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Sodium in PDB 5b4v: Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate

Enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate

All present enzymatic activity of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate:
1.1.1.30;

Protein crystallography data

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate, PDB code: 5b4v was solved by H.Kanazawa, M.Tsunoda, M.M.Hoque, K.Suzuki, T.Yamamoto, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.03 / 1.50
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.770, 62.770, 119.310, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 16.3

Other elements in 5b4v:

The structure of Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate (pdb code 5b4v). 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 D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate, PDB code: 5b4v:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5b4v

Go back to Sodium Binding Sites List in 5b4v
Sodium binding site 1 out of 3 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate


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 D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:13.6
occ:0.50
 O A:HOH424 2.3 18.4 1.0
OXT A:ARG260 2.4 15.3 1.0
O A:HOH432 2.4 20.0 1.0
C A:ARG260 3.4 12.4 1.0
O A:ARG260 3.7 14.7 1.0
O A:HOH440 3.7 27.8 1.0
CG1 A:VAL147 3.7 11.7 1.0
O A:THR258 4.3 12.7 1.0
CB A:VAL147 4.6 8.4 1.0
CA A:ARG260 4.8 10.0 1.0
O A:TRP257 4.8 9.1 1.0
O A:HOH623 4.8 29.9 1.0
C A:THR258 4.8 9.3 1.0
CA A:THR258 4.9 8.3 1.0
N A:ARG260 5.0 9.7 1.0

Sodium binding site 2 out of 3 in 5b4v

Go back to Sodium Binding Sites List in 5b4v
Sodium binding site 2 out of 3 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate


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 D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:24.5
occ:1.00
 O A:HOH457 2.2 27.4 1.0
O A:ALA112 2.8 8.8 1.0
O A:HOH593 3.0 18.6 1.0
O A:LEU64 3.1 12.4 1.0
O A:SER65 3.3 14.6 1.0
C A:SER65 3.5 13.6 1.0
N A:ALA117 3.5 7.3 1.0
CB A:SER116 3.6 8.2 1.0
C A:ALA112 3.7 7.5 1.0
CD2 A:HIS120 3.8 8.2 1.0
C A:SER116 3.8 6.9 1.0
CA A:SER65 3.9 11.6 1.0
CA A:ALA117 3.9 8.1 1.0
N A:ALA67 4.1 11.1 1.0
CB A:ALA117 4.1 7.8 1.0
C A:LEU64 4.2 11.3 1.0
CA A:ALA112 4.2 7.5 1.0
N A:ASP66 4.2 12.6 1.0
C A:ASP66 4.2 11.9 1.0
CB A:ALA112 4.3 9.1 1.0
CA A:SER116 4.3 7.3 1.0
CA A:ALA67 4.3 10.4 1.0
O A:SER116 4.4 7.0 1.0
O A:HOH461 4.4 14.1 1.0
NE2 A:HIS120 4.4 9.6 1.0
N A:SER65 4.5 11.7 1.0
O A:ASP66 4.6 12.9 1.0
CA A:ASP66 4.6 14.3 1.0
OG1 A:THR70 4.6 11.2 1.0
CB A:ALA67 4.7 12.9 1.0
N A:LEU113 4.8 8.2 1.0
OG A:SER116 4.8 9.4 1.0
CG A:HIS120 4.9 7.4 1.0
O A:HOH468 5.0 9.8 1.0

Sodium binding site 3 out of 3 in 5b4v

Go back to Sodium Binding Sites List in 5b4v
Sodium binding site 3 out of 3 in the Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate


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 D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and An Inhibitor Methylmalonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:35.9
occ:1.00
 OD1 A:ASP85 2.6 12.5 1.0
O A:GLY4 3.1 22.2 1.0
NZ A:LYS6 3.2 29.4 1.0
CG A:ASP85 3.5 12.4 1.0
OD2 A:ASP85 3.7 14.1 1.0
C A:GLY4 4.0 21.1 1.0
CD A:LYS6 4.0 18.8 1.0
CE A:LYS6 4.0 24.6 1.0
CA A:LYS5 4.1 12.0 1.0
CG A:LYS6 4.2 13.6 1.0
N A:LYS6 4.4 9.8 1.0
N A:LYS5 4.5 16.6 1.0
C A:LYS5 4.6 11.2 1.0
O A:HOH427 4.7 24.9 1.0
CD A:LYS5 4.8 16.1 1.0
CB A:ASP85 4.9 10.5 1.0
CB A:LYS6 4.9 12.1 1.0

Reference:

H.Kanazawa, M.M.Hoque, M.Tsunoda, K.Suzuki, T.Yamamoto, G.Kawai, J.Kondo, A.Takenaka. Structural Insights Into the Catalytic Reaction Trigger and Inhibition of D-3-Hydroxybutyrate Dehydrogenase Acta Crystallogr.,Sect.F V. 72 507 2016.
ISSN: ESSN 2053-230X
PubMed: 27380367
DOI: 10.1107/S2053230X16007767
Page generated: Mon Oct 7 20:03:51 2024

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