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Sodium in PDB 3sjl: Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex

Enzymatic activity of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex

All present enzymatic activity of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex:
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of the P107S-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3sjl 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) 29.39 / 1.63
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.606, 89.001, 104.812, 67.05, 79.51, 79.72
R / Rfree (%) 14.2 / 18

Other elements in 3sjl:

The structure of Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex (pdb code 3sjl). 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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex, PDB code: 3sjl:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3sjl

Go back to Sodium Binding Sites List in 3sjl
Sodium binding site 1 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:31.8
occ:1.00
 OG1 A:THR233 2.3 37.3 1.0
OD1 A:ASN231 2.3 24.3 1.0
O A:HOH934 2.4 19.4 1.0
O A:HOH854 2.4 23.9 1.0
O A:HOH492 2.5 18.7 1.0
O A:HOH381 2.7 26.0 1.0
CG A:ASN231 3.3 23.7 1.0
CB A:THR233 3.5 34.0 1.0
ND2 A:ASN231 3.6 22.1 1.0
CG2 A:THR233 3.8 34.7 1.0
N A:THR233 3.8 29.5 1.0
CA A:THR233 4.2 33.8 1.0
N A:ALA234 4.3 31.4 1.0
O A:HOH980 4.5 28.5 1.0
CB A:ASN231 4.6 22.3 1.0
N A:GLU232 4.7 27.4 1.0
C A:THR233 4.7 33.9 1.0
C A:ASN231 4.7 25.7 1.0
CA A:ASN231 4.8 25.1 1.0
C A:GLU232 4.9 30.7 1.0

Sodium binding site 2 out of 4 in 3sjl

Go back to Sodium Binding Sites List in 3sjl
Sodium binding site 2 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:26.5
occ:1.00
 O A:ILE255 2.3 25.1 1.0
O A:LEU250 2.4 22.2 1.0
O A:HOH1653 2.4 22.6 1.0
O A:HOH947 2.5 15.8 1.0
O A:HOH777 2.5 19.7 1.0
O A:ARG252 2.6 22.7 1.0
C A:ILE255 3.4 23.6 1.0
C A:ARG252 3.5 21.6 1.0
C A:LEU250 3.5 21.2 1.0
N A:ILE255 3.8 24.7 1.0
C A:ALA251 3.9 22.9 1.0
CA A:ILE255 4.0 23.8 1.0
N A:ARG252 4.0 21.4 1.0
N A:GLY254 4.1 27.2 1.0
CA A:PRO253 4.1 25.0 1.0
OE1 A:GLU256 4.2 43.7 1.0
CB A:ILE255 4.2 22.6 1.0
O A:ALA251 4.2 24.5 1.0
N A:PRO253 4.2 24.8 1.0
CA A:ALA251 4.2 21.7 1.0
N A:ALA251 4.3 20.0 1.0
C A:PRO253 4.4 25.9 1.0
CA A:ARG252 4.4 20.9 1.0
CD1 A:LEU250 4.5 18.6 1.0
CD A:GLU256 4.5 41.2 1.0
CA A:LEU250 4.5 19.6 1.0
N A:GLU256 4.5 23.1 1.0
OE2 A:GLU256 4.7 46.6 1.0
C A:GLY254 4.7 27.6 1.0
CG A:LEU250 4.8 18.1 1.0
CA A:GLU256 4.9 26.1 1.0

Sodium binding site 3 out of 4 in 3sjl

Go back to Sodium Binding Sites List in 3sjl
Sodium binding site 3 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:30.1
occ:1.00
 O B:HOH999 2.3 21.8 1.0
O B:HOH1146 2.4 20.5 1.0
OD1 B:ASN231 2.4 22.0 1.0
O B:HOH409 2.4 16.0 1.0
OG1 B:THR233 2.4 30.7 1.0
O B:HOH1109 2.6 19.5 1.0
CG B:ASN231 3.2 19.9 1.0
ND2 B:ASN231 3.5 18.3 1.0
CB B:THR233 3.7 27.7 1.0
O B:HOH1889 3.9 23.4 1.0
CG2 B:THR233 4.0 31.9 1.0
N B:THR233 4.0 24.0 1.0
CA B:THR233 4.3 26.4 1.0
O B:HOH1842 4.4 25.8 1.0
O B:HOH2179 4.4 23.3 1.0
N B:ALA234 4.4 22.5 1.0
CB B:ASN231 4.6 16.9 1.0
N B:GLU232 4.7 21.3 1.0
C B:ASN231 4.8 19.2 1.0
CA B:ASN231 4.8 18.8 1.0
C B:THR233 4.9 24.9 1.0
O B:HOH1424 4.9 16.4 1.0

Sodium binding site 4 out of 4 in 3sjl

Go back to Sodium Binding Sites List in 3sjl
Sodium binding site 4 out of 4 in the Crystal Structure of the P107S-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 P107S-Maug/Pre-Methylamine Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:24.3
occ:1.00
 O B:ILE255 2.2 20.9 1.0
O B:LEU250 2.4 19.0 1.0
O B:HOH517 2.4 15.7 1.0
O B:HOH1261 2.5 19.8 1.0
O B:HOH818 2.5 24.4 1.0
O B:ARG252 2.6 20.7 1.0
C B:ILE255 3.4 21.0 1.0
C B:ARG252 3.5 20.5 1.0
C B:LEU250 3.6 17.5 1.0
N B:ILE255 3.7 22.8 1.0
C B:ALA251 4.0 18.9 1.0
CA B:ILE255 4.0 20.8 1.0
N B:ARG252 4.0 18.2 1.0
N B:GLY254 4.1 25.9 1.0
CA B:PRO253 4.1 23.7 1.0
CB B:ILE255 4.2 19.6 1.0
O B:ALA251 4.2 20.9 1.0
CA B:ALA251 4.2 19.5 1.0
N B:PRO253 4.2 22.1 1.0
OE2 B:GLU256 4.3 40.7 1.0
N B:ALA251 4.3 17.6 1.0
C B:PRO253 4.4 22.8 1.0
CA B:ARG252 4.4 19.3 1.0
OE1 B:GLU256 4.4 39.1 1.0
CD1 B:LEU250 4.5 21.2 1.0
CD B:GLU256 4.5 32.3 1.0
N B:GLU256 4.6 20.5 1.0
CA B:LEU250 4.6 16.4 1.0
C B:GLY254 4.7 28.1 1.0
CG B:LEU250 4.8 18.7 1.0
CA B:GLU256 4.8 21.3 1.0
CA B:GLY254 5.0 26.5 1.0

Reference:

M.Feng, L.M.Jensen, E.T.Yukl, X.Wei, A.Liu, C.M.Wilmot, V.L.Davidson. Proline 107 Is A Major Determinant in Maintaining the Structure of the Distal Pocket and Reactivity of the High-Spin Heme of Maug. Biochemistry V. 51 1598 2012.
ISSN: ISSN 0006-2960
PubMed: 22299652
DOI: 10.1021/BI201882E
Page generated: Mon Oct 7 12:58:24 2024

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