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Sodium in PDB 3rn1: Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3rn1 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) 43.46 / 1.93
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.527, 83.524, 107.782, 109.94, 91.54, 105.78
R / Rfree (%) 14.4 / 19.2

Other elements in 3rn1:

The structure of Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex 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 W199E-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 3rn1). 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 W199E-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3rn1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3rn1

Go back to Sodium Binding Sites List in 3rn1
Sodium binding site 1 out of 4 in the Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex


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 W199E-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:23.6
occ:1.00
 O A:HOH844 2.3 14.6 1.0
O A:HOH918 2.4 18.2 1.0
OD1 A:ASN231 2.4 16.8 1.0
O A:HOH488 2.4 19.8 1.0
O A:HOH380 2.5 13.4 1.0
OG1 A:THR233 2.6 20.0 1.0
CG A:ASN231 3.2 14.0 1.0
ND2 A:ASN231 3.5 12.8 1.0
CB A:THR233 3.7 18.4 1.0
N A:THR233 3.8 16.8 1.0
O A:HOH1036 3.9 21.4 1.0
O A:HOH866 4.0 26.0 1.0
CG2 A:THR233 4.0 21.5 1.0
CA A:THR233 4.3 17.7 1.0
O A:HOH1357 4.3 25.7 1.0
N A:ALA234 4.4 15.1 1.0
O A:HOH963 4.5 25.5 1.0
N A:GLU232 4.5 14.4 1.0
CB A:ASN231 4.6 13.1 1.0
O A:HOH451 4.6 9.4 1.0
C A:ASN231 4.7 14.7 1.0
C A:THR233 4.8 16.3 1.0
CA A:ASN231 4.8 13.4 1.0
C A:GLU232 5.0 16.9 1.0

Sodium binding site 2 out of 4 in 3rn1

Go back to Sodium Binding Sites List in 3rn1
Sodium binding site 2 out of 4 in the Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex


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 W199E-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:29.0
occ:1.00
 O A:LEU250 2.4 19.4 1.0
O A:HOH931 2.4 26.1 1.0
O A:ILE255 2.5 24.1 1.0
O A:ARG252 2.7 21.1 1.0
O A:HOH768 2.8 26.2 1.0
C A:ILE255 3.6 24.0 1.0
C A:LEU250 3.6 18.2 1.0
C A:ARG252 3.6 21.3 1.0
C A:ALA251 4.0 19.9 1.0
N A:ILE255 4.0 24.1 1.0
O A:ALA251 4.1 18.6 1.0
CA A:ILE255 4.2 23.6 1.0
N A:ARG252 4.2 19.2 1.0
CB A:ILE255 4.2 22.7 1.0
CA A:ALA251 4.2 20.3 1.0
CA A:PRO253 4.3 24.6 1.0
N A:PRO253 4.3 22.6 1.0
N A:GLY254 4.4 24.1 1.0
N A:ALA251 4.4 17.7 1.0
OE1 A:GLU256 4.4 47.5 1.0
C A:PRO253 4.6 24.2 1.0
CA A:ARG252 4.6 19.8 1.0
CD1 A:LEU250 4.6 18.5 1.0
CA A:LEU250 4.6 16.4 1.0
OE2 A:GLU256 4.6 45.6 1.0
N A:GLU256 4.7 24.3 1.0
CD A:GLU256 4.7 42.4 1.0
CG A:LEU250 4.9 19.4 1.0
C A:GLY254 4.9 25.2 1.0
CA A:GLU256 5.0 25.9 1.0

Sodium binding site 3 out of 4 in 3rn1

Go back to Sodium Binding Sites List in 3rn1
Sodium binding site 3 out of 4 in the Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex


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 W199E-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:36.8
occ:1.00
 O B:HOH1088 2.3 21.1 1.0
O B:HOH413 2.4 17.7 1.0
O B:HOH981 2.4 28.2 1.0
O B:HOH1123 2.4 21.5 1.0
OD1 B:ASN231 2.5 17.8 1.0
OG1 B:THR233 2.7 28.4 1.0
CG B:ASN231 3.3 18.0 1.0
ND2 B:ASN231 3.4 15.2 1.0
O B:HOH1002 3.7 25.0 1.0
CB B:THR233 3.9 23.6 1.0
CG2 B:THR233 4.1 25.8 1.0
N B:THR233 4.1 20.4 1.0
CA B:THR233 4.5 21.8 1.0
O B:HOH778 4.5 17.4 1.0
CB B:ASN231 4.7 16.3 1.0
N B:ALA234 4.7 16.9 1.0
N B:GLU232 4.9 18.8 1.0
C B:ASN231 4.9 17.8 1.0
CA B:ASN231 5.0 16.7 1.0

Sodium binding site 4 out of 4 in 3rn1

Go back to Sodium Binding Sites List in 3rn1
Sodium binding site 4 out of 4 in the Crystal Structure of the W199E-Maug/Pre-Methylamine Dehydrogenase Complex


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 W199E-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:25.0
occ:1.00
 O B:LEU250 2.4 16.1 1.0
O B:ILE255 2.4 23.3 1.0
O B:HOH1229 2.5 20.6 1.0
O B:HOH513 2.5 17.2 1.0
O B:HOH809 2.5 24.8 1.0
O B:ARG252 2.5 15.7 1.0
C B:ARG252 3.5 17.5 1.0
C B:ILE255 3.5 21.5 1.0
C B:LEU250 3.6 13.9 1.0
N B:ILE255 3.9 22.1 1.0
C B:ALA251 3.9 16.8 1.0
N B:GLY254 4.0 21.7 1.0
N B:ARG252 4.0 15.2 1.0
CA B:PRO253 4.1 20.5 1.0
CA B:ILE255 4.1 19.7 1.0
N B:PRO253 4.2 19.5 1.0
CB B:ILE255 4.2 18.5 1.0
O B:ALA251 4.2 17.7 1.0
OE2 B:GLU256 4.2 43.6 1.0
CA B:ALA251 4.2 16.1 1.0
C B:PRO253 4.3 20.4 1.0
N B:ALA251 4.4 13.9 1.0
CA B:ARG252 4.4 15.2 1.0
CD1 B:LEU250 4.5 17.7 1.0
CA B:LEU250 4.6 13.9 1.0
N B:GLU256 4.6 23.1 1.0
C B:GLY254 4.7 22.4 1.0
CD B:GLU256 4.8 40.7 1.0
CG B:LEU250 4.9 13.6 1.0
CA B:GLY254 4.9 23.2 1.0
CA B:GLU256 5.0 24.9 1.0

Reference:

L.M.R.Jensen, C.M.Wilmot. Mutagenesis of TRYPTOPHAN199 Reveals That Electron Hopping Is Required For Maug-Dependent Tryptophan Tryptophylquinone Biosynthesis To Be Published.
Page generated: Mon Oct 7 12:50:48 2024

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