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Sodium in PDB 5m67: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine

Enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine

All present enzymatic activity of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine:
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 and 2'-Deoxyadenosine, PDB code: 5m67 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) 43.63 / 1.54
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.484, 174.532, 96.620, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.6

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 and 2'-Deoxyadenosine (pdb code 5m67). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine, PDB code: 5m67:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5m67

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Sodium binding site 1 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine


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 and 2'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:13.9
occ:1.00
 O A:HOH878 2.4 14.3 1.0
O A:MET390 2.5 13.6 1.0
O C:HOH814 2.5 15.1 1.0
O A:HOH922 2.5 14.2 1.0
O A:HIS392 2.7 13.7 1.0
OE1 A:GLN62 2.8 14.1 1.0
CD A:GLN62 3.2 13.8 1.0
NE2 A:GLN62 3.3 15.3 1.0
C A:MET390 3.6 13.3 1.0
C A:HIS392 3.7 14.3 1.0
CB A:MET390 3.8 12.3 1.0
N6 A:ADE504 3.8 11.0 1.0
O A:GLY391 3.9 12.1 1.0
CA A:PRO393 4.0 11.3 1.0
C A:GLY391 4.1 12.2 1.0
N A:PRO393 4.2 12.4 1.0
O A:HOH935 4.3 15.6 1.0
CA A:MET390 4.3 10.8 1.0
CG A:GLN62 4.3 13.0 1.0
NE2 A:GLN88 4.4 14.1 1.0
C A:PRO393 4.5 12.1 1.0
N A:GLY391 4.5 11.0 1.0
CB C:ASP249 4.5 12.8 1.0
N A:HIS392 4.6 11.7 1.0
N A:SER394 4.6 12.2 1.0
CA A:GLY391 4.7 12.3 1.0
CA A:HIS392 4.8 13.4 1.0
O C:ASP249 4.8 13.1 1.0
O C:HOH709 4.8 16.7 1.0
OE1 A:GLN88 4.9 14.3 1.0
CG C:ASP249 4.9 17.0 1.0

Sodium binding site 2 out of 5 in 5m67

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Sodium binding site 2 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine


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 and 2'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:24.8
occ:1.00
 O D:HOH994 2.4 49.7 1.0
O A:HOH1038 2.5 53.2 1.0
O B:HOH783 2.5 29.2 1.0
O C:HOH807 2.6 26.7 1.0
O A:HOH846 2.6 28.0 1.0
O D:HOH791 2.6 27.3 1.0
O A:HOH1021 3.9 39.7 1.0
O B:HOH1049 4.0 43.1 1.0
O D:HOH998 4.1 40.3 1.0
O C:HOH983 4.1 36.2 1.0
OE1 B:GLN275 4.3 23.0 1.0
OE1 A:GLN275 4.3 21.7 1.0
O A:HOH1076 4.3 29.0 1.0
O B:HOH1089 4.3 33.9 1.0
OE1 D:GLN275 4.3 21.6 1.0
OE1 C:GLN275 4.4 21.0 1.0
O C:HOH1036 4.4 33.8 1.0
O D:HOH1044 4.4 30.9 1.0
NE2 B:GLN275 4.7 22.5 1.0
NE2 A:GLN275 4.7 20.0 1.0
NE2 C:GLN275 4.7 20.3 1.0
NE2 D:GLN275 4.7 20.3 1.0
CD B:GLN275 4.9 20.7 1.0
CD A:GLN275 4.9 17.9 1.0
CD D:GLN275 4.9 20.8 1.0
CD C:GLN275 5.0 20.9 1.0

Sodium binding site 3 out of 5 in 5m67

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Sodium binding site 3 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine


