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Sodium in PDB 3pxs: Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:

Enzymatic activity of Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:

All present enzymatic activity of Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase::
1.4.99.3;

Protein crystallography data

The structure of Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:, PDB code: 3pxs was solved by E.T.Yukl, B.R.Goblirsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.49 / 2.22
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.530, 83.520, 107.780, 109.94, 91.54, 105.78
R / Rfree (%) 17.7 / 22.9

Other elements in 3pxs:

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

Sodium binding site 1 out of 4 in 3pxs

Go back to Sodium Binding Sites List in 3pxs
Sodium binding site 1 out of 4 in the Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:


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 Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase: within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na374

b:25.5
occ:1.00
 O A:HOH808 2.3 22.2 1.0
O A:HOH686 2.3 15.1 1.0
O A:HOH418 2.4 15.0 1.0
OD1 A:ASN231 2.4 25.5 1.0
O A:HOH426 2.4 15.9 1.0
OG1 A:THR233 2.9 29.6 1.0
CG A:ASN231 3.3 26.9 1.0
ND2 A:ASN231 3.6 24.2 1.0
O A:HOH681 3.9 29.2 1.0
CB A:THR233 4.1 29.8 1.0
N A:THR233 4.2 29.7 1.0
CG2 A:THR233 4.4 30.2 1.0
O A:HOH752 4.5 10.9 1.0
CB A:ASN231 4.7 27.0 1.0
N A:ALA234 4.7 28.5 1.0
CA A:THR233 4.7 29.8 1.0
N A:GLU232 4.7 29.5 1.0
C A:ASN231 4.9 28.6 1.0
CA A:ASN231 5.0 27.7 1.0
O A:VAL283 5.0 23.9 1.0

Sodium binding site 2 out of 4 in 3pxs

Go back to Sodium Binding Sites List in 3pxs
Sodium binding site 2 out of 4 in the Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:


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 Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase: within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na375

b:30.0
occ:1.00
 O A:HOH1052 2.3 32.8 1.0
O A:LEU250 2.4 26.9 1.0
O A:HOH727 2.4 23.1 1.0
O A:HOH973 2.5 22.4 1.0
O A:ILE255 2.5 31.8 1.0
O A:ARG252 2.7 28.4 1.0
C A:LEU250 3.6 26.6 1.0
C A:ARG252 3.6 28.1 1.0
C A:ILE255 3.6 31.8 1.0
C A:ALA251 4.0 27.1 1.0
OE2 A:GLU256 4.0 37.2 1.0
O A:ALA251 4.1 27.3 1.0
N A:ILE255 4.1 31.2 1.0
OE1 A:GLU256 4.2 37.3 1.0
N A:ARG252 4.2 27.2 1.0
CA A:PRO253 4.2 29.3 1.0
CA A:ILE255 4.2 31.4 1.0
N A:PRO253 4.3 28.8 1.0
N A:GLY254 4.3 30.1 1.0
CA A:ALA251 4.3 26.9 1.0
CB A:ILE255 4.3 31.1 1.0
N A:ALA251 4.4 26.7 1.0
CD A:GLU256 4.4 36.8 1.0
CA A:ARG252 4.5 27.5 1.0
C A:PRO253 4.6 29.8 1.0
CD1 A:LEU250 4.6 27.1 1.0
CA A:LEU250 4.6 26.2 1.0
N A:GLU256 4.7 32.2 1.0
CG A:LEU250 4.8 26.7 1.0
C A:GLY254 4.9 31.2 1.0

Sodium binding site 3 out of 4 in 3pxs

Go back to Sodium Binding Sites List in 3pxs
Sodium binding site 3 out of 4 in the Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:


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 Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase: within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na374

b:32.8
occ:1.00
 O B:HOH391 2.4 25.2 1.0
O B:HOH944 2.4 22.1 1.0
O B:HOH945 2.4 25.9 1.0
O B:HOH888 2.5 29.1 1.0
OD1 B:ASN231 2.5 23.1 1.0
OG1 B:THR233 2.7 26.3 1.0
CG B:ASN231 3.4 23.5 1.0
ND2 B:ASN231 3.8 22.8 1.0
O B:HOH540 3.8 23.2 1.0
CB B:THR233 3.9 26.5 1.0
N B:THR233 4.2 26.1 1.0
CG2 B:THR233 4.2 26.9 1.0
CA B:THR233 4.6 26.4 1.0
O B:HOH740 4.7 19.1 1.0
N B:ALA234 4.7 25.5 1.0
CB B:ASN231 4.8 23.6 1.0
N B:GLU232 4.8 25.1 1.0
C B:ASN231 5.0 24.6 1.0

Sodium binding site 4 out of 4 in 3pxs

Go back to Sodium Binding Sites List in 3pxs
Sodium binding site 4 out of 4 in the Crystal Structure of Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase:


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 Diferrous Maug in Complex with Pre-Methylamine Dehydrogenase: within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na375

b:31.1
occ:1.00
 O B:HOH748 2.3 25.2 1.0
O B:LEU250 2.4 25.1 1.0
O B:HOH713 2.5 20.9 1.0
O B:ILE255 2.5 28.8 1.0
O B:HOH420 2.5 21.4 1.0
O B:ARG252 2.7 25.9 1.0
C B:ARG252 3.6 25.8 1.0
C B:LEU250 3.6 24.7 1.0
C B:ILE255 3.7 29.0 1.0
O B:ALA251 3.9 25.1 1.0
C B:ALA251 3.9 24.8 1.0
CA B:PRO253 4.1 27.1 1.0
N B:ILE255 4.1 28.4 1.0
N B:PRO253 4.2 26.4 1.0
N B:GLY254 4.2 27.9 1.0
N B:ARG252 4.3 24.7 1.0
CA B:ALA251 4.3 24.5 1.0
CA B:ILE255 4.3 28.4 1.0
N B:ALA251 4.4 24.5 1.0
CB B:ILE255 4.4 27.9 1.0
OE1 B:GLU256 4.5 37.6 1.0
OE2 B:GLU256 4.5 36.4 1.0
C B:PRO253 4.5 27.4 1.0
CD1 B:LEU250 4.6 25.2 1.0
CA B:ARG252 4.6 25.3 1.0
CD B:GLU256 4.6 35.8 1.0
CA B:LEU250 4.7 24.6 1.0
N B:GLU256 4.7 29.7 1.0
CG B:LEU250 4.9 25.6 1.0
C B:GLY254 5.0 28.7 1.0

Reference:

E.T.Yukl, B.R.Goblirsch, V.L.Davidson, C.M.Wilmot. Crystal Structures of Co and No Adducts of Maug in Complex with Pre-Methylamine Dehydrogenase: Implications For the Mechanism of Dioxygen Activation. Biochemistry V. 50 2931 2011.
ISSN: ISSN 0006-2960
PubMed: 21355604
DOI: 10.1021/BI200023N
Page generated: Mon Oct 7 12:23:28 2024

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