.0
C A:LEU250 3.5 34.1 1.0
N A:ILE255 3.8 39.0 1.0
C A:ALA251 3.8 35.0 1.0
N A:ARG252 3.8 35.9 1.0
CA A:PRO253 4.0 40.7 1.0
CA A:ILE255 4.0 38.4 1.0
N A:PRO253 4.1 39.6 1.0
CB A:ILE255 4.1 38.0 1.0
N A:GLY254 4.1 40.7 1.0
O A:ALA251 4.2 35.3 1.0
CA A:ALA251 4.2 34.8 1.0
CA A:ARG252 4.3 35.5 1.0
N A:ALA251 4.3 33.7 1.0
C A:PRO253 4.3 40.8 1.0
OE1 A:GLU256 4.4 57.4 1.0
CA A:LEU250 4.5 32.5 1.0
CD1 A:LEU250 4.5 34.4 1.0
N A:GLU256 4.6 37.5 1.0
C A:GLY254 4.7 41.6 1.0
CD A:GLU256 4.8 53.9 1.0
CA A:GLU256 4.9 37.8 1.0
O A:LEU249 4.9 29.8 1.0
CG A:LEU250 5.0 35.5 1.0

Sodium binding site 3 out of 4 in 3sxt

Go back to Sodium Binding Sites List in 3sxt
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:40.0
occ:1.00
 OD1 B:ASN231 2.2 39.2 1.0
O B:HOH704 2.3 18.5 1.0
O B:HOH700 2.4 24.2 1.0
OG1 B:THR233 2.4 38.7 1.0
O B:HOH681 2.5 24.0 1.0
O B:HOH534 2.6 20.9 1.0
CG B:ASN231 3.1 35.0 1.0
ND2 B:ASN231 3.4 34.0 1.0
CB B:THR233 3.7 40.4 1.0
N B:THR233 3.8 40.1 1.0
O B:HOH826 4.0 24.3 1.0
CG2 B:THR233 4.1 37.4 1.0
CA B:THR233 4.3 39.7 1.0
CB B:ASN231 4.5 32.6 1.0
N B:GLU232 4.5 34.7 1.0
N B:ALA234 4.5 37.6 1.0
O B:HOH636 4.6 19.7 1.0
C B:ASN231 4.7 34.0 1.0
CA B:ASN231 4.8 31.6 1.0
C B:THR233 4.9 39.9 1.0
C B:GLU232 4.9 40.1 1.0

Sodium binding site 4 out of 4 in 3sxt

Go back to Sodium Binding Sites List in 3sxt
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:39.4
occ:1.00
 O B:ILE255 2.3 39.0 1.0
O B:HOH720 2.4 24.7 1.0
O B:HOH642 2.4 33.7 1.0
O B:LEU250 2.4 37.3 1.0
O B:ARG252 2.5 37.9 1.0
O B:HOH590 3.0 31.3 1.0
C B:ILE255 3.4 40.0 1.0
C B:ARG252 3.4 37.2 1.0
C B:LEU250 3.5 34.5 1.0
N B:ILE255 3.8 39.1 1.0
C B:ALA251 3.9 36.7 1.0
N B:ARG252 4.0 35.1 1.0
CA B:ILE255 4.0 39.1 1.0
O B:ALA251 4.1 35.0 1.0
CA B:PRO253 4.1 40.2 1.0
CB B:ILE255 4.2 37.2 1.0
N B:PRO253 4.2 39.0 1.0
CA B:ALA251 4.2 36.1 1.0
N B:GLY254 4.2 41.7 1.0
CD1 B:LEU250 4.3 32.9 1.0
N B:ALA251 4.3 34.8 1.0
CA B:ARG252 4.4 35.5 1.0
CA B:LEU250 4.5 33.1 1.0
C B:PRO253 4.5 39.6 1.0
N B:GLU256 4.5 41.1 1.0
OE2 B:GLU256 4.7 58.8 1.0
C B:GLY254 4.8 41.7 1.0
CD B:GLU256 4.8 59.5 1.0
OE1 B:GLU256 4.9 64.5 1.0
CA B:GLU256 4.9 43.3 1.0
CG B:LEU250 4.9 34.9 1.0
O B:LEU249 5.0 27.9 1.0

Reference:

L.M.R.Jensen, C.M.Wilmot. Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of Maug To Be Published.
Page generated: Mon Oct 7 13:01:45 2024

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