Sodium in PDB 6wqp: GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis

Protein crystallography data

The structure of GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis, PDB code: 6wqp was solved by C.M.Bianchetti, C.A.Bingman, R.W.Smith, E.M.Glasgow, B.G.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.37 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.980, 85.850, 87.200, 90.00, 96.54, 90.00
R / Rfree (%) 20.3 / 24.2

Sodium Binding Sites:

The binding sites of Sodium atom in the GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis (pdb code 6wqp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis, PDB code: 6wqp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6wqp

Go back to Sodium Binding Sites List in 6wqp
Sodium binding site 1 out of 2 in the GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:28.5
occ:1.00
O A:HOH594 2.3 19.0 1.0
O A:HOH771 2.3 25.1 1.0
O A:ILE81 2.5 18.0 1.0
O A:THR84 2.6 16.1 1.0
O A:HOH659 2.6 31.7 1.0
O A:HOH708 2.6 26.3 1.0
H A:THR84 3.3 16.6 1.0
HB A:THR84 3.6 20.8 1.0
C A:ILE81 3.7 15.9 1.0
HA A:ASP82 3.7 20.8 1.0
C A:THR84 3.7 14.4 1.0
HH22 A:ARG138 3.9 15.8 1.0
HG13 A:ILE81 4.0 23.9 1.0
N A:THR84 4.0 14.1 1.0
HG12 A:ILE81 4.0 23.9 1.0
O A:HOH525 4.2 21.0 1.0
O A:HOH570 4.2 23.9 1.0
CA A:THR84 4.2 13.7 1.0
CA A:ASP82 4.3 17.5 1.0
CB A:THR84 4.3 17.5 1.0
C A:ASP82 4.4 14.2 1.0
CG1 A:ILE81 4.5 20.1 1.0
HA A:ILE81 4.5 22.2 1.0
N A:ASP82 4.5 14.8 1.0
O A:HOH751 4.5 33.5 1.0
O A:HOH758 4.7 38.5 1.0
CA A:ILE81 4.7 18.6 1.0
NH2 A:ARG138 4.7 13.4 1.0
N A:HIS83 4.7 13.5 1.0
O A:ASP82 4.7 20.1 1.0
HA2 A:GLY85 4.7 20.4 1.0
H A:HIS83 4.8 15.9 1.0
HG22 A:THR84 4.8 23.7 1.0
N A:GLY85 4.8 17.5 1.0
HH21 A:ARG138 4.9 15.8 1.0

Sodium binding site 2 out of 2 in 6wqp

Go back to Sodium Binding Sites List in 6wqp
Sodium binding site 2 out of 2 in the GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:21.6
occ:1.00
O B:HOH768 2.2 27.9 1.0
O B:ILE81 2.4 15.2 1.0
O B:HOH694 2.4 17.9 1.0
O B:THR84 2.5 15.8 1.0
O B:HOH636 2.6 26.7 1.0
O B:HOH732 2.8 29.7 1.0
H B:THR84 3.2 18.2 1.0
HA B:ASP82 3.5 16.1 1.0
HB B:THR84 3.6 19.0 1.0
C B:ILE81 3.6 13.4 1.0
C B:THR84 3.6 13.9 1.0
HG12 B:ILE81 3.9 18.0 1.0
N B:THR84 3.9 15.3 1.0
HH22 B:ARG138 4.0 14.6 1.0
CA B:THR84 4.1 13.3 1.0
CA B:ASP82 4.2 13.6 1.0
O B:HOH673 4.2 18.2 1.0
HG13 B:ILE81 4.2 18.0 1.0
C B:ASP82 4.3 16.6 1.0
O B:HOH514 4.3 19.0 1.0
CB B:THR84 4.3 16.0 1.0
N B:ASP82 4.4 13.5 1.0
HA B:ILE81 4.4 13.6 1.0
CG1 B:ILE81 4.5 15.2 1.0
O B:ASP82 4.6 16.6 1.0
N B:HIS83 4.6 12.7 1.0
CA B:ILE81 4.6 11.5 1.0
O B:HOH759 4.6 31.3 1.0
NH2 B:ARG138 4.7 12.3 1.0
HA2 B:GLY85 4.7 21.9 1.0
H B:HIS83 4.7 15.0 1.0
N B:GLY85 4.8 13.8 1.0
HG22 B:THR84 4.8 24.0 1.0
HH21 B:ARG138 4.9 14.6 1.0

Reference:

C.M.Bianchetti, C.A.Bingman, R.W.Smith, E.M.Glasgow, B.G.Fox. GH5-4 Broad Specificity Endoglucanase From Ruminococcus Champanellensis To Be Published.
Page generated: Tue Dec 15 15:43:38 2020

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