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Sodium in PDB 3rmz: Crystal Structure of the W199F-Maug/Pre-Methylamine Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the W199F-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the W199F-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the W199F-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3rmz 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 / 1.72
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 (%) 13.8 / 18.1

Other elements in 3rmz:

The structure of Crystal Structure of the W199F-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 W199F-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 3rmz). 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 W199F-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3rmz:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3rmz

Go back to Sodium Binding Sites List in 3rmz
Sodium binding site 1 out of 4 in the Crystal Structure of the W199F-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 W199F-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:23.2
occ:1.00
 O A:HOH934 2.3 17.6 1.0
OD1 A:ASN231 2.4 19.5 1.0
O A:HOH854 2.4 17.0 1.0
OG1 A:THR233 2.4 23.9 1.0
O A:HOH382 2.4 13.0 1.0
O A:HOH492 2.4 17.3 1.0
CG A:ASN231 3.2 18.6 1.0
ND2 A:ASN231 3.5 19.6 1.0
CB A:THR233 3.6 21.2 1.0
N A:THR233 3.9 19.2 1.0
O A:HOH1056 3.9 17.9 1.0
O A:HOH878 4.0 24.6 1.0
CG2 A:THR233 4.0 25.0 1.0
CA A:THR233 4.2 21.6 1.0
O A:HOH1425 4.3 24.0 1.0
N A:ALA234 4.4 18.6 1.0
O A:HOH453 4.5 15.1 1.0
O A:HOH980 4.5 27.7 1.0
CB A:ASN231 4.6 18.4 1.0
N A:GLU232 4.6 19.7 1.0
C A:ASN231 4.7 20.4 1.0
C A:THR233 4.8 20.6 1.0
CA A:ASN231 4.8 19.9 1.0
C A:GLU232 5.0 21.0 1.0

Sodium binding site 2 out of 4 in 3rmz

Go back to Sodium Binding Sites List in 3rmz
Sodium binding site 2 out of 4 in the Crystal Structure of the W199F-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 W199F-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.8
occ:1.00
 O A:LEU250 2.3 20.6 1.0
O A:HOH1611 2.4 26.5 1.0
O A:ILE255 2.4 24.9 1.0
O A:HOH947 2.5 21.2 1.0
O A:ARG252 2.6 20.6 1.0
O A:HOH777 2.7 28.7 1.0
C A:LEU250 3.5 19.9 1.0
C A:ILE255 3.5 24.1 1.0
C A:ARG252 3.6 22.5 1.0
N A:ILE255 3.9 22.5 1.0
C A:ALA251 4.0 21.6 1.0
N A:ARG252 4.0 19.8 1.0
CA A:ILE255 4.1 22.1 1.0
CA A:PRO253 4.2 25.5 1.0
CB A:ILE255 4.2 21.7 1.0
O A:ALA251 4.2 20.3 1.0
N A:GLY254 4.2 24.1 1.0
N A:PRO253 4.3 24.2 1.0
CA A:ALA251 4.3 21.2 1.0
N A:ALA251 4.3 19.9 1.0
OE2 A:GLU256 4.3 43.7 1.0
CD1 A:LEU250 4.4 19.1 1.0
C A:PRO253 4.5 24.9 1.0
CA A:ARG252 4.5 20.4 1.0
CA A:LEU250 4.5 17.7 1.0
N A:GLU256 4.6 23.7 1.0
CD A:GLU256 4.7 43.1 1.0
OE1 A:GLU256 4.7 47.5 1.0
CG A:LEU250 4.7 17.1 1.0
C A:GLY254 4.8 24.8 1.0
CG2 A:ILE255 5.0 22.9 1.0
O A:LEU249 5.0 17.4 1.0
CA A:GLU256 5.0 26.4 1.0

Sodium binding site 3 out of 4 in 3rmz

Go back to Sodium Binding Sites List in 3rmz
Sodium binding site 3 out of 4 in the Crystal Structure of the W199F-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 W199F-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:22.5
occ:1.00
 O B:HOH1109 2.3 15.8 1.0
OD1 B:ASN231 2.4 19.2 1.0
OG1 B:THR233 2.4 22.2 1.0
O B:HOH999 2.4 20.0 1.0
O B:HOH1146 2.4 19.6 1.0
O B:HOH411 2.4 14.3 1.0
CG B:ASN231 3.2 16.0 1.0
ND2 B:ASN231 3.4 16.1 1.0
CB B:THR233 3.6 18.9 1.0
O B:HOH1020 3.8 19.2 1.0
N B:THR233 3.9 18.0 1.0
CG2 B:THR233 4.0 23.4 1.0
O B:HOH1474 4.0 25.7 1.0
CA B:THR233 4.3 18.8 1.0
O B:HOH1564 4.3 29.6 1.0
O B:HOH787 4.5 15.2 1.0
N B:ALA234 4.5 16.6 1.0
CB B:ASN231 4.6 14.1 1.0
O B:HOH1367 4.7 25.3 1.0
N B:GLU232 4.8 17.4 1.0
C B:ASN231 4.8 17.4 1.0
C B:THR233 4.9 17.4 1.0
CA B:ASN231 4.9 16.8 1.0

Sodium binding site 4 out of 4 in 3rmz

Go back to Sodium Binding Sites List in 3rmz
Sodium binding site 4 out of 4 in the Crystal Structure of the W199F-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 W199F-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:24.4
occ:1.00
 O B:ILE255 2.4 21.6 1.0
O B:LEU250 2.4 17.3 1.0
O B:HOH1261 2.4 22.7 1.0
O B:HOH818 2.4 27.4 1.0
O B:HOH517 2.5 21.9 1.0
O B:ARG252 2.6 19.1 1.0
C B:ARG252 3.5 20.0 1.0
C B:ILE255 3.5 20.2 1.0
C B:LEU250 3.5 16.5 1.0
N B:ILE255 3.8 22.4 1.0
C B:ALA251 3.8 19.2 1.0
N B:ARG252 4.0 16.8 1.0
CA B:PRO253 4.0 23.0 1.0
N B:GLY254 4.1 23.6 1.0
CA B:ILE255 4.1 19.4 1.0
O B:ALA251 4.1 20.1 1.0
N B:PRO253 4.1 21.8 1.0
OE2 B:GLU256 4.2 36.8 1.0
CA B:ALA251 4.2 19.1 1.0
CB B:ILE255 4.2 19.4 1.0
N B:ALA251 4.3 17.1 1.0
C B:PRO253 4.4 23.0 1.0
CA B:ARG252 4.4 18.6 1.0
CD1 B:LEU250 4.5 19.7 1.0
CA B:LEU250 4.5 14.8 1.0
CD B:GLU256 4.6 36.5 1.0
N B:GLU256 4.6 19.4 1.0
C B:GLY254 4.7 24.8 1.0
OE1 B:GLU256 4.8 43.2 1.0
CG B:LEU250 4.8 15.3 1.0
CA B:GLU256 5.0 22.6 1.0
CA B:GLY254 5.0 24.6 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 12:50:32 2024

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