Atomistry » Sodium » PDB 5m1y-5mfs » 5m67
Atomistry »
  Sodium »
    PDB 5m1y-5mfs »
      5m67 »

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

Go back to Sodium Binding Sites List in 5m67
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

Go back to Sodium Binding Sites List in 5m67
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

Go back to Sodium Binding Sites List in 5m67
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

Go back to Sodium Binding Sites List in 5m67
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

Go back to Sodium Binding Sites List in 5m67
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 Oct 7 22:29:44 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy