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Sodium in PDB 5m5k: S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin

Enzymatic activity of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin

All present enzymatic activity of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin:
3.3.1.1;

Protein crystallography data

The structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin, PDB code: 5m5k was solved by T.Manszewski, J.Mueller-Dieckamann, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.82 / 1.84
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.162, 176.283, 102.349, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.2

Sodium Binding Sites:

The binding sites of Sodium atom in the S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin (pdb code 5m5k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin, PDB code: 5m5k:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5m5k

Go back to Sodium Binding Sites List in 5m5k
Sodium binding site 1 out of 3 in the S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:26.0
occ:1.00
 O A:HOH840 2.5 29.6 1.0
O C:HOH770 2.6 25.4 1.0
O A:MET390 2.7 18.5 1.0
O A:HIS392 2.7 23.6 1.0
O A:HOH805 2.8 21.5 1.0
OE1 A:GLN62 3.2 24.1 1.0
NE2 A:GLN62 3.3 23.4 1.0
CD A:GLN62 3.4 21.7 1.0
C A:HIS392 3.6 18.9 1.0
C A:MET390 3.7 16.4 1.0
CB A:MET390 3.8 21.6 1.0
O A:GLY391 3.8 18.9 1.0
CA A:PRO393 3.8 22.4 1.0
N6 A:ADN502 3.8 15.5 1.0
N A:PRO393 4.1 19.3 1.0
C A:GLY391 4.1 18.2 1.0
O A:HOH838 4.3 26.7 1.0
CA A:MET390 4.4 19.9 1.0
CG A:GLN62 4.5 21.3 1.0
C A:PRO393 4.5 19.2 1.0
CB C:ASP249 4.5 19.1 1.0
NE2 A:GLN88 4.6 20.2 1.0
N A:HIS392 4.6 18.4 1.0
N A:GLY391 4.6 19.9 1.0
N A:SER394 4.6 17.7 1.0
CA A:GLY391 4.7 18.0 1.0
CA A:HIS392 4.7 17.6 1.0
O C:HOH663 4.7 28.6 1.0
CG C:ASP249 4.8 23.9 1.0
O C:ASP249 4.8 23.1 1.0
O C:HOH728 4.8 31.5 1.0
OD1 C:ASP249 5.0 21.5 1.0

Sodium binding site 2 out of 3 in 5m5k

Go back to Sodium Binding Sites List in 5m5k
Sodium binding site 2 out of 3 in the S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:23.6
occ:1.00
 O B:HOH801 2.6 27.3 1.0
O B:HOH879 2.7 20.6 1.0
O B:MET390 2.7 14.2 1.0
O D:HOH711 2.8 22.2 1.0
O B:HIS392 2.9 16.8 1.0
OE1 B:GLN62 3.1 17.4 1.0
NE2 B:GLN62 3.3 15.1 1.0
CD B:GLN62 3.3 19.7 1.0
C B:MET390 3.7 14.3 1.0
C B:HIS392 3.7 16.0 1.0
CB B:MET390 3.7 16.2 1.0
O B:GLY391 3.8 15.3 1.0
N6 B:ADN502 3.9 16.2 1.0
CA B:PRO393 3.9 19.2 1.0
C B:GLY391 4.1 14.1 1.0
N B:PRO393 4.2 16.1 1.0
CA B:MET390 4.3 16.4 1.0
CB D:ASP249 4.4 18.4 1.0
O B:HOH892 4.5 26.4 1.0
CG B:GLN62 4.5 16.8 1.0
NE2 B:GLN88 4.5 15.9 1.0
C B:PRO393 4.5 17.7 1.0
N B:HIS392 4.6 12.9 1.0
O D:HOH744 4.6 26.1 1.0
N B:GLY391 4.6 14.1 1.0
N B:SER394 4.7 15.8 1.0
CA B:GLY391 4.7 14.4 1.0
CG D:ASP249 4.8 26.7 1.0
O D:HOH671 4.8 25.2 1.0
O D:ASP249 4.8 21.0 1.0
CA B:HIS392 4.8 12.4 1.0
OD1 D:ASP249 5.0 21.5 1.0

Sodium binding site 3 out of 3 in 5m5k

Go back to Sodium Binding Sites List in 5m5k
Sodium binding site 3 out of 3 in the S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine and Cordycepin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:25.5
occ:1.00
 O C:HOH863 2.4 27.5 1.0
O A:HOH744 2.8 26.0 1.0
O C:MET390 2.8 19.7 1.0
O C:HIS392 2.8 14.9 1.0
O C:HOH798 2.8 22.4 1.0
OE1 C:GLN62 3.3 22.7 1.0
NE2 C:GLN62 3.4 21.2 1.0
CD C:GLN62 3.5 19.7 1.0
C C:HIS392 3.6 14.3 1.0
C C:MET390 3.7 19.5 1.0
CB C:MET390 3.7 20.5 1.0
O C:GLY391 3.8 18.0 1.0
CA C:PRO393 3.8 18.9 1.0
N6 C:ADN502 4.0 17.5 1.0
N C:PRO393 4.0 15.2 1.0
C C:GLY391 4.1 17.9 1.0
CB A:ASP249 4.3 18.8 1.0
O C:HOH851 4.3 25.8 1.0
CA C:MET390 4.4 17.2 1.0
C C:PRO393 4.5 21.5 1.0
N C:HIS392 4.6 17.1 1.0
N C:GLY391 4.6 15.2 1.0
CG C:GLN62 4.6 17.3 1.0
N C:SER394 4.6 18.3 1.0
O A:HOH699 4.6 27.8 1.0
O A:ASP249 4.6 21.0 1.0
NE2 C:GLN88 4.6 17.3 1.0
CA C:GLY391 4.7 13.6 1.0
CG A:ASP249 4.7 24.0 1.0
CA C:HIS392 4.7 15.2 1.0
OD1 A:ASP249 4.9 22.9 1.0
O C:HOH778 4.9 26.1 1.0
O C:HOH700 4.9 20.3 1.0
CB C:PRO393 5.0 17.4 1.0

Reference:

T.Manszewski, K.Szpotkowski, M.Jaskolski. Crystallographic and Saxs Studies of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii. Iucrj V. 4 271 2017.
ISSN: ESSN 2052-2525
PubMed: 28512574
DOI: 10.1107/S2052252517002433
Page generated: Mon Aug 18 00:58:08 2025

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