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Sodium in PDB 3w8d: 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: 3w8d 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) 22.92 / 1.37
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.740, 62.740, 119.220, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 3w8d:

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 3w8d). 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: 3w8d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3w8d

Go back to Sodium Binding Sites List in 3w8d
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:9.5
occ:0.50
 O A:HOH705 2.3 18.9 1.0
OXT A:ARG260 2.4 10.9 1.0
O A:HOH476 2.4 15.7 1.0
C A:ARG260 3.4 8.4 1.0
O A:ARG260 3.7 9.9 1.0
CG1 A:VAL147 3.7 9.1 1.0
O A:HOH505 3.7 18.4 1.0
O A:THR258 4.4 8.8 1.0
CB A:VAL147 4.7 8.2 1.0
CA A:ARG260 4.8 8.2 1.0
O A:TRP257 4.8 8.0 1.0
O A:HOH608 4.8 27.3 1.0
O A:HOH610 4.9 27.4 0.5
CA A:THR258 4.9 6.5 1.0
C A:THR258 4.9 6.8 1.0
N A:ARG260 4.9 8.1 1.0

Sodium binding site 2 out of 3 in 3w8d

Go back to Sodium Binding Sites List in 3w8d
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:21.1
occ:1.00
 O A:HOH447 2.0 26.2 1.0
O A:ALA112 2.8 7.9 1.0
O A:LEU64 3.0 11.2 1.0
O A:HOH454 3.0 19.7 1.0
O A:SER65 3.4 14.1 1.0
N A:ALA117 3.4 6.5 1.0
CB A:SER116 3.6 7.0 1.0
C A:SER65 3.6 10.9 1.0
C A:SER116 3.7 6.7 1.0
CA A:ALA117 3.7 6.7 1.0
CD2 A:HIS120 3.7 6.7 1.0
C A:ALA112 3.8 7.3 1.0
CA A:SER65 3.9 10.4 1.0
CB A:ALA117 4.0 8.1 1.0
C A:LEU64 4.1 9.8 1.0
N A:ALA67 4.1 10.2 1.0
C A:ASP66 4.2 11.1 1.0
CA A:ALA112 4.2 5.9 1.0
N A:ASP66 4.2 11.3 1.0
O A:SER116 4.3 6.8 1.0
CA A:SER116 4.3 7.0 1.0
CA A:ALA67 4.3 10.0 1.0
CB A:ALA112 4.4 8.9 1.0
NE2 A:HIS120 4.4 9.0 1.0
O A:HOH428 4.5 14.2 1.0
O A:ASP66 4.5 11.5 1.0
N A:SER65 4.6 9.6 1.0
OG1 A:THR70 4.6 9.2 1.0
CA A:ASP66 4.7 12.4 1.0
CB A:ALA67 4.7 10.4 1.0
N A:LEU113 4.8 7.1 1.0
CG A:HIS120 4.8 6.4 1.0
OG A:SER116 4.8 8.3 1.0
N A:SER116 5.0 5.8 1.0

Sodium binding site 3 out of 3 in 3w8d

Go back to Sodium Binding Sites List in 3w8d
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:34.4
occ:1.00
 O A:HOH640 2.2 39.1 1.0
OD1 A:ASP85 2.7 10.7 1.0
O A:GLY4 3.2 20.8 1.0
NZ A:LYS6 3.2 26.5 1.0
CG A:ASP85 3.4 10.3 1.0
OD2 A:ASP85 3.6 11.5 1.0
CE A:LYS6 3.9 21.2 1.0
CD A:LYS6 3.9 17.1 1.0
CG A:LYS6 4.2 11.4 1.0
C A:GLY4 4.2 19.4 1.0
CA A:LYS5 4.2 11.6 1.0
O A:HOH647 4.3 34.0 1.0
O A:HOH673 4.4 50.5 1.0
O A:HOH516 4.5 22.5 1.0
N A:LYS6 4.5 8.8 1.0
N A:LYS5 4.6 15.1 1.0
C A:LYS5 4.7 10.5 1.0
CD A:LYS5 4.9 13.5 1.0
CB A:ASP85 4.9 8.0 1.0
CB A:LYS6 4.9 10.1 1.0

Reference:

H.Kanazawa, M.Tsunoda, M.M.Hoque, K.Suzuki, T.Yamamoto, A.Takenaka. X-Ray Diffraction of D-3-Hydroxybutyrate Dehydrogenase From Alcaligenes Faecalis Complexed with Nad+ and Methylmalonate To Be Published.
Page generated: Mon Oct 7 13:54:25 2024

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