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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

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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

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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

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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

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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 Oct 8 08:33:22 2024

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