Atomistry » Sodium » PDB 6eqv-6f1h » 6exi
Atomistry »
  Sodium »
    PDB 6eqv-6f1h »
      6exi »

Sodium in PDB 6exi: Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine

Enzymatic activity of Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine

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

Protein crystallography data

The structure of Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine, PDB code: 6exi 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) 47.08 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.635, 124.360, 92.721, 90.00, 103.71, 90.00
R / Rfree (%) 17.3 / 21.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine (pdb code 6exi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine, PDB code: 6exi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6exi

Go back to Sodium Binding Sites List in 6exi
Sodium binding site 1 out of 4 in the Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:20.6
occ:1.00
 O A:HOH672 2.3 22.1 1.0
O A:MET390 2.6 21.8 1.0
O C:HOH687 2.6 20.2 1.0
O A:HOH831 2.6 19.0 1.0
O A:HIS392 2.8 21.8 1.0
OE1 A:GLN62 3.1 19.4 1.0
NE2 A:GLN62 3.3 19.9 1.0
CD A:GLN62 3.3 19.4 1.0
C A:MET390 3.6 21.4 1.0
C A:HIS392 3.7 21.2 1.0
CB A:MET390 3.7 22.0 1.0
O A:GLY391 3.8 20.4 1.0
CA A:PRO393 4.0 22.0 1.0
N6 A:ADN502 4.0 18.2 1.0
C A:GLY391 4.1 20.5 1.0
N A:PRO393 4.2 21.2 1.0
O A:HOH800 4.2 20.4 1.0
CA A:MET390 4.3 21.6 1.0
CG A:GLN62 4.4 18.9 1.0
NE2 A:GLN88 4.4 19.2 1.0
CB C:ASP249 4.5 20.5 1.0
N A:GLY391 4.5 20.8 1.0
C A:PRO393 4.6 22.7 1.0
N A:SER394 4.6 21.0 1.0
CA A:GLY391 4.7 20.6 1.0
N A:HIS392 4.7 20.5 1.0
O C:ASP249 4.7 19.7 1.0
O C:HOH726 4.8 23.9 1.0
CG C:ASP249 4.8 20.7 1.0
CA A:HIS392 4.8 20.5 1.0
O A:HOH726 5.0 22.7 1.0

Sodium binding site 2 out of 4 in 6exi

Go back to Sodium Binding Sites List in 6exi
Sodium binding site 2 out of 4 in the Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:18.2
occ:1.00
 O B:HOH857 2.4 18.6 1.0
O B:HOH787 2.5 18.9 1.0
O D:HOH759 2.6 18.2 1.0
O B:MET390 2.6 21.9 1.0
O B:HIS392 2.8 18.5 1.0
OE1 B:GLN62 2.9 18.4 1.0
CD B:GLN62 3.3 18.6 1.0
NE2 B:GLN62 3.3 19.1 1.0
C B:MET390 3.6 22.0 1.0
CB B:MET390 3.7 21.2 1.0
C B:HIS392 3.8 18.2 1.0
N6 B:ADN502 3.8 15.9 1.0
O B:GLY391 4.0 16.7 1.0
CA B:PRO393 4.0 17.9 1.0
O B:HOH784 4.1 19.4 1.0
C B:GLY391 4.2 16.9 1.0
N B:PRO393 4.3 18.2 1.0
CA B:MET390 4.3 21.9 1.0
NE2 B:GLN88 4.4 18.6 1.0
CG B:GLN62 4.4 18.5 1.0
CB D:ASP249 4.5 18.4 1.0
C B:PRO393 4.5 18.4 1.0
N B:GLY391 4.6 16.8 1.0
N B:SER394 4.6 17.2 1.0
O D:HOH690 4.7 21.8 1.0
N B:HIS392 4.7 19.1 1.0
CA B:GLY391 4.7 17.0 1.0
O D:ASP249 4.8 18.1 1.0
CA B:HIS392 4.9 18.6 1.0
CG B:MET390 4.9 20.0 1.0
OE1 B:GLN88 4.9 18.4 1.0
CG D:ASP249 4.9 18.5 1.0

