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Sodium in PDB 5ohg: Enolase in Complex with Rnase E

Enzymatic activity of Enolase in Complex with Rnase E

All present enzymatic activity of Enolase in Complex with Rnase E:
3.1.26.12; 4.2.1.11;

Protein crystallography data

The structure of Enolase in Complex with Rnase E, PDB code: 5ohg was solved by D.Du, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.24 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.683, 116.923, 107.776, 90.00, 105.43, 90.00
R / Rfree (%) 16.1 / 19.7

Other elements in 5ohg:

The structure of Enolase in Complex with Rnase E also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Enolase in Complex with Rnase E (pdb code 5ohg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Enolase in Complex with Rnase E, PDB code: 5ohg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5ohg

Go back to Sodium Binding Sites List in 5ohg
Sodium binding site 1 out of 5 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Enolase in Complex with Rnase E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:17.0
occ:1.00
 O A:ASN162 2.7 30.5 1.0
O A:GLY157 2.7 24.6 1.0
OD1 A:ASN162 2.7 27.3 1.0
O A:ALA160 2.7 30.4 1.0
O A:HOH918 2.9 31.9 1.0
O A:VAL164 2.9 28.4 1.0
N A:GLY157 3.2 26.1 1.0
C A:GLY157 3.6 27.5 1.0
C A:ASN162 3.6 29.2 1.0
CA A:GLY157 3.7 22.9 1.0
C A:GLY156 3.7 24.7 1.0
N A:ASN162 3.7 28.1 1.0
C A:ALA160 3.8 32.5 1.0
CG A:ASN162 3.9 28.8 1.0
O A:HOH769 4.0 39.1 1.0
C A:VAL164 4.0 27.9 1.0
N A:VAL164 4.0 28.7 1.0
CA A:GLY156 4.0 25.5 1.0
CA A:ASN162 4.2 29.5 1.0
C A:ASP161 4.4 34.9 1.0
O A:GLY156 4.5 24.0 1.0
CA A:VAL164 4.5 28.1 1.0
N A:ASN163 4.5 29.1 1.0
CA A:ASP161 4.6 37.7 1.0
N A:ASP161 4.6 33.9 1.0
O A:HOH677 4.7 35.4 1.0
CB A:ASN162 4.7 30.9 1.0
C A:ASN163 4.7 32.8 1.0
N A:ALA160 4.7 26.6 1.0
CA A:ALA160 4.7 29.6 1.0
CA A:ASN163 4.9 30.1 1.0
N A:GLU158 4.9 24.7 1.0
CB A:ALA160 4.9 31.5 1.0
ND2 A:ASN162 4.9 26.9 1.0
CB A:VAL164 5.0 26.1 1.0

Sodium binding site 2 out of 5 in 5ohg

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Sodium binding site 2 out of 5 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Enolase in Complex with Rnase E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:18.9
occ:1.00
 O B:ALA160 2.6 33.6 1.0
O B:ASN162 2.8 27.4 1.0
OD1 B:ASN162 2.8 29.7 1.0
O B:GLY157 2.8 27.7 1.0
O B:HOH873 2.9 28.2 1.0
O B:VAL164 3.1 32.3 1.0
N B:GLY157 3.2 28.2 1.0
C B:ASN162 3.6 32.2 1.0
C B:GLY157 3.6 30.8 1.0
N B:ASN162 3.6 34.8 1.0
C B:GLY156 3.7 29.2 1.0
O B:HOH828 3.7 42.1 1.0
C B:ALA160 3.7 34.5 1.0
CA B:GLY157 3.7 25.0 1.0
CG B:ASN162 4.0 33.0 1.0
CA B:GLY156 4.0 28.7 1.0
C B:VAL164 4.1 30.8 1.0
N B:VAL164 4.2 33.2 1.0
CA B:ASN162 4.2 29.4 1.0
C B:ASP161 4.3 39.5 1.0
O B:GLY156 4.4 23.9 1.0
CA B:ASP161 4.5 41.7 1.0
N B:ASP161 4.5 37.6 1.0
CA B:ALA160 4.6 32.9 1.0
N B:ALA160 4.6 31.5 1.0
N B:ASN163 4.6 31.8 1.0
CA B:VAL164 4.7 31.3 1.0
CB B:ASN162 4.7 32.6 1.0
CB B:ALA160 4.8 28.6 1.0
C B:ASN163 4.9 35.8 1.0
N B:GLU158 4.9 30.4 1.0
CA B:ASN163 5.0 30.7 1.0

Sodium binding site 3 out of 5 in 5ohg

Go back to Sodium Binding Sites List in 5ohg
Sodium binding site 3 out of 5 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Enolase in Complex with Rnase E within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na502

b:14.4
occ:1.00
 O H:ALA160 2.7 23.7 1.0
O H:GLY157 2.7 21.3 1.0
OD1 H:ASN162 2.7 21.9 1.0
O H:ASN162 2.8 23.8 1.0
O H:HOH927 2.9 30.1 1.0
O H:VAL164 3.0 22.4 1.0
N H:GLY157 3.2 19.5 1.0
C H:GLY157 3.6 18.8 1.0
O H:HOH752 3.6 41.0 1.0
C H:ASN162 3.7 26.2 1.0
CA H:GLY157 3.7 18.1 1.0
C H:GLY156 3.7 19.8 1.0
C H:ALA160 3.7 30.3 1.0
N H:ASN162 3.8 26.8 1.0
CG H:ASN162 3.9 24.0 1.0
C H:VAL164 4.0 23.0 1.0
CA H:GLY156 4.1 19.5 1.0
N H:VAL164 4.1 24.3 1.0
CA H:ASN162 4.2 23.0 1.0
O H:GLY156 4.4 18.4 1.0
O H:HOH984 4.4 37.9 1.0
C H:ASP161 4.5 34.2 1.0
N H:ALA160 4.6 23.1 1.0
N H:ASP161 4.6 31.8 1.0
CA H:ALA160 4.6 26.1 1.0
CA H:VAL164 4.6 21.8 1.0
N H:ASN163 4.6 26.9 1.0
CA H:ASP161 4.7 34.6 1.0
CB H:ASN162 4.7 22.7 1.0
O H:HOH666 4.7 34.9 1.0
CB H:ALA160 4.8 26.2 1.0
C H:ASN163 4.8 30.5 1.0
N H:GLU158 4.8 22.1 1.0
ND2 H:ASN162 4.9 19.5 1.0
CA H:ASN163 5.0 29.4 1.0

