Cadmium 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:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom
Sodium	(Na)	6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 17 binding sites of Cadmium where determined in the Structure of Fungal Beta-Mannosidase From Glycoside Hydrolase Family 2 of Trichoderma Harzianum, PDB code: 4cvu:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 17 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 Cadmium with other atoms in the Cd 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:Cd1978 b:39.4 occ:1.00 O A:HOH3043 2.2 24.8 1.0 O A:HOH3044 2.2 24.4 1.0 NE2 A:HIS62 2.3 31.4 1.0 O A:HOH3726 2.5 28.2 1.0 CD2 A:HIS62 3.2 30.9 1.0 CE1 A:HIS62 3.3 30.8 1.0 ND1 A:HIS62 4.4 30.9 1.0 CG A:HIS62 4.4 31.8 1.0 OE1 A:GLU69 4.4 35.5 1.0 O A:HOH3024 4.5 46.3 1.0 CB A:GLU69 4.7 38.1 1.0 O A:HOH3346 4.8 49.4 1.0

Cadmium binding site 2 out of 17 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 Cadmium with other atoms in the Cd 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:Cd1979 b:43.9 occ:1.00 O A:HOH3058 2.2 33.3 1.0 ND2 A:ASN72 2.5 33.3 1.0 O A:HOH3727 2.6 28.1 1.0 O A:HOH3051 2.7 37.2 1.0 CG A:ASN72 3.4 33.8 1.0 CB A:ASN72 3.5 34.8 1.0 OD1 A:ASN72 4.5 35.9 1.0 O A:HOH3057 4.7 49.8 1.0 N A:GLU69 4.9 39.1 1.0 O A:HOH3728 5.0 41.3 1.0

Cadmium binding site 3 out of 17 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 Cadmium with other atoms in the Cd 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:Cd1980 b:58.6 occ:1.00 ND2 A:ASN75 2.4 35.0 1.0 O A:HOH3728 2.6 41.3 1.0 O A:HOH3050 2.7 27.4 1.0 CG A:ASN75 3.1 35.7 1.0 OD1 A:ASN75 3.2 36.6 1.0 O A:HOH3051 3.3 37.2 1.0 O A:HOH3060 4.1 45.0 1.0 N A:GLY68 4.6 42.0 1.0 CB A:ASN75 4.6 35.6 1.0 CD2 A:LEU79 4.7 42.9 1.0 OD2 A:ASP78 4.8 50.4 1.0 CA A:GLY68 4.9 42.4 1.0

Cadmium binding site 4 out of 17 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 Cadmium with other atoms in the Cd 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:Cd1981 b:50.5 occ:1.00 O A:HOH3434 1.8 29.2 1.0 O A:HOH3435 2.2 55.3 1.0 OD2 A:ASP547 2.4 55.0 1.0 OD2 A:ASP549 2.4 52.6 1.0 OD1 A:ASP547 2.7 47.4 1.0 CG A:ASP547 2.9 49.3 1.0 CG A:ASP549 3.3 49.4 1.0 CB A:ASP549 3.5 51.5 1.0 O A:HOH3433 3.9 59.4 1.0 CB A:ASP547 4.3 49.7 1.0 OD1 A:ASP549 4.4 51.7 1.0 N A:ASP549 4.6 47.7 1.0 CA A:ASP549 4.7 50.8 1.0

Cadmium binding site 5 out of 17 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 Cadmium with other atoms in the Cd 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:Cd1982 b:72.3 occ:1.00 OD2 A:ASP660 2.6 47.5 1.0 OD1 A:ASP660 2.6 42.7 1.0 CG A:ASP660 2.9 43.7 1.0 C8 A:NAG1946 4.3 44.6 1.0 O3 A:NAG1946 4.4 47.1 1.0 CB A:ASP660 4.4 42.2 1.0 N2 A:NAG1946 4.4 44.8 1.0 C7 A:NAG1946 4.7 47.0 1.0 C3 A:NAG1946 4.8 44.9 1.0

