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Sodium in PDB 6tn6: X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila

Enzymatic activity of X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila

All present enzymatic activity of X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila:
3.2.1.78;

Protein crystallography data

The structure of X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila, PDB code: 6tn6 was solved by V.M.Da Silva, F.M.Squina, M.Sperenca, L.Martin, J.R.C.Muniz, W.Garcia, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.69 / 1.45
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 174.710, 174.710, 174.710, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 15.1

Other elements in 6tn6:

The structure of X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila (pdb code 6tn6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila, PDB code: 6tn6:

Sodium binding site 1 out of 1 in 6tn6

Go back to Sodium Binding Sites List in 6tn6
Sodium binding site 1 out of 1 in the X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Endo-Beta-1,4-Mannanase From Thermotoga Petrophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na920

b:36.0
occ:1.00
 HA A:ASN44 2.4 22.5 1.0
HD2 A:TYR45 2.7 25.6 1.0
HB3 A:ASN43 2.8 21.5 1.0
H A:TYR45 2.8 23.4 1.0
O A:HOH1348 3.0 24.9 1.0
CA A:ASN44 3.0 18.8 1.0
N A:TYR45 3.0 19.5 1.0
CH2 A:TRP350 3.1 21.5 1.0
HB2 A:MET351 3.1 29.0 0.7
HB2 A:MET351 3.1 21.3 0.3
N A:ASN44 3.2 18.2 1.0
CZ3 A:TRP350 3.2 22.9 1.0
HE3 A:MET351 3.2 31.3 0.7
HB3 A:TYR45 3.2 24.7 1.0
HH2 A:TRP350 3.2 25.8 1.0
C A:ASN43 3.2 18.2 1.0
HE2 A:MET351 3.3 28.0 0.3
C A:ASN44 3.3 18.3 1.0
HB3 A:MET351 3.4 29.0 0.7
HZ3 A:TRP350 3.4 27.5 1.0
HB2 A:ASN43 3.4 21.5 1.0
O A:ASN43 3.4 19.4 1.0
CD2 A:TYR45 3.5 21.4 1.0
CB A:ASN43 3.5 17.9 1.0
CZ2 A:TRP350 3.5 22.4 1.0
HB3 A:MET351 3.6 21.3 0.3
SD A:MET351 3.6 25.6 0.7
H A:ASN44 3.6 21.8 1.0
CB A:MET351 3.7 24.2 0.7
CE A:MET351 3.7 26.1 0.7
CE3 A:TRP350 3.7 19.6 1.0
CB A:MET351 3.8 17.8 0.3
HE1 A:MET351 3.8 31.3 0.7
CB A:TYR45 3.8 20.6 1.0
HZ2 A:TRP350 3.9 26.9 1.0
CE2 A:TRP350 3.9 20.4 1.0
CA A:TYR45 4.0 19.7 1.0
CA A:ASN43 4.0 17.7 1.0
CG A:TYR45 4.0 20.6 1.0
CD2 A:TRP350 4.1 19.3 1.0
HE3 A:TRP350 4.2 23.5 1.0
HA A:TYR45 4.2 23.7 1.0
CE A:MET351 4.2 23.4 0.3
CG A:MET351 4.2 21.6 0.7
O A:ASN44 4.3 20.1 1.0
CE2 A:TYR45 4.4 22.9 1.0
HG2 A:MET351 4.4 31.2 0.3
HE2 A:TYR45 4.4 27.5 1.0
CB A:ASN44 4.5 19.3 1.0
HA A:ASN43 4.5 21.2 1.0
CG A:MET351 4.6 26.0 0.3
HE2 A:MET351 4.6 31.3 0.7
HE3 A:MET351 4.6 28.0 0.3
HB2 A:ASN44 4.7 23.2 1.0
HB2 A:TYR45 4.7 24.7 1.0
HA A:MET351 4.7 22.6 0.3
CG A:ASN43 4.7 18.8 1.0
HE1 A:MET351 4.8 28.0 0.3
HG2 A:MET351 4.8 25.9 0.7
HA A:MET351 4.9 24.0 0.7
HG3 A:MET351 4.9 25.9 0.7
CA A:MET351 4.9 18.8 0.3
NE1 A:TRP350 4.9 21.8 1.0
CA A:MET351 5.0 20.0 0.7
SD A:MET351 5.0 25.7 0.3

Reference:

V.M.Da Silva, A.D.Cabral, M.Sperenca, F.M.Squina, J.R.C.Muniz, L.Martin, Y.Nicolet, W.Garcia. High-Resolution Structure of A Modular Hyperthermostable Endo-Beta-1,4-Mannanase From Thermotoga Petrophila: the Ancillary Immunoglobulin-Like Module Is A Thermostabilizing Domain Biochem.Biophys.Acta 2020PROTEINS & Proteomics.
ISSN: ISSN 1570-9639
Page generated: Tue Oct 8 14:00:00 2024

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