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 Adenine and 2'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:13.4
occ:1.00
 O B:HOH847 2.3 14.1 1.0
O B:MET390 2.5 13.0 1.0
O D:HOH842 2.5 14.3 1.0
O B:HOH899 2.6 14.5 1.0
O B:HIS392 2.7 12.5 1.0
OE1 B:GLN62 2.9 12.5 1.0
CD B:GLN62 3.2 12.0 1.0
NE2 B:GLN62 3.3 13.4 1.0
C B:MET390 3.5 11.8 1.0
C B:HIS392 3.6 13.0 1.0
CB B:MET390 3.8 14.0 1.0
N6 B:ADE503 3.9 11.8 1.0
O B:GLY391 3.9 13.6 1.0
CA B:PRO393 4.0 12.0 1.0
C B:GLY391 4.1 11.9 1.0
N B:PRO393 4.2 11.6 1.0
CA B:MET390 4.3 11.2 1.0
NE2 B:GLN88 4.3 12.1 1.0
O B:HOH965 4.3 14.8 1.0
CG B:GLN62 4.4 11.8 1.0
N B:GLY391 4.5 12.2 1.0
C B:PRO393 4.5 13.1 1.0
CB D:ASP249 4.5 12.4 1.0
N B:HIS392 4.6 10.8 1.0
CA B:GLY391 4.6 11.2 1.0
N B:SER394 4.6 12.2 1.0
CA B:HIS392 4.8 10.9 1.0
O B:HOH779 4.8 15.1 1.0
O D:ASP249 4.8 12.8 1.0
OE1 B:GLN88 4.9 13.6 1.0
CG D:ASP249 4.9 13.7 1.0
O D:HOH718 5.0 14.3 1.0

Sodium binding site 4 out of 5 in 5m67

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Sodium binding site 4 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine


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 Adenine and 2'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:14.9
occ:1.00
 O C:HOH791 2.3 15.8 1.0
O C:MET390 2.5 13.6 1.0
O A:HOH828 2.5 15.5 1.0
O C:HOH878 2.6 14.9 1.0
O C:HIS392 2.7 13.2 1.0
OE1 C:GLN62 2.9 15.8 1.0
CD C:GLN62 3.2 14.7 1.0
NE2 C:GLN62 3.3 16.3 1.0
C C:MET390 3.5 12.3 1.0
C C:HIS392 3.6 13.3 1.0
CB C:MET390 3.7 12.2 1.0
N6 C:3D1503 3.8 13.0 1.0
O C:GLY391 3.9 14.1 1.0
CA C:PRO393 3.9 13.3 1.0
C C:GLY391 4.1 12.4 1.0
N C:PRO393 4.2 12.8 1.0
CA C:MET390 4.3 11.3 1.0
O C:HOH937 4.4 17.4 1.0
NE2 C:GLN88 4.4 13.8 1.0
CG C:GLN62 4.4 13.5 1.0
N C:GLY391 4.5 12.6 1.0
CB A:ASP249 4.5 13.9 1.0
C C:PRO393 4.5 14.5 1.0
N C:HIS392 4.6 11.2 1.0
CA C:GLY391 4.6 12.8 1.0
N C:SER394 4.6 13.6 1.0
CA C:HIS392 4.7 12.9 1.0
O A:HOH755 4.8 16.6 1.0
O A:ASP249 4.8 14.2 1.0
OE1 C:GLN88 4.9 14.6 1.0
CG A:ASP249 4.9 14.6 1.0

Sodium binding site 5 out of 5 in 5m67

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Sodium binding site 5 out of 5 in the Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii in Complex with Adenine and 2'-Deoxyadenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:14.6
occ:1.00
 O D:HOH766 2.4 15.2 1.0
O D:MET390 2.5 14.4 1.0
O B:HOH815 2.5 16.5 1.0
O D:HOH898 2.6 15.8 1.0
O D:HIS392 2.7 13.6 1.0
OE1 D:GLN62 2.9 17.2 1.0
CD D:GLN62 3.3 16.5 1.0
NE2 D:GLN62 3.3 17.2 1.0
C D:MET390 3.5 12.5 1.0
C D:HIS392 3.6 11.5 1.0
N6 D:3D1503 3.7 13.4 1.0
CB D:MET390 3.8 15.2 1.0
O D:GLY391 3.9 13.0 1.0
CA D:PRO393 4.0 11.7 1.0
C D:GLY391 4.1 9.8 1.0
N D:PRO393 4.2 11.8 1.0
CA D:MET390 4.3 14.2 1.0
O D:HOH927 4.3 16.1 1.0
NE2 D:GLN88 4.4 14.9 1.0
CG D:GLN62 4.5 13.8 1.0
CB B:ASP249 4.5 13.6 1.0
C D:PRO393 4.5 12.8 1.0
N D:GLY391 4.5 12.2 1.0
N D:HIS392 4.6 11.4 1.0
N D:SER394 4.6 13.7 1.0
CA D:GLY391 4.6 11.1 1.0
CA D:HIS392 4.7 12.1 1.0
O B:HOH706 4.8 17.7 1.0
O B:ASP249 4.8 15.0 1.0
CG B:ASP249 4.9 16.7 1.0
OE1 D:GLN88 4.9 15.0 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 00:58:41 2025

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