Sodium in PDB 3x2f: A Thermophilic S-Adenosylhomocysteine Hydrolase

All present enzymatic activity of A Thermophilic S-Adenosylhomocysteine Hydrolase:
3.3.1.1;

The structure of A Thermophilic S-Adenosylhomocysteine Hydrolase, PDB code: 3x2f was solved by Y.Zheng, T.P.Ko, C.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.04
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.600, 148.600, 84.160, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 23

The binding sites of Sodium atom in the A Thermophilic S-Adenosylhomocysteine Hydrolase (pdb code 3x2f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the A Thermophilic S-Adenosylhomocysteine Hydrolase, PDB code: 3x2f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the A Thermophilic S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Thermophilic S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:14.8 occ:0.50 OD1 A:ASP74 2.5 28.6 1.0 O A:GLN72 2.5 33.8 1.0 OE2 A:GLU77 2.8 41.9 1.0 CD A:GLU77 3.7 39.7 1.0 CG A:ASP74 3.7 32.2 1.0 C A:GLN72 3.7 35.6 1.0 OE1 A:GLU77 3.9 40.1 1.0 CB A:GLN72 3.9 38.5 1.0 N A:ASP74 4.0 26.0 1.0 CA A:ASP74 4.1 26.9 1.0 C A:ASP73 4.4 28.0 1.0 CA A:GLN72 4.4 37.3 1.0 CB A:ASP74 4.5 25.3 1.0 OD2 A:ASP74 4.6 32.1 1.0 N A:ASP73 4.8 31.5 1.0 O A:ASP73 4.8 28.1 1.0 CG A:GLU77 4.9 35.4 1.0 CA A:ASP73 5.0 30.9 1.0

Sodium binding site 2 out of 3 in the A Thermophilic S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Thermophilic S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:39.2 occ:1.00 O A:HOH686 2.5 21.1 1.0 OD1 A:ASP384 2.5 34.9 1.0 O A:HOH683 2.6 40.7 1.0 O A:HOH682 2.7 50.4 1.0 O A:HOH684 2.7 20.2 1.0 CG A:ASP384 3.5 32.6 1.0 O A:HOH685 3.7 26.5 1.0 O A:VAL388 4.1 21.4 1.0 CA A:ASP384 4.2 25.5 1.0 OD2 A:ASP384 4.3 36.8 1.0 CB A:ASP384 4.3 27.7 1.0 N A:ASP384 4.5 23.5 1.0 O A:HOH696 4.6 45.2 1.0

Sodium binding site 3 out of 3 in the A Thermophilic S-Adenosylhomocysteine Hydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Thermophilic S-Adenosylhomocysteine Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:35.8 occ:1.00 O B:MET363 2.5 30.1 1.0 O B:HOH844 2.5 30.8 1.0 O B:HIS360 2.5 29.3 1.0 O2 B:NO3523 2.6 37.7 1.0 O B:HOH842 2.8 56.8 1.0 O3 B:NO3523 3.3 38.3 1.0 N B:NO3523 3.3 38.2 1.0 C B:MET363 3.6 31.7 1.0 C B:HIS360 3.6 28.6 1.0 CD B:PRO160 3.7 26.2 1.0 N B:MET363 4.2 30.2 1.0 CA B:ARG361 4.2 31.2 1.0 CG B:PRO160 4.2 29.6 1.0 CA B:MET363 4.3 30.8 1.0 C B:ARG361 4.4 31.2 1.0 N B:ARG361 4.4 28.0 1.0 O B:ARG361 4.4 31.5 1.0 O1 B:NO3523 4.5 39.0 1.0 O B:HOH666 4.5 46.8 1.0 CB B:MET363 4.6 31.4 1.0 CA B:HIS360 4.6 28.9 1.0 N B:SER364 4.7 30.3 1.0 ND1 B:HIS360 4.8 28.5 1.0 CB B:HIS360 4.9 28.6 1.0 CA B:SER364 4.9 30.9 1.0 N B:PRO160 4.9 25.8 1.0 C B:SER364 4.9 31.6 1.0 CB B:PRO160 4.9 25.4 1.0 O B:HOH698 4.9 23.2 1.0 N B:LYS362 5.0 30.7 1.0 O B:SER364 5.0 32.4 1.0

Y.Zheng, C.C.Chen, T.P.Ko, X.Xiao, Y.Yang, C.H.Huang, G.Qian, W.Shao, R.T.Guo. Crystal Structures of S-Adenosylhomocysteine Hydrolase From the Thermophilic Bacterium Thermotoga Maritima J.Struct.Biol. 2015.
ISSN: ESSN 1095-8657
PubMed: 25791616
DOI: 10.1016/J.JSB.2015.03.002