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Sodium in PDB 4fa4: Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days

Enzymatic activity of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days

All present enzymatic activity of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days:
1.4.9.1; 1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days, PDB code: 4fa4 was solved by E.T.Yukl, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.46 / 2.14
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.530, 83.520, 107.780, 109.92, 91.52, 105.78
R / Rfree (%) 16.3 / 22.7

Other elements in 4fa4:

The structure of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days 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 Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days (pdb code 4fa4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days, PDB code: 4fa4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4fa4

Go back to Sodium Binding Sites List in 4fa4
Sodium binding site 1 out of 3 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days


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 Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:61.1
occ:1.00
O A:LEU250 2.1 41.5 1.0
O A:ILE255 2.3 47.3 1.0
O A:ARG252 2.8 40.3 1.0
C A:LEU250 3.3 40.6 1.0
C A:ILE255 3.5 46.6 1.0
C A:ARG252 3.7 40.5 1.0
C A:ALA251 4.0 41.7 1.0
CA A:ALA251 4.1 41.7 1.0
N A:ARG252 4.2 40.9 1.0
CA A:ILE255 4.2 45.0 1.0
N A:ALA251 4.2 40.8 1.0
N A:ILE255 4.2 45.3 1.0
OE2 A:GLU256 4.2 58.3 1.0
CB A:ILE255 4.2 43.8 1.0
CD1 A:LEU250 4.2 37.0 1.0
O A:ALA251 4.3 42.5 1.0
CA A:LEU250 4.3 39.3 1.0
CA A:PRO253 4.4 43.7 1.0
CG A:LEU250 4.4 41.6 1.0
N A:PRO253 4.4 42.1 1.0
N A:GLY254 4.5 44.7 1.0
OE1 A:GLU256 4.5 61.0 1.0
N A:GLU256 4.6 47.2 1.0
CA A:ARG252 4.6 39.8 1.0
CD A:GLU256 4.6 58.9 1.0
O A:HOH565 4.7 33.4 1.0
C A:PRO253 4.8 44.5 1.0
CA A:GLU256 4.9 48.3 1.0
O A:LEU249 4.9 37.5 1.0
CB A:LEU250 5.0 39.0 1.0
C A:GLY254 5.0 46.2 1.0

Sodium binding site 2 out of 3 in 4fa4

Go back to Sodium Binding Sites List in 4fa4
Sodium binding site 2 out of 3 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days


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 Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:38.4
occ:1.00
OD1 B:ASN231 2.2 31.6 1.0
OG1 B:THR233 2.3 31.8 1.0
O B:HOH688 2.4 35.9 1.0
O B:HOH756 2.5 30.6 1.0
O B:HOH572 2.5 21.9 1.0
O B:HOH657 2.8 24.8 1.0
CG B:ASN231 3.2 30.2 1.0
ND2 B:ASN231 3.5 25.4 1.0
CB B:THR233 3.5 33.6 1.0
N B:THR233 3.7 31.9 1.0
CG2 B:THR233 3.8 31.8 1.0
O B:HOH603 3.8 30.4 1.0
CA B:THR233 4.1 32.8 1.0
N B:ALA234 4.3 30.6 1.0
O B:HOH706 4.4 23.0 1.0
CB B:ASN231 4.5 29.2 1.0
O B:HOH663 4.6 24.8 1.0
N B:GLU232 4.6 30.2 1.0
C B:THR233 4.7 31.8 1.0
C B:ASN231 4.7 30.5 1.0
C B:GLU232 4.8 32.1 1.0
O B:HOH737 4.8 25.0 1.0
CA B:ASN231 4.8 29.9 1.0

Sodium binding site 3 out of 3 in 4fa4

Go back to Sodium Binding Sites List in 4fa4
Sodium binding site 3 out of 3 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days


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 Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 10 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:42.3
occ:1.00
O B:LEU250 2.2 29.4 1.0
O B:ILE255 2.2 34.0 1.0
O B:HOH713 2.3 40.1 1.0
O B:HOH638 2.4 37.0 1.0
O B:ARG252 2.7 32.3 1.0
C B:ILE255 3.4 36.1 1.0
C B:LEU250 3.4 30.0 1.0
C B:ARG252 3.7 32.1 1.0
N B:ILE255 3.8 36.0 1.0
OE2 B:GLU256 3.9 48.3 1.0
C B:ALA251 4.0 30.4 1.0
CA B:ILE255 4.0 35.6 1.0
CA B:PRO253 4.1 34.4 1.0
N B:ARG252 4.2 29.6 1.0
CA B:ALA251 4.2 29.4 1.0
N B:GLY254 4.2 36.2 1.0
N B:ALA251 4.2 29.1 1.0
O B:ALA251 4.4 30.8 1.0
CB B:ILE255 4.4 34.9 1.0
N B:PRO253 4.4 33.3 1.0
CA B:LEU250 4.4 29.4 1.0
CD1 B:LEU250 4.4 30.0 1.0
C B:PRO253 4.4 35.3 1.0
N B:GLU256 4.5 36.2 1.0
O B:HOH694 4.5 41.3 1.0
CD B:GLU256 4.5 46.6 1.0
CA B:ARG252 4.6 30.4 1.0
C B:GLY254 4.7 37.3 1.0
CG B:LEU250 4.8 31.2 1.0
CA B:GLU256 4.8 36.7 1.0
OE1 B:GLU256 4.9 51.4 1.0

Reference:

E.T.Yukl, F.Liu, J.Krzystek, S.Shin, L.M.Jensen, V.L.Davidson, C.M.Wilmot, A.Liu. Diradical Intermediate Within the Context of Tryptophan Tryptophylquinone Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 110 4569 2013.
ISSN: ISSN 0027-8424
PubMed: 23487750
DOI: 10.1073/PNAS.1215011110
Page generated: Tue Dec 15 06:39:50 2020

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