Sodium binding site 3 out of 4 in 6exi

Go back to Sodium Binding Sites List in 6exi
Sodium binding site 3 out of 4 in the Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:22.2
occ:1.00
 O C:MET390 2.5 19.8 1.0
O C:HOH771 2.6 22.3 1.0
O C:HOH821 2.6 20.5 1.0
O A:HOH693 2.6 21.7 1.0
O C:HIS392 2.8 19.2 1.0
OE1 C:GLN62 2.9 20.5 1.0
CD C:GLN62 3.2 20.4 1.0
NE2 C:GLN62 3.3 20.9 1.0
C C:MET390 3.6 19.7 1.0
C C:HIS392 3.7 19.2 1.0
CB C:MET390 3.8 21.2 1.0
N6 C:ADN502 3.9 16.9 1.0
O C:GLY391 4.0 19.1 1.0
CA C:PRO393 4.0 19.6 1.0
C C:GLY391 4.2 19.0 1.0
N C:PRO393 4.2 19.3 1.0
CA C:MET390 4.3 20.3 1.0
O C:HOH827 4.3 21.7 1.0
CG C:GLN62 4.4 20.0 1.0
NE2 C:GLN88 4.4 21.9 1.0
C C:PRO393 4.5 19.7 1.0
N C:GLY391 4.5 19.3 1.0
CB A:ASP249 4.5 21.8 1.0
N C:HIS392 4.6 19.0 1.0
N C:SER394 4.7 19.9 1.0
CA C:GLY391 4.7 19.1 1.0
O A:ASP249 4.8 21.4 1.0
CA C:HIS392 4.8 19.0 1.0
O C:HOH684 4.9 22.6 1.0
CG A:ASP249 4.9 21.8 1.0

Sodium binding site 4 out of 4 in 6exi

Go back to Sodium Binding Sites List in 6exi
Sodium binding site 4 out of 4 in the Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Nad-Free Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii Complexed with Adenosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:22.4
occ:1.00
 O D:HOH808 2.4 21.8 1.0
O B:HOH732 2.7 19.6 1.0
O D:HOH821 2.7 21.2 1.0
O D:MET390 2.7 21.2 1.0
O D:HIS392 2.8 20.4 1.0
OE1 D:GLN62 3.1 20.1 1.0
CD D:GLN62 3.3 20.4 1.0
NE2 D:GLN62 3.4 21.1 1.0
C D:MET390 3.7 20.7 1.0
C D:HIS392 3.7 19.8 1.0
CB D:MET390 3.7 21.7 1.0
CA D:PRO393 3.9 20.0 1.0
N6 D:ADN502 3.9 19.9 1.0
O D:GLY391 4.0 19.0 1.0
N D:PRO393 4.2 19.6 1.0
O D:HOH815 4.2 21.2 1.0
C D:GLY391 4.2 19.4 1.0
CA D:MET390 4.3 21.0 1.0
CG D:GLN62 4.4 19.9 1.0
CB B:ASP249 4.5 20.2 1.0
C D:PRO393 4.5 20.8 1.0
NE2 D:GLN88 4.6 20.6 1.0
N D:SER394 4.6 20.1 1.0
N D:GLY391 4.6 19.8 1.0
N D:HIS392 4.7 19.6 1.0
O B:ASP249 4.7 20.2 1.0
O B:HOH760 4.7 22.3 1.0
CA D:GLY391 4.8 19.8 1.0
CA D:HIS392 4.8 19.4 1.0
CG B:ASP249 4.9 20.3 1.0
O B:HOH799 4.9 22.1 1.0

Reference:

L.L.Kailing, D.Bertinetti, C.E.Paul, T.Manszewski, M.Jaskolski, F.W.Herberg, I.V.Pavlidis. S-Adenosyl-L-Homocysteine Hydrolase Inhibition By A Synthetic Nicotinamide Cofactor Biomimetic. Front Microbiol V. 9 505 2018.
ISSN: ESSN 1664-302X
PubMed: 29619018
DOI: 10.3389/FMICB.2018.00505
Page generated: Tue Dec 15 12:12:52 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