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Sodium in PDB 5ldu: Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta

Protein crystallography data

The structure of Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta, PDB code: 5ldu was solved by K.M.Polyakov, T.V.Fedorova, D.S.Loginov, O.S.Savinova, V.S.Lamzin, O.V.Koroleva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.30
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 160.650, 160.650, 53.460, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 21

Other elements in 5ldu:

The structure of Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta (pdb code 5ldu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta, PDB code: 5ldu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ldu

Go back to Sodium Binding Sites List in 5ldu
Sodium binding site 1 out of 2 in the Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na517

b:12.6
occ:0.50
O A:SER225 2.1 27.0 1.0
O A:ALA103 2.2 23.1 1.0
O A:HOH849 2.3 32.1 1.0
O A:HOH805 2.4 26.4 1.0
O A:HOH617 2.6 28.6 1.0
O A:HOH801 2.8 27.1 1.0
C A:SER225 3.3 24.7 1.0
C A:ALA103 3.4 21.7 1.0
N A:ALA103 4.0 22.0 1.0
OD1 A:ASN227 4.0 19.2 1.0
N A:VAL226 4.1 22.1 1.0
CA A:VAL226 4.1 20.3 1.0
N A:ASN227 4.2 20.3 1.0
CA A:ALA103 4.2 21.5 1.0
CA A:SER225 4.3 24.1 1.0
N A:GLY104 4.3 21.0 1.0
CA A:GLY104 4.4 20.4 1.0
CG A:ASN227 4.4 21.1 1.0
CB A:SER225 4.4 23.9 1.0
ND2 A:ASN227 4.5 17.6 1.0
C A:VAL226 4.5 20.8 1.0
O A:HOH800 4.5 19.7 1.0
OE1 A:GLU222 4.6 27.9 1.0
O A:HOH786 4.6 23.7 1.0
O A:HOH606 4.6 26.1 1.0
CB A:ALA103 4.6 20.7 1.0
OG A:SER225 4.6 22.9 1.0

Sodium binding site 2 out of 2 in 5ldu

Go back to Sodium Binding Sites List in 5ldu
Sodium binding site 2 out of 2 in the Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na518

b:50.6
occ:1.00
OD1 A:ASN292 2.3 44.4 1.0
CG A:ASN292 3.3 38.3 1.0
ND2 A:ASN292 3.6 34.5 1.0
O A:THR290 4.6 26.6 1.0
CB A:ASN292 4.7 33.8 1.0

Reference:

T.V.Fedorova, K.M.Polyakov, D.S.Loginov, O.S.Savinova, E.A.Vavilova, A.M.Chulkin, V.S.Lamzin, O.V.Koroleva. First Structure of Recombinant High-Redox Potential Laccase From Basidiomycete Trametes Hirsuta. To Be Published.
Page generated: Tue Dec 15 11:13:00 2020

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