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Sodium in PDB 5m66: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine

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

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

Protein crystallography data

The structure of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine, PDB code: 5m66 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) 46.90 / 1.95
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.437, 173.622, 97.425, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.1

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 Adenosine (pdb code 5m66). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine, PDB code: 5m66:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5m66

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Sodium binding site 1 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine


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 Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:24.5
occ:1.00
 O A:HOH670 2.3 18.1 1.0
O A:MET390 2.5 22.1 1.0
O A:HOH767 2.5 21.3 1.0
O A:HIS392 2.7 23.0 1.0
O A:HOH729 2.7 24.9 1.0
OE1 A:GLN62 2.9 21.5 1.0
CD A:GLN62 3.3 25.9 1.0
NE2 A:GLN62 3.4 19.8 1.0
C A:MET390 3.5 25.1 1.0
C A:HIS392 3.6 23.0 1.0
CB A:MET390 3.7 25.7 1.0
O A:GLY391 3.8 14.6 1.0
N6 A:ADN502 3.8 25.8 1.0
CA A:PRO393 4.0 18.5 1.0
C A:GLY391 4.1 14.3 1.0
N A:PRO393 4.2 19.0 1.0
CA A:MET390 4.2 19.8 1.0
OE1 A:GLN88 4.3 33.2 1.0
O A:HOH773 4.5 23.1 1.0
N A:GLY391 4.5 17.8 1.0
CG A:GLN62 4.5 17.3 1.0
CB C:ASP249 4.5 14.8 1.0
N A:HIS392 4.5 17.0 1.0
C A:PRO393 4.6 13.9 1.0
CA A:GLY391 4.6 18.6 1.0
N A:SER394 4.7 15.7 1.0
CA A:HIS392 4.7 19.4 1.0
O C:HOH648 4.8 31.3 1.0
O C:ASP249 4.8 24.8 1.0
CG C:ASP249 4.8 24.1 1.0
O A:HOH690 4.9 26.6 1.0
NE2 A:GLN88 4.9 19.0 1.0

Sodium binding site 2 out of 4 in 5m66

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Sodium binding site 2 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine


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 Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:21.2
occ:1.00
 O B:HOH773 2.3 23.2 1.0
O B:MET390 2.4 21.1 1.0
O B:HOH757 2.5 20.2 1.0
O D:HOH638 2.6 20.8 1.0
O B:HIS392 2.8 22.9 1.0
OE1 B:GLN62 2.8 20.5 1.0
NE2 B:GLN62 3.2 17.4 1.0
CD B:GLN62 3.2 29.5 1.0
C B:MET390 3.5 21.9 1.0
CB B:MET390 3.7 19.7 1.0
C B:HIS392 3.7 20.1 1.0
N6 B:ADN502 3.9 20.2 1.0
CA B:PRO393 3.9 19.6 1.0
O B:GLY391 4.0 17.4 1.0
C B:GLY391 4.2 20.1 1.0
O B:HOH766 4.2 19.5 1.0
N B:PRO393 4.2 23.2 1.0
CA B:MET390 4.2 16.5 1.0
NE2 B:GLN88 4.3 18.0 1.0
CG B:GLN62 4.4 27.9 1.0
N B:GLY391 4.5 19.1 1.0
CB D:ASP249 4.5 27.4 1.0
C B:PRO393 4.5 21.0 1.0
CA B:GLY391 4.6 18.8 1.0
N B:HIS392 4.7 23.3 1.0
N B:SER394 4.7 22.8 1.0
O B:HOH653 4.7 27.4 1.0
O D:ASP249 4.8 22.3 1.0
OE1 B:GLN88 4.8 21.5 1.0
CA B:HIS392 4.8 19.7 1.0
CG D:ASP249 4.9 28.2 1.0
O D:HOH664 5.0 26.5 1.0

Sodium binding site 3 out of 4 in 5m66

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Sodium binding site 3 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine


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

b:27.8
occ:1.00
 O C:HOH709 2.2 26.4 1.0
O C:MET390 2.4 23.7 1.0
O C:HOH746 2.5 22.7 1.0
O A:HOH704 2.6 21.8 1.0
O C:HIS392 2.7 21.7 1.0
OE1 C:GLN62 2.9 25.5 1.0
CD C:GLN62 3.3 28.6 1.0
NE2 C:GLN62 3.4 21.8 1.0
C C:MET390 3.5 27.4 1.0
C C:HIS392 3.6 21.8 1.0
CB C:MET390 3.7 21.6 1.0
N6 C:ADN502 3.7 27.9 1.0
O C:GLY391 3.8 20.4 1.0
CA C:PRO393 4.0 19.9 1.0
C C:GLY391 4.1 20.8 1.0
N C:PRO393 4.1 18.7 1.0
CA C:MET390 4.2 18.3 1.0
NE2 C:GLN88 4.3 30.4 1.0
N C:GLY391 4.4 20.1 1.0
N C:HIS392 4.5 26.1 1.0
CG C:GLN62 4.5 26.4 1.0
CB A:ASP249 4.5 25.6 1.0
C C:PRO393 4.5 24.9 1.0
O C:HOH772 4.5 26.5 1.0
CA C:GLY391 4.6 23.6 1.0
N C:SER394 4.7 19.9 1.0
CA C:HIS392 4.7 15.6 1.0
O A:HOH632 4.8 24.3 1.0
CG A:ASP249 4.8 35.2 1.0
O C:HOH702 4.9 31.9 1.0
O A:ASP249 4.9 22.8 1.0
OE1 C:GLN88 4.9 24.9 1.0
OD1 A:ASP249 4.9 26.9 1.0
CG C:MET390 5.0 20.4 1.0

Sodium binding site 4 out of 4 in 5m66

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Sodium binding site 4 out of 4 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:34.9
occ:1.00
 O D:MET390 2.5 20.6 1.0
O D:HOH714 2.6 25.9 1.0
O D:HOH732 2.6 22.9 1.0
O B:HOH663 2.6 24.7 1.0
O D:HIS392 2.7 22.4 1.0
NE2 D:GLN62 3.0 26.4 1.0
OE1 D:GLN62 3.3 29.6 1.0
CD D:GLN62 3.3 30.9 1.0
C D:MET390 3.6 22.5 1.0
C D:HIS392 3.6 24.8 1.0
N6 D:ADN502 3.7 23.8 1.0
O D:GLY391 3.8 24.6 1.0
CB D:MET390 3.8 21.0 1.0
CA D:PRO393 4.0 17.0 1.0
C D:GLY391 4.1 22.5 1.0
N D:PRO393 4.1 19.8 1.0
O D:HOH723 4.3 25.4 1.0
CA D:MET390 4.3 18.6 1.0
OE1 D:GLN88 4.5 41.3 1.0
C D:PRO393 4.5 22.0 1.0
CG D:GLN62 4.5 26.9 1.0
N D:GLY391 4.5 20.7 1.0
N D:HIS392 4.5 24.1 1.0
CA D:GLY391 4.6 22.1 1.0
N D:SER394 4.7 18.0 1.0
CB B:ASP249 4.7 23.6 1.0
CA D:HIS392 4.7 22.9 1.0
O B:HOH718 4.8 33.6 1.0
O B:ASP249 4.9 21.2 1.0
O B:HOH650 4.9 22.5 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 Oct 7 22:29:35 2024

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