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Sodium in PDB 6sl8: Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab)

Enzymatic activity of Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab)

All present enzymatic activity of Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab):
2.3.1.178;

Protein crystallography data

The structure of Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab), PDB code: 6sl8 was solved by A.A.Richter, S.Kobus, L.Czech, A.Hoeppner, E.Bremer, S.H.J.Smits, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.24 / 1.53
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.979, 57.979, 134.461, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab) (pdb code 6sl8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab), PDB code: 6sl8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6sl8

Go back to Sodium Binding Sites List in 6sl8
Sodium binding site 1 out of 3 in the Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:39.9
occ:1.00
 O A:DAB202 2.6 58.5 0.8
OXT A:DAB202 3.0 34.4 0.8
C A:DAB202 3.1 41.5 0.8
O A:HOH302 3.1 41.2 1.0
N A:LYS94 3.1 29.3 1.0
CA A:GLY91 3.4 34.5 1.0
C A:GLY91 3.5 30.7 1.0
N A:ALA93 3.6 27.6 1.0
CB A:LYS94 3.7 31.0 1.0
CB A:ALA93 3.8 27.9 1.0
O A:GLY91 3.9 30.4 1.0
N A:ILE92 3.9 30.4 1.0
CA A:ALA93 3.9 25.8 1.0
N A:GLY91 4.0 34.2 1.0
CA A:LYS94 4.0 27.6 1.0
C A:ALA93 4.0 26.4 1.0
CA A:DAB202 4.4 46.8 0.8
C A:ILE92 4.4 28.9 1.0
CD1 A:LEU126 4.6 31.3 1.0
O A:HOH355 4.6 43.9 1.0
CG A:DAB202 4.7 38.4 0.8
CB A:DAB202 4.7 43.4 0.8
CA A:ILE92 4.8 29.1 1.0
NA A:NA204 4.8 40.1 1.0

Sodium binding site 2 out of 3 in 6sl8

Go back to Sodium Binding Sites List in 6sl8
Sodium binding site 2 out of 3 in the Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:40.1
occ:1.00
 OXT A:DAB202 2.6 34.4 0.8
O A:HIS87 2.8 37.7 1.0
N A:GLN90 2.9 41.9 1.0
N A:ILE92 3.1 30.4 1.0
N A:GLY91 3.4 34.2 1.0
C A:DAB202 3.4 41.5 0.8
CA A:GLN90 3.5 41.2 1.0
N A:ARG89 3.5 40.9 1.0
CB A:ILE92 3.5 30.6 1.0
C A:GLN90 3.5 34.5 1.0
CB A:GLN90 3.6 44.0 1.0
CG1 A:ILE92 3.6 33.4 1.0
C A:ARG88 3.8 37.7 1.0
O A:HOH302 3.8 41.2 1.0
CA A:ILE92 3.8 29.1 1.0
N A:DAB202 3.9 47.7 0.8
CD1 A:ILE92 3.9 37.8 1.0
C A:HIS87 3.9 33.8 1.0
O A:DAB202 3.9 58.5 0.8
C A:ARG89 4.0 48.8 1.0
CG1 A:VAL83 4.0 33.8 1.0
CA A:ARG88 4.0 36.7 1.0
C A:GLY91 4.1 30.7 1.0
CA A:ARG89 4.1 49.5 1.0
CG A:GLN90 4.2 45.0 1.0
CA A:GLY91 4.2 34.5 1.0
O A:GLN90 4.3 38.5 1.0
CA A:DAB202 4.3 46.8 0.8
O A:ARG88 4.4 44.1 1.0
N A:ALA93 4.4 27.6 1.0
N A:ARG88 4.4 34.8 1.0
C A:ILE92 4.7 28.9 1.0
NA A:NA203 4.8 39.9 1.0
CG2 A:ILE92 4.9 30.0 1.0
CG2 A:VAL83 5.0 31.3 1.0

Sodium binding site 3 out of 3 in 6sl8

Go back to Sodium Binding Sites List in 6sl8
Sodium binding site 3 out of 3 in the Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Diaminobutyrate Acetyltransferase Ecta From Paenibacillus Lautus in Complex with Its Substrate L-2,4-Diaminobutyric Acid (Dab) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:33.0
occ:1.00
 OXT A:DAB201 2.6 26.2 1.0
OD1 A:ASN35 2.9 27.5 1.0
NE1 A:TRP79 3.0 24.6 1.0
C A:DAB201 3.5 24.8 1.0
ND2 A:ASN35 3.5 19.3 1.0
CG A:ASN35 3.6 22.1 1.0
NE2 A:GLN80 3.7 23.7 1.0
O A:ASP33 3.7 26.2 1.0
CE2 A:TRP79 3.8 25.6 1.0
CZ2 A:TRP79 3.9 26.3 1.0
O A:DAB201 4.0 23.8 1.0
CB A:ASP33 4.0 27.4 1.0
CD1 A:TRP79 4.1 21.7 1.0
CD A:GLN80 4.2 24.8 1.0
C A:ASP33 4.5 24.5 1.0
CA A:DAB201 4.5 24.4 1.0
CG A:GLN80 4.7 20.4 1.0
OE1 A:GLN80 4.7 24.3 1.0
CA A:ASP33 4.8 24.0 1.0
OD2 A:ASP33 4.8 26.7 1.0

Reference:

A.Richter, S.Kobus, L.Czech, A.Hoeppner, J.Zarzycki, T.Erb, L.Lauterbach, J.S.Dickschat, E.Bremer, S.H.J.Smits. The Architecture of the Diaminobutyrate Acetyltransferase Active Site Provides Mechanistic Insight Into the Biosynthesis of the Chemical Chaperone Ectoine J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Tue Oct 8 13:29:49 2024

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