Sodium in PDB 4cvu: Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum

The structure of Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum, PDB code: 4cvu 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)	117.70 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	166.456, 166.456, 121.452, 90.00, 90.00, 90.00
R / Rfree (%)	23.35 / 26.254

The structure of Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum also contains other interesting chemical elements:

Cadmium	(Cd)	17 atoms
Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum (pdb code 4cvu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum, PDB code: 4cvu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of 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 From Glycoside Hydrolase Family 2 of Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1995 b:54.0 occ:1.00 O A:HOH3558 2.4 40.8 1.0 OE1 A:GLU754 3.1 51.7 1.0 OE2 A:GLU754 3.3 59.0 1.0 CD A:GLU754 3.5 54.0 1.0 O A:HOH3557 4.2 62.4 1.0 NH1 A:ARG692 4.5 45.7 1.0 O A:HOH3592 4.7 60.1 1.0 CG A:GLU754 4.9 53.1 1.0

Sodium binding site 2 out of 6 in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of 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 From Glycoside Hydrolase Family 2 of Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1996 b:48.1 occ:1.00 O A:HOH3117 2.2 46.0 1.0 OD2 A:ASP129 2.6 50.2 1.0 O A:HOH3393 3.1 59.5 1.0 CG A:ASP129 3.5 48.0 1.0 OD1 A:ASP129 3.7 44.6 1.0 C6 A:MAN1954 3.9 62.8 1.0 C4 A:MAN1954 4.0 60.5 1.0 O4 A:MAN1954 4.1 52.8 1.0 ND2 A:ASN463 4.1 42.2 1.0 CG A:ASN463 4.4 39.9 1.0 CB A:ASN463 4.4 41.2 1.0 O A:HOH3396 4.5 46.2 1.0 C5 A:MAN1954 4.5 61.5 1.0 O A:ASP459 4.5 48.4 1.0 CB A:ASP129 4.9 46.4 1.0

Sodium binding site 3 out of 6 in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of 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 From Glycoside Hydrolase Family 2 of Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1997 b:30.6 occ:1.00 OD2 A:ASP409 2.2 36.7 1.0 O A:HOH3735 2.8 59.1 1.0 CG A:ASP409 3.0 34.6 1.0 OD1 A:ASP409 3.0 34.6 1.0 O A:HOH3364 3.8 54.7 1.0 O A:HOH3351 4.1 73.8 1.0 CB A:ASP409 4.4 33.8 1.0 NE2 A:GLN919 4.6 42.4 1.0 CG A:GLN919 4.8 41.0 1.0 NH2 A:ARG439 4.8 40.7 1.0 O A:ASN405 4.9 35.5 1.0

Sodium binding site 4 out of 6 in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1998 b:40.7 occ:1.00 OG1 A:THR505 2.0 63.2 1.0 OD2 A:ASP502 2.6 60.9 1.0 OD1 A:ASP502 2.6 59.0 1.0 O A:HOH3736 2.6 57.2 1.0 CG A:ASP502 2.9 59.9 1.0 O A:HOH3737 3.2 65.0 1.0 CB A:THR505 3.3 57.8 1.0 N A:THR505 4.0 56.2 1.0 CA A:THR505 4.2 55.0 1.0 CG2 A:THR505 4.3 61.4 1.0 CB A:ASP502 4.5 56.4 1.0 CB A:ALA504 4.5 59.8 1.0 C A:ALA504 4.8 58.3 1.0

Sodium binding site 5 out of 6 in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1999 b:33.2 occ:1.00 O A:ALA504 2.5 59.1 1.0 O A:HOH3414 2.5 48.2 1.0 C A:ALA504 3.6 58.3 1.0 N A:THR505 4.4 56.2 1.0 CA A:THR505 4.5 55.0 1.0 CA A:ALA504 4.5 58.9 1.0 CB A:ALA504 4.7 59.8 1.0 CD A:PRO507 5.0 50.9 1.0

Sodium binding site 6 out of 6 in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2004 b:37.5 occ:1.00 O A:HOH3448 2.7 46.2 1.0 CD A:CD1988 3.5 74.5 1.0 O A:HOH3730 4.0 51.3 1.0 O A:HOH3428 4.0 47.1 1.0 O A:HOH3408 4.1 42.3 1.0 OD1 A:ASP571 4.4 50.2 1.0 O A:ASP569 4.5 41.3 1.0 O A:HOH3429 4.8 48.0 1.0

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