Sodium binding site 4 out of 5 in 5ohg

Go back to Sodium Binding Sites List in 5ohg
Sodium binding site 4 out of 5 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Enolase in Complex with Rnase E within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na502

b:27.1
occ:1.00
 O I:HOH701 2.9 20.8 1.0
O I:ASP55 2.9 29.4 1.0
N I:GLY63 3.1 22.1 1.0
N I:ASP55 3.1 29.7 1.0
O I:ARG58 3.1 20.8 1.0
C I:GLY61 3.2 25.7 1.0
CB I:ASP55 3.3 27.9 1.0
CA I:GLY61 3.4 25.2 1.0
CB I:ASP53 3.4 22.6 1.0
CA I:ASP55 3.5 28.2 1.0
O I:GLY61 3.5 27.3 1.0
N I:LYS62 3.6 20.0 1.0
C I:ASP55 3.6 30.1 1.0
CA I:GLY63 3.7 18.7 1.0
N I:GLY54 3.9 24.8 1.0
N I:GLY61 3.9 23.2 1.0
CB I:ARG58 4.0 20.6 1.0
C I:ARG58 4.1 23.5 1.0
C I:GLY54 4.1 30.1 1.0
C I:LYS62 4.1 20.2 1.0
OD2 I:ASP53 4.3 24.6 1.0
C I:ASP53 4.3 28.8 1.0
CA I:ASP53 4.3 25.2 1.0
CG I:ASP53 4.4 22.4 1.0
CA I:LYS62 4.4 20.6 1.0
CA I:GLY54 4.5 27.7 1.0
C I:GLY63 4.5 21.0 1.0
O I:GLY63 4.5 19.7 1.0
CG I:ASP55 4.5 32.9 1.0
CA I:ARG58 4.5 26.4 1.0
N I:ASP53 4.6 21.1 1.0
O I:HOH620 4.7 24.6 1.0
N I:ARG58 4.7 25.8 1.0
N I:LYS56 4.9 27.9 1.0

Sodium binding site 5 out of 5 in 5ohg

Go back to Sodium Binding Sites List in 5ohg
Sodium binding site 5 out of 5 in the Enolase in Complex with Rnase E


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Enolase in Complex with Rnase E within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na503

b:17.5
occ:1.00
 O I:ASN162 2.7 28.5 1.0
OD1 I:ASN162 2.7 23.4 1.0
O I:HOH873 2.7 35.2 1.0
O I:GLY157 2.9 22.4 1.0
O I:ALA160 2.9 28.2 1.0
O I:VAL164 2.9 27.8 1.0
N I:GLY157 3.2 23.5 1.0
O I:HOH730 3.4 48.1 1.0
C I:ASN162 3.5 27.2 1.0
O I:HOH690 3.6 39.2 1.0
C I:GLY157 3.7 23.6 1.0
CA I:GLY157 3.7 18.4 1.0
C I:GLY156 3.8 23.1 1.0
N I:ASN162 3.8 34.1 1.0
N I:VAL164 3.9 28.7 1.0
C I:ALA160 3.9 31.9 1.0
CG I:ASN162 3.9 27.6 1.0
C I:VAL164 4.0 27.3 1.0
CA I:GLY156 4.1 19.9 1.0
CA I:ASN162 4.2 29.4 1.0
N I:ASN163 4.4 28.6 1.0
CA I:VAL164 4.5 31.6 1.0
C I:ASN163 4.6 34.9 1.0
O I:GLY156 4.6 21.9 1.0
C I:ASP161 4.6 38.1 1.0
O I:HOH803 4.6 38.4 1.0
CB I:ASN162 4.7 25.0 1.0
CA I:ASN163 4.7 31.0 1.0
CA I:ALA160 4.7 30.2 1.0
N I:ALA160 4.8 26.4 1.0
N I:ASP161 4.8 35.2 1.0
CB I:ALA160 4.9 27.5 1.0
CB I:VAL164 4.9 29.3 1.0
CA I:ASP161 5.0 41.4 1.0
ND2 I:ASN162 5.0 21.9 1.0
N I:GLU158 5.0 27.4 1.0

Reference:

H.A.Bruce, D.Du, D.Matak-Vinkovic, K.J.Bandyra, R.W.Broadhurst, E.Martin, F.Sobott, A.V.Shkumatov, B.F.Luisi. Analysis of the Natively Unstructured Rna/Protein-Recognition Core in the Escherichia Coli Rna Degradosome and Its Interactions with Regulatory Rna/Hfq Complexes. Nucleic Acids Res. V. 46 387 2018.
ISSN: ESSN 1362-4962
PubMed: 29136196
DOI: 10.1093/NAR/GKX1083
Page generated: Tue Dec 15 11:24:49 2020

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