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Sodium in PDB 5m65: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine:
3.3.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine, PDB code: 5m65 was solved by T.Manszewski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.87 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.665, 103.051, 90.654, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 21.3

Other elements in 5m65:

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine (pdb code 5m65). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine, PDB code: 5m65:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5m65

Go back to Sodium Binding Sites List in 5m65
Sodium binding site 1 out of 2 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine


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 S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:34.2
occ:1.00
 O A:HOH650 2.4 33.4 1.0
O A:MET390 2.6 21.0 1.0
O A:HOH797 2.7 25.2 1.0
O A:HIS392 3.2 18.9 1.0
OE1 A:GLN62 3.3 28.1 1.0
NE2 A:GLN62 3.5 31.9 1.0
CB A:MET390 3.5 23.5 1.0
CD A:GLN62 3.5 28.6 1.0
C A:MET390 3.6 22.4 1.0
O A:GLY391 3.7 20.6 1.0
C A:HIS392 3.9 20.2 1.0
CA A:PRO393 4.1 18.5 1.0
N6 A:ADE502 4.1 21.8 1.0
C A:GLY391 4.2 17.9 1.0
CA A:MET390 4.2 22.2 1.0
N A:PRO393 4.3 20.4 1.0
O A:HOH834 4.4 35.7 1.0
N A:GLY391 4.5 16.8 1.0
O A:HOH735 4.5 20.4 1.0
NE2 A:GLN88 4.5 19.4 1.0
CG A:GLN62 4.6 22.2 1.0
CA A:GLY391 4.7 19.7 1.0
CG A:MET390 4.7 23.4 1.0
N A:SER394 4.7 14.4 1.0
C A:PRO393 4.7 16.9 1.0
N A:HIS392 4.8 15.5 1.0
CA A:HIS392 5.0 14.7 1.0

Sodium binding site 2 out of 2 in 5m65

Go back to Sodium Binding Sites List in 5m65
Sodium binding site 2 out of 2 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine


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 S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:39.6
occ:1.00
 O B:HOH801 2.3 24.8 1.0
O B:MET390 2.5 21.5 1.0
O B:HOH804 2.7 31.0 1.0
O B:HIS392 3.0 22.9 1.0
OE1 B:GLN62 3.2 28.8 1.0
NE2 B:GLN62 3.4 22.4 1.0
CD B:GLN62 3.4 22.2 1.0
C B:MET390 3.5 25.9 1.0
CB B:MET390 3.6 24.1 1.0
O B:GLY391 3.8 19.2 1.0
C B:HIS392 3.8 23.8 1.0
N6 B:ADE502 4.0 44.5 1.0
C B:GLY391 4.1 16.2 1.0
CA B:PRO393 4.1 21.6 1.0
CA B:MET390 4.2 26.0 1.0
N B:PRO393 4.3 19.7 1.0
N B:GLY391 4.4 21.6 1.0
OE1 B:GLN88 4.4 19.3 1.0
CG B:GLN62 4.5 20.0 1.0
O B:HOH819 4.5 41.1 1.0
CA B:GLY391 4.6 14.8 1.0
N B:HIS392 4.6 16.3 1.0
C B:PRO393 4.8 19.6 1.0
CA B:HIS392 4.8 17.9 1.0
N B:SER394 4.8 15.1 1.0
CG B:MET390 4.9 24.1 1.0

Reference:

T.Manszewski, K.Szpotkowski, M.Jaskolski. Crystallographic and Saxs Studies Ofs-Adenosyl-L-Homocysteine Hydrolase Frombradyrhizobium Elkanii. Iucrj V. 4 271 2017.
ISSN: ESSN 2052-2525
PubMed: 28512574
DOI: 10.1107/S2052252517002433
Page generated: Tue Dec 15 11:16:07 2020

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