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Sodium in PDB 3eqn: Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)

Enzymatic activity of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)

All present enzymatic activity of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A):
3.2.1.58;

Protein crystallography data

The structure of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A), PDB code: 3eqn was solved by T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, M.Samejima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.21 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.281, 67.148, 105.183, 81.04, 76.34, 61.45
R / Rfree (%) 14.9 / 18.4

Other elements in 3eqn:

The structure of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) (pdb code 3eqn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A), PDB code: 3eqn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3eqn

Go back to Sodium Binding Sites List in 3eqn
Sodium binding site 1 out of 4 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na759

b:19.9
occ:1.00
 OE1 A:GLU597 2.0 24.6 1.0
NE2 A:HIS557 2.2 19.4 1.0
O A:HOH1532 2.4 38.0 1.0
CE1 A:HIS557 2.5 16.6 1.0
CD A:GLU597 3.0 20.6 1.0
OE2 A:GLU597 3.4 20.5 1.0
O A:HOH1531 3.4 32.3 1.0
CD2 A:HIS557 3.5 18.2 1.0
ND1 A:HIS557 3.8 19.1 1.0
CG A:GLU597 4.3 16.3 1.0
O A:HOH1279 4.3 41.5 1.0
CG A:HIS557 4.3 14.8 1.0
CB A:GLU597 4.7 13.5 1.0
CG2 A:THR559 4.7 13.8 1.0
CE2 A:PHE653 4.9 23.4 1.0
CA A:THR559 5.0 13.9 1.0
CB A:THR559 5.0 13.5 1.0

Sodium binding site 2 out of 4 in 3eqn

Go back to Sodium Binding Sites List in 3eqn
Sodium binding site 2 out of 4 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na760

b:29.7
occ:1.00
 OD1 A:ASP78 2.2 17.1 1.0
O A:HOH1496 2.3 37.2 1.0
O A:HOH1495 2.4 32.8 1.0
O A:HOH1434 2.8 35.3 1.0
O A:HOH1494 2.8 43.9 1.0
O A:HOH1010 3.0 31.8 1.0
CG A:ASP78 3.1 15.3 1.0
OD2 A:ASP78 3.3 15.5 1.0
O A:HOH946 4.1 17.7 1.0
O A:HOH1459 4.2 34.7 1.0
CB A:ASP78 4.5 13.5 1.0
CA A:ASP78 4.9 13.6 1.0
N A:ASP78 4.9 14.2 1.0

Sodium binding site 3 out of 4 in 3eqn

Go back to Sodium Binding Sites List in 3eqn
Sodium binding site 3 out of 4 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na759

b:21.1
occ:1.00
 OE1 B:GLU597 1.9 20.6 1.0
NE2 B:HIS557 2.2 20.4 1.0
O B:HOH1494 2.3 41.5 1.0
CE1 B:HIS557 2.4 18.0 1.0
O B:HOH1556 2.7 35.6 1.0
CD B:GLU597 3.0 19.1 1.0
O B:HOH808 3.4 24.6 1.0
OE2 B:GLU597 3.5 22.1 1.0
CD2 B:HIS557 3.6 17.6 1.0
ND1 B:HIS557 3.7 18.2 1.0
CG B:GLU597 4.3 16.0 1.0
CG B:HIS557 4.3 14.2 1.0
CE B:MET595 4.6 21.8 1.0
CG2 B:THR559 4.7 13.0 1.0
CB B:GLU597 4.8 12.5 1.0
CE2 B:PHE653 4.8 22.9 1.0

Sodium binding site 4 out of 4 in 3eqn

Go back to Sodium Binding Sites List in 3eqn
Sodium binding site 4 out of 4 in the Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Beta-1,3-Glucanase From Phanerochaete Chrysosporium (LAM55A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na760

b:29.2
occ:1.00
 OD1 B:ASP78 2.2 17.7 1.0
O B:HOH1470 2.8 30.9 1.0
O B:HOH1356 2.9 28.0 1.0
O B:HOH1462 2.9 37.1 1.0
CG B:ASP78 3.1 16.5 1.0
O B:HOH1005 3.1 29.4 1.0
OD2 B:ASP78 3.4 17.0 1.0
O B:HOH1062 4.0 20.4 1.0
O B:HOH1408 4.2 33.2 1.0
CB B:ASP78 4.5 13.9 1.0
CA B:ASP78 4.8 14.1 1.0
N B:ASP78 4.8 15.2 1.0
O B:GLY76 4.9 19.9 1.0

Reference:

T.Ishida, S.Fushinobu, R.Kawai, M.Kitaoka, K.Igarashi, M.Samejima. Crystal Structure of Glycoside Hydrolase Family 55 Beta -1,3-Glucanase From the Basidiomycete Phanerochaete Chrysosporium J.Biol.Chem. V. 284 10100 2009.
ISSN: ISSN 0021-9258
PubMed: 19193645
DOI: 10.1074/JBC.M808122200
Page generated: Mon Oct 7 08:54:53 2024

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