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Sodium in PDB 3rn0: Crystal Structure of the W199K-Maug/Pre-Methylamine Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the W199K-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the W199K-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the W199K-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3rn0 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) 39.58 / 1.91
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 (%) 17.3 / 23

Other elements in 3rn0:

The structure of Crystal Structure of the W199K-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 W199K-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 3rn0). 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 W199K-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3rn0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3rn0

Go back to Sodium Binding Sites List in 3rn0
Sodium binding site 1 out of 4 in the Crystal Structure of the W199K-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 W199K-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:45.8
occ:1.00
 O A:HOH478 2.2 19.9 1.0
O A:HOH849 2.3 23.3 1.0
OD1 A:ASN231 2.4 38.6 1.0
O A:HOH379 2.5 11.1 1.0
O A:HOH789 2.5 21.7 1.0
OG1 A:THR233 2.6 42.0 1.0
CG A:ASN231 3.3 37.5 1.0
ND2 A:ASN231 3.6 37.5 1.0
CB A:THR233 3.7 43.5 1.0
N A:THR233 3.9 43.3 1.0
CG2 A:THR233 3.9 44.6 1.0
O A:HOH805 4.2 22.1 1.0
CA A:THR233 4.3 43.1 1.0
N A:ALA234 4.4 39.1 1.0
O A:HOH453 4.6 13.1 1.0
CB A:ASN231 4.6 36.5 1.0
N A:GLU232 4.7 40.9 1.0
C A:ASN231 4.7 39.0 1.0
C A:THR233 4.8 41.5 1.0
CA A:ASN231 4.8 38.5 1.0
O A:HOH883 5.0 36.3 1.0

Sodium binding site 2 out of 4 in 3rn0

Go back to Sodium Binding Sites List in 3rn0
Sodium binding site 2 out of 4 in the Crystal Structure of the W199K-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 W199K-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:37.4
occ:1.00
 O A:LEU250 2.2 34.8 1.0
O A:HOH861 2.3 33.4 1.0
O A:ILE255 2.4 39.1 1.0
O A:ARG252 2.5 39.9 1.0
C A:ARG252 3.4 37.8 1.0
C A:LEU250 3.4 33.0 1.0
C A:ILE255 3.6 39.1 1.0
C A:ALA251 3.8 37.5 1.0
N A:ILE255 4.0 40.1 1.0
O A:ALA251 4.0 39.0 1.0
N A:ARG252 4.0 37.5 1.0
CA A:PRO253 4.1 40.4 1.0
CA A:ALA251 4.1 36.8 1.0
CA A:ILE255 4.1 38.2 1.0
CB A:ILE255 4.1 36.9 1.0
N A:PRO253 4.1 39.2 1.0
N A:ALA251 4.2 34.6 1.0
N A:GLY254 4.3 41.1 1.0
OE2 A:GLU256 4.4 58.1 1.0
CA A:ARG252 4.4 36.9 1.0
CD1 A:LEU250 4.4 30.1 1.0
CA A:LEU250 4.5 31.6 1.0
C A:PRO253 4.5 40.9 1.0
N A:GLU256 4.7 39.5 1.0
CG A:LEU250 4.8 32.5 1.0
C A:GLY254 4.9 41.3 1.0
CG2 A:ILE255 4.9 37.2 1.0

Sodium binding site 3 out of 4 in 3rn0

Go back to Sodium Binding Sites List in 3rn0
Sodium binding site 3 out of 4 in the Crystal Structure of the W199K-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 W199K-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:41.1
occ:1.00
 O B:HOH973 2.3 26.1 1.0
OD1 B:ASN231 2.4 30.8 1.0
O B:HOH897 2.4 31.7 1.0
O B:HOH998 2.5 21.1 1.0
OG1 B:THR233 2.5 34.9 1.0
O B:HOH410 2.9 23.7 1.0
CG B:ASN231 3.4 30.1 1.0
CB B:THR233 3.6 33.0 1.0
ND2 B:ASN231 3.7 28.7 1.0
N B:THR233 3.9 31.4 1.0
CG2 B:THR233 3.9 32.6 1.0
CA B:THR233 4.2 31.3 1.0
N B:ALA234 4.5 26.8 1.0
O B:HOH733 4.6 25.9 1.0
CB B:ASN231 4.7 27.1 1.0
N B:GLU232 4.7 29.8 1.0
C B:ASN231 4.8 28.1 1.0
C B:THR233 4.8 30.7 1.0
CA B:ASN231 4.9 28.3 1.0

Sodium binding site 4 out of 4 in 3rn0

Go back to Sodium Binding Sites List in 3rn0
Sodium binding site 4 out of 4 in the Crystal Structure of the W199K-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 W199K-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:35.5
occ:1.00
 O B:LEU250 2.3 28.1 1.0
O B:ILE255 2.3 30.2 1.0
O B:HOH762 2.4 29.8 1.0
O B:HOH1082 2.5 25.9 1.0
O B:HOH502 2.6 26.6 1.0
O B:ARG252 2.7 27.6 1.0
C B:LEU250 3.5 27.5 1.0
C B:ILE255 3.5 32.0 1.0
C B:ARG252 3.6 29.1 1.0
C B:ALA251 3.8 28.8 1.0
N B:ILE255 3.9 33.8 1.0
O B:ALA251 4.0 30.8 1.0
N B:ARG252 4.0 27.5 1.0
CA B:ILE255 4.1 32.2 1.0
CA B:ALA251 4.1 27.4 1.0
CA B:PRO253 4.2 33.6 1.0
CD1 B:LEU250 4.2 22.9 1.0
N B:GLY254 4.2 35.1 1.0
CB B:ILE255 4.2 31.4 1.0
OE2 B:GLU256 4.3 49.0 1.0
N B:ALA251 4.3 25.9 1.0
N B:PRO253 4.4 32.1 1.0
C B:PRO253 4.5 34.8 1.0
CA B:LEU250 4.5 25.3 1.0
CA B:ARG252 4.5 28.2 1.0
N B:GLU256 4.6 31.0 1.0
CD B:GLU256 4.7 47.4 1.0
CG B:LEU250 4.7 26.6 1.0
C B:GLY254 4.8 35.8 1.0
CA B:GLU256 4.9 34.1 1.0
O B:LEU249 5.0 22.5 1.0

Reference:

N.A.Tarboush, L.M.Jensen, E.T.Yukl, J.Geng, A.Liu, C.M.Wilmot, V.L.Davidson. Mutagenesis of TRYPTOPHAN199 Suggests That Hopping Is Required For Maug-Dependent Tryptophan Tryptophylquinone Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 108 16956 2011.
ISSN: ISSN 0027-8424
PubMed: 21969534
DOI: 10.1073/PNAS.1109423108
Page generated: Mon Oct 7 12:50:38 2024

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