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Sodium in PDB 4uoj: Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum

Protein crystallography data

The structure of Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum, PDB code: 4uoj was solved by J.R.C.Muniz, R.Aparicio, J.C.Santos, A.S.Nascimento, A.M.Golubev, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.23 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 165.161, 165.631, 123.562, 90.00, 90.00, 90.00
R / Rfree (%) 17.851 / 20.113

Other elements in 4uoj:

The structure of Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum also contains other interesting chemical elements:

Cadmium (Cd) 28 atoms
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum (pdb code 4uoj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum, PDB code: 4uoj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4uoj

Go back to Sodium Binding Sites List in 4uoj
Sodium binding site 1 out of 3 in the Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1995

b:48.6
occ:1.00
NE2 A:HIS565 2.9 61.4 1.0
CD2 A:HIS565 3.8 59.7 1.0
CE1 A:HIS565 3.9 61.1 1.0
CG A:PRO369 4.1 57.3 1.0
CG A:HIS565 4.9 59.4 1.0
ND1 A:HIS565 4.9 60.7 1.0

Sodium binding site 2 out of 3 in 4uoj

Go back to Sodium Binding Sites List in 4uoj
Sodium binding site 2 out of 3 in the Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1996

b:55.8
occ:1.00
OE1 A:GLU489 3.1 69.6 1.0
OE1 A:GLU594 3.4 56.3 1.0
OE2 A:GLU489 3.6 40.9 1.0
O A:HOH2177 3.6 38.6 1.0
OE2 A:GLU594 3.7 59.5 1.0
CD A:GLU489 3.7 62.0 1.0
O A:HOH2181 3.8 49.0 1.0
NE1 A:TRP422 3.9 39.5 1.0
CD A:GLU594 3.9 60.5 1.0
ND2 A:ASN488 4.0 43.1 1.0
OD1 A:ASN488 4.3 47.2 1.0
CH2 A:TRP706 4.3 39.5 1.0
CZ3 A:TRP706 4.5 38.6 1.0
CZ2 A:TRP706 4.5 39.7 1.0
CG A:ASN488 4.6 48.6 1.0
CD1 A:TRP422 4.7 38.6 1.0
CE2 A:TRP422 4.7 38.9 1.0
CE3 A:TRP706 4.8 37.8 1.0
OH A:TYR573 4.8 46.9 1.0
CE2 A:TRP706 4.9 38.5 1.0
NE1 A:TRP200 5.0 40.5 1.0

Sodium binding site 3 out of 3 in 4uoj

Go back to Sodium Binding Sites List in 4uoj
Sodium binding site 3 out of 3 in the Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1992

b:57.1
occ:1.00
OE1 B:GLU489 3.2 64.0 1.0
OE1 B:GLU594 3.4 56.5 1.0
O B:HOH2173 3.5 38.2 1.0
OE2 B:GLU489 3.7 40.5 1.0
CD B:GLU489 3.7 60.4 1.0
NE1 B:TRP422 3.7 37.1 1.0
OE2 B:GLU594 3.8 59.5 1.0
ND2 B:ASN488 3.8 44.6 1.0
CD B:GLU594 3.9 60.3 1.0
O B:HOH2175 4.3 49.2 1.0
OD1 B:ASN488 4.3 49.2 1.0
CH2 B:TRP706 4.3 36.0 1.0
CZ3 B:TRP706 4.5 34.9 1.0
CG B:ASN488 4.5 48.5 1.0
CZ2 B:TRP706 4.5 35.9 1.0
CD1 B:TRP422 4.6 36.5 1.0
CE2 B:TRP422 4.6 36.8 1.0
CE3 B:TRP706 4.8 33.8 1.0
CE2 B:TRP706 4.9 34.9 1.0
CZ2 B:TRP422 4.9 37.2 1.0
OH B:TYR573 4.9 42.8 1.0
NE1 B:TRP200 5.0 38.3 1.0

Reference:

A.S.Nascimento, J.R.C.Muniz, R.Aparicio, A.M.Golubev, I.Polikarpov. Insights Into the Structure and Function of Fungal Beta- Mannosidases From Glycoside Hydrolase Family 2 Based on Multiple Crystal Structures of the Trichoderma Harzianum Enzyme. Febs J. V. 281 4165 2014.
ISSN: ISSN 1742-464X
PubMed: 24975648
DOI: 10.1111/FEBS.12894
Page generated: Tue Dec 15 08:39:35 2020

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