Atomistry » Sodium » PDB 5m1e-5mfr » 5m67
Atomistry »
  Sodium »
    PDB 5m1e-5mfr »
      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: Tue Dec 15 11:16:09 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy