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Sodium in PDB 4fa9: Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 Days

Enzymatic activity of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 Days

All present enzymatic activity of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 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 30 Days, PDB code: 4fa9 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) 44.49 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.530, 83.540, 107.780, 109.94, 91.54, 105.78
R / Rfree (%) 15.7 / 21.4

Other elements in 4fa9:

The structure of Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 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 30 Days (pdb code 4fa9). 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 Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 Days, PDB code: 4fa9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4fa9

Go back to Sodium Binding Sites List in 4fa9
Sodium binding site 1 out of 4 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 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 30 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:55.8
occ:1.00
 OD1 A:ASN231 2.4 51.9 1.0
OG1 A:THR233 2.6 54.4 1.0
CG A:ASN231 3.3 46.9 1.0
ND2 A:ASN231 3.6 44.0 1.0
O A:HOH576 3.8 25.0 1.0
CB A:THR233 3.8 53.5 1.0
N A:THR233 4.0 53.1 1.0
CG2 A:THR233 4.1 54.9 1.0
CA A:THR233 4.4 52.7 1.0
N A:ALA234 4.6 47.8 1.0
CB A:ASN231 4.6 48.0 1.0
N A:GLU232 4.7 51.9 1.0
C A:ASN231 4.7 49.9 1.0
CA A:ASN231 4.8 48.6 1.0
O A:VAL283 5.0 45.3 1.0
C A:THR233 5.0 50.6 1.0

Sodium binding site 2 out of 4 in 4fa9

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Sodium binding site 2 out of 4 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 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 30 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:52.0
occ:1.00
 O A:LEU250 2.1 40.4 1.0
O A:ILE255 2.4 47.6 1.0
O A:ARG252 2.7 42.0 1.0
C A:LEU250 3.3 39.2 1.0
C A:ILE255 3.5 46.7 1.0
C A:ARG252 3.6 41.6 1.0
C A:ALA251 3.9 41.0 1.0
N A:ILE255 4.0 45.2 1.0
N A:ARG252 4.0 40.9 1.0
CA A:ILE255 4.1 45.3 1.0
CB A:ILE255 4.1 44.4 1.0
CA A:PRO253 4.2 45.1 1.0
CD1 A:LEU250 4.2 40.7 1.0
CA A:ALA251 4.2 40.9 1.0
N A:ALA251 4.2 39.7 1.0
N A:GLY254 4.2 46.2 1.0
OE2 A:GLU256 4.2 60.5 1.0
O A:ALA251 4.2 41.0 1.0
N A:PRO253 4.3 42.8 1.0
OE1 A:GLU256 4.3 62.3 1.0
CA A:LEU250 4.3 38.6 1.0
CA A:ARG252 4.5 40.1 1.0
C A:PRO253 4.5 45.4 1.0
CD A:GLU256 4.5 59.2 1.0
CG A:LEU250 4.6 40.9 1.0
N A:GLU256 4.6 47.5 1.0
C A:GLY254 4.8 46.3 1.0
CA A:GLU256 4.9 49.2 1.0
CG2 A:ILE255 5.0 41.1 1.0
O A:LEU249 5.0 36.3 1.0

Sodium binding site 3 out of 4 in 4fa9

Go back to Sodium Binding Sites List in 4fa9
Sodium binding site 3 out of 4 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 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 30 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:42.1
occ:1.00
 O B:LEU250 2.2 31.9 1.0
O B:ILE255 2.3 35.9 1.0
O B:HOH679 2.4 33.5 1.0
O B:ARG252 2.6 31.2 1.0
C B:LEU250 3.4 31.1 1.0
C B:ILE255 3.5 36.3 1.0
C B:ARG252 3.7 32.5 1.0
N B:ILE255 3.7 36.4 1.0
C B:ALA251 3.8 32.7 1.0
CA B:ILE255 4.0 36.0 1.0
CA B:ALA251 4.1 31.5 1.0
CB B:ILE255 4.1 34.0 1.0
O B:ALA251 4.1 34.1 1.0
N B:ARG252 4.1 30.7 1.0
CD1 B:LEU250 4.1 31.4 1.0
N B:ALA251 4.2 30.7 1.0
CA B:PRO253 4.2 35.0 1.0
N B:GLY254 4.3 36.7 1.0
CA B:LEU250 4.4 30.3 1.0
N B:PRO253 4.4 34.0 1.0
OE2 B:GLU256 4.5 60.8 1.0
C B:PRO253 4.5 36.3 1.0
CA B:ARG252 4.6 31.0 1.0
N B:GLU256 4.6 37.0 1.0
CG B:LEU250 4.6 31.9 1.0
C B:GLY254 4.7 37.3 1.0
OE1 B:GLU256 4.7 59.2 1.0
CD B:GLU256 4.7 56.4 1.0
O B:LEU249 4.9 28.5 1.0
CG2 B:ILE255 5.0 33.9 1.0
CA B:GLU256 5.0 38.9 1.0

Sodium binding site 4 out of 4 in 4fa9

Go back to Sodium Binding Sites List in 4fa9
Sodium binding site 4 out of 4 in the Crystal Structure of Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 Days


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 Wt Maug in Complex with Pre-Methylamine Dehydrogenase Aged 30 Days within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:38.5
occ:1.00
 OG1 B:THR233 2.3 37.2 1.0
O B:HOH621 2.3 27.0 1.0
OD1 B:ASN231 2.4 32.9 1.0
O B:HOH608 2.6 24.9 1.0
O B:HOH694 2.6 26.8 1.0
CG B:ASN231 3.3 31.3 1.0
ND2 B:ASN231 3.5 30.1 1.0
CB B:THR233 3.5 37.3 1.0
CG2 B:THR233 3.8 38.0 1.0
O B:HOH617 3.8 32.2 1.0
N B:THR233 3.9 35.3 1.0
CA B:THR233 4.2 36.0 1.0
N B:ALA234 4.3 32.0 1.0
CB B:ASN231 4.6 29.4 1.0
N B:GLU232 4.7 32.8 1.0
C B:THR233 4.7 34.5 1.0
C B:ASN231 4.7 31.0 1.0
CA B:ASN231 4.9 30.2 1.0
O B:HOH627 4.9 30.8 1.0
C B:GLU232 5.0 34.5 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: Mon Oct 7 15:18:38 2024

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