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Sodium in PDB 3fpc: Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh

Enzymatic activity of Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh

All present enzymatic activity of Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh:
1.1.1.2;

Protein crystallography data

The structure of Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh, PDB code: 3fpc was solved by F.Felix, E.Goihberg, L.Shimon, Y.Burstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.77 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.742, 82.429, 118.249, 90.00, 99.89, 90.00
R / Rfree (%) 11.6 / 15.5

Other elements in 3fpc:

The structure of Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh also contains other interesting chemical elements:

Arsenic (As) 4 atoms
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh (pdb code 3fpc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh, PDB code: 3fpc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3fpc

Go back to Sodium Binding Sites List in 3fpc
Sodium binding site 1 out of 2 in the Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na361

b:28.5
occ:1.00
OG C:SER103 2.2 7.2 0.5
O C:HOH754 2.6 26.2 1.0
O C:SER103 2.7 8.4 0.5
O C:SER103 2.7 8.8 0.5
NZ C:LYS111 2.8 20.5 1.0
O C:ALA108 3.0 7.4 1.0
N C:ASP89 3.1 7.3 1.0
CE C:LYS111 3.4 11.7 1.0
CB C:SER103 3.4 6.4 0.5
OD2 C:ASP89 3.4 13.5 0.5
C C:ALA108 3.5 6.3 1.0
C C:SER103 3.7 6.4 0.5
CA C:GLY109 3.7 5.0 1.0
C C:SER103 3.7 7.0 0.5
CB C:ASP89 3.7 5.7 0.5
CB C:SER103 3.8 9.4 0.5
N C:GLY109 3.8 5.9 1.0
CA C:PRO88 3.8 7.2 1.0
CG C:ASP89 3.8 9.5 0.5
O C:HOH2023 3.8 25.6 1.0
C C:PRO88 3.9 5.7 1.0
CB C:ASP89 3.9 7.0 0.5
CA C:ASP89 4.0 5.9 0.5
OG C:SER103 4.0 12.5 0.5
CA C:ASP89 4.0 6.4 0.5
CA C:SER103 4.1 6.3 0.5
CA C:SER103 4.3 7.3 0.5
CB C:ALA108 4.4 8.7 1.0
O C:THR87 4.6 7.2 1.0
CA C:ALA108 4.6 5.7 1.0
CD C:LYS111 4.6 7.0 1.0
CB C:PRO88 4.6 9.6 1.0
N C:SER103 4.6 5.8 0.5
OD1 C:ASP89 4.7 10.8 0.5
N C:SER103 4.7 6.4 0.5
C C:GLY109 4.7 6.0 1.0
O C:ASP89 4.7 8.7 1.0
CG C:LYS111 4.7 8.1 1.0
O C:HOH1081 4.7 32.4 1.0
N C:GLY104 4.8 8.3 1.0
C C:ASP89 4.9 6.7 1.0
N C:PRO88 4.9 5.9 1.0
O C:GLY109 5.0 6.0 1.0

Sodium binding site 2 out of 2 in 3fpc

Go back to Sodium Binding Sites List in 3fpc
Sodium binding site 2 out of 2 in the Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Chimera of Alcohol Dehydrogenase By Exchange of the Cofactor Binding Domain Res 153-294 of T. Brockii Adh By E. Histolytica Adh within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na361

b:24.6
occ:1.00
OG D:SER103 2.2 11.3 0.5
O D:SER103 2.7 10.0 0.5
O D:HOH2019 2.7 27.6 1.0
O D:SER103 2.8 10.2 0.5
N D:ASP89 3.0 8.1 1.0
O D:ALA108 3.0 8.9 1.0
NZ D:LYS111 3.0 25.6 1.0
CB D:SER103 3.3 10.3 0.5
CE D:LYS111 3.5 12.8 1.0
C D:ALA108 3.5 7.1 1.0
OD2 D:ASP89 3.6 14.7 0.5
C D:SER103 3.6 9.1 0.5
C D:SER103 3.7 8.8 0.5
CB D:ASP89 3.7 6.4 0.5
CA D:PRO88 3.7 7.0 1.0
CA D:GLY109 3.7 6.8 1.0
O D:HOH2016 3.8 19.7 1.0
CB D:ASP89 3.8 8.3 0.5
CB D:SER103 3.8 10.4 0.5
N D:GLY109 3.8 6.5 1.0
C D:PRO88 3.8 6.8 1.0
CG D:ASP89 3.8 11.0 0.5
OG D:SER103 3.9 8.8 0.5
CA D:ASP89 3.9 6.4 0.5
CA D:ASP89 3.9 6.8 0.5
CA D:SER103 4.0 9.2 0.5
CA D:SER103 4.2 9.4 0.5
CB D:PRO88 4.4 11.4 1.0
CB D:ALA108 4.5 7.9 1.0
O D:ASP89 4.6 9.8 1.0
N D:SER103 4.6 9.0 0.5
O D:HOH650 4.6 26.3 1.0
O D:THR87 4.6 7.2 1.0
CA D:ALA108 4.6 6.1 1.0
N D:SER103 4.6 9.0 0.5
OD1 D:ASP89 4.7 9.2 0.5
C D:GLY109 4.7 6.1 1.0
N D:GLY104 4.7 8.4 1.0
CD D:LYS111 4.7 8.7 1.0
C D:ASP89 4.7 6.7 1.0
CG D:LYS111 4.8 7.7 1.0
N D:PRO88 4.9 5.9 1.0
O D:PRO88 4.9 6.6 1.0
O D:GLY109 5.0 8.2 1.0

Reference:

E.Goihberg, M.Peretz, S.Tel-Or, O.Dym, L.Shimon, F.Frolow, Y.Burstein. Biochemical and Structural Properties of Chimeras Constructed By Exchange of Cofactor-Binding Domains in Alcohol Dehydrogenases From Thermophilic and Mesophilic Microorganisms Biochemistry V. 49 1943 2010.
ISSN: ISSN 0006-2960
PubMed: 20102159
DOI: 10.1021/BI901730X
Page generated: Tue Dec 15 06:11:00 2020

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