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Sodium in PDB 3pxt: Crystal Structure of Ferrous Co Adduct of Maug in Complex with Pre- Methylamine Dehydrogenase

Enzymatic activity of Crystal Structure of Ferrous Co Adduct of Maug in Complex with Pre- Methylamine Dehydrogenase

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

Protein crystallography data

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

Resolution Low / High (Å) 44.49 / 2.16
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 / 22.6

Other elements in 3pxt:

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

Sodium binding site 1 out of 3 in 3pxt

Go back to Sodium Binding Sites List in 3pxt
Sodium binding site 1 out of 3 in the Crystal Structure of Ferrous Co Adduct of 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 Ferrous Co Adduct of Maug in Complex with Pre- Methylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na374

b:39.8
occ:1.00
 O A:HOH519 2.2 25.8 1.0
O A:HOH382 2.4 19.7 1.0
O A:HOH680 2.5 23.3 1.0
O A:HOH388 2.5 16.6 1.0
OD1 A:ASN231 2.5 31.9 1.0
OG1 A:THR233 2.6 31.7 1.0
CG A:ASN231 3.4 31.4 1.0
ND2 A:ASN231 3.7 29.4 1.0
CB A:THR233 3.9 32.4 1.0
N A:THR233 4.1 32.7 1.0
O A:HOH908 4.3 19.6 1.0
CG2 A:THR233 4.4 32.8 1.0
CA A:THR233 4.6 32.3 1.0
O A:HOH862 4.6 27.1 1.0
N A:ALA234 4.6 30.6 1.0
N A:GLU232 4.7 33.1 1.0
CB A:ASN231 4.7 31.1 1.0
C A:ASN231 4.9 32.4 1.0
O A:VAL283 4.9 27.0 1.0
CA A:ASN231 5.0 31.6 1.0

Sodium binding site 2 out of 3 in 3pxt

Go back to Sodium Binding Sites List in 3pxt
Sodium binding site 2 out of 3 in the Crystal Structure of Ferrous Co Adduct of 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 Ferrous Co Adduct of Maug in Complex with Pre- Methylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na375

b:41.6
occ:1.00
 O A:HOH865 2.2 29.9 1.0
O A:HOH1080 2.4 34.1 1.0
O A:LEU250 2.5 29.4 1.0
O A:HOH436 2.5 24.6 1.0
O A:ILE255 2.5 34.4 1.0
O A:ARG252 2.9 31.2 1.0
C A:ILE255 3.7 34.1 1.0
C A:LEU250 3.7 28.7 1.0
C A:ARG252 3.7 31.0 1.0
C A:ALA251 4.0 29.6 1.0
N A:ILE255 4.0 33.4 1.0
O A:ALA251 4.1 30.0 1.0
OE2 A:GLU256 4.2 42.9 1.0
CA A:ILE255 4.2 33.6 1.0
N A:ARG252 4.3 29.9 1.0
CA A:PRO253 4.4 32.1 1.0
CB A:ILE255 4.4 32.9 1.0
N A:PRO253 4.4 31.4 1.0
CA A:ALA251 4.4 29.5 1.0
N A:GLY254 4.4 33.0 1.0
OE1 A:GLU256 4.4 42.4 1.0
N A:ALA251 4.5 28.9 1.0
CD A:GLU256 4.6 41.4 1.0
CA A:ARG252 4.6 30.2 1.0
CD1 A:LEU250 4.6 29.2 1.0
CA A:LEU250 4.7 28.1 1.0
C A:PRO253 4.7 32.5 1.0
N A:GLU256 4.8 34.7 1.0
CG A:LEU250 4.8 29.2 1.0
C A:GLY254 4.9 33.7 1.0

Sodium binding site 3 out of 3 in 3pxt

Go back to Sodium Binding Sites List in 3pxt
Sodium binding site 3 out of 3 in the Crystal Structure of Ferrous Co Adduct of 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 Ferrous Co Adduct of Maug in Complex with Pre- Methylamine Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na374

b:35.1
occ:1.00
 O B:HOH974 2.3 26.8 1.0
O B:HOH444 2.4 19.9 1.0
O B:HOH440 2.4 20.2 1.0
OG1 B:THR233 2.5 26.8 1.0
O B:HOH437 2.6 23.2 1.0
OD1 B:ASN231 2.6 26.5 1.0
CG B:ASN231 3.5 25.4 1.0
O B:HOH447 3.6 22.8 1.0
ND2 B:ASN231 3.8 24.6 1.0
CB B:THR233 3.9 27.6 1.0
O B:HOH913 4.1 31.7 1.0
N B:THR233 4.2 26.8 1.0
CG2 B:THR233 4.3 28.0 1.0
O B:HOH779 4.5 23.6 1.0
CA B:THR233 4.6 27.2 1.0
N B:ALA234 4.8 26.1 1.0
CB B:ASN231 4.9 24.8 1.0
N B:GLU232 5.0 26.3 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: Tue Dec 15 06:22:05 2020

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