Cadmium binding site 6 out of 17 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 Cadmium with other atoms in the Cd 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:Cd1983 b:52.8 occ:1.00 O A:HOH3380 2.1 40.9 1.0 OD2 A:ASP430 2.3 47.5 1.0 OD2 A:ASP434 2.5 43.3 1.0 O A:HOH3300 2.6 37.4 1.0 OD1 A:ASP434 2.6 43.6 1.0 OD1 A:ASP430 2.7 45.5 1.0 CG A:ASP430 2.9 43.5 1.0 CG A:ASP434 2.9 41.5 1.0 O A:HOH3298 4.2 53.5 1.0 CB A:ASP430 4.4 42.7 1.0 CB A:ASP434 4.4 39.7 1.0 CE1 A:HIS478 4.4 40.0 1.0 O A:ASP430 4.5 41.0 1.0 O A:HOH3302 4.6 36.3 1.0 CD A:CD1984 4.6 76.5 1.0 C A:ASP430 4.8 40.3 1.0 CE1 A:HIS477 4.8 45.8 1.0

Cadmium binding site 7 out of 17 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 Cadmium with other atoms in the Cd binding site number 7 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:Cd1984 b:76.5 occ:1.00 O A:HOH3379 2.4 35.2 1.0 OD1 A:ASP430 2.7 45.5 1.0 O A:HOH3298 2.7 53.5 1.0 NE2 A:HIS477 2.8 46.8 1.0 CG A:ASP430 3.0 43.5 1.0 O A:HOH3209 3.2 51.6 1.0 CB A:ASP430 3.3 42.7 1.0 NE2 A:HIS478 3.6 40.4 1.0 CE1 A:HIS477 3.6 45.8 1.0 OD2 A:ASP430 3.7 47.5 1.0 O A:ARG474 3.7 41.4 1.0 NE A:ARG344 3.7 45.5 1.0 CD2 A:HIS477 3.8 45.6 1.0 CD A:ARG344 4.1 46.6 1.0 CE1 A:HIS478 4.3 40.0 1.0 CA A:ASP430 4.4 41.7 1.0 CD2 A:HIS478 4.5 39.2 1.0 O A:HOH3208 4.5 48.4 1.0 CZ A:ARG344 4.6 44.8 1.0 CD A:CD1983 4.6 52.8 1.0 O A:HOH3300 4.6 37.4 1.0 CG A:ARG474 4.6 43.1 1.0 C A:ARG474 4.8 41.5 1.0 ND1 A:HIS477 4.8 47.3 1.0 NH2 A:ARG344 4.8 45.4 1.0 CG A:HIS477 4.9 45.2 1.0

Cadmium binding site 8 out of 17 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 Cadmium with other atoms in the Cd binding site number 8 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:Cd1985 b:51.2 occ:1.00 O A:HOH3366 2.1 42.0 1.0 O A:HOH3278 2.3 33.8 1.0 OE1 A:GLU412 2.5 37.9 1.0 CD A:GLU412 3.2 40.8 1.0 OE2 A:GLU412 3.3 40.4 1.0 O A:HOH3129 4.1 60.8 1.0 NE A:ARG316 4.3 36.2 1.0 O A:ARG439 4.5 40.1 1.0 CG A:GLU412 4.6 38.4 1.0 NH2 A:ARG316 4.6 36.8 1.0 O A:HOH3281 4.9 45.5 1.0 CZ A:ARG316 4.9 36.2 1.0 CB A:GLU412 5.0 37.2 1.0

Cadmium binding site 9 out of 17 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 Cadmium with other atoms in the Cd binding site number 9 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:Cd1986 b:59.5 occ:1.00 OE2 A:GLU381 2.2 45.6 1.0 O A:HOH3563 2.4 37.4 1.0 O A:HOH3322 2.5 33.8 1.0 O A:HOH3323 2.6 36.9 1.0 OE1 A:GLU381 2.7 41.6 1.0 CD A:GLU381 2.8 43.1 1.0 NE A:ARG699 3.9 43.9 1.0 NE2 A:GLN362 4.1 48.8 1.0 CG A:GLU381 4.3 42.8 1.0 CD1 A:ILE367 4.3 48.7 1.0 NH2 A:ARG699 4.5 45.6 1.0 CD A:ARG699 4.7 42.9 1.0 CZ A:ARG699 4.7 43.9 1.0 CG A:GLN362 4.9 52.3 1.0 CG A:ARG699 4.9 42.1 1.0 CD A:GLN362 4.9 49.7 1.0

Cadmium binding site 10 out of 17 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 Cadmium with other atoms in the Cd binding site number 10 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:Cd1987 b:81.6 occ:1.00 OE2 A:GLU438 2.4 40.4 1.0 O A:HOH3729 2.4 60.2 1.0 OE1 A:GLU438 2.7 42.2 1.0 O A:HOH3357 2.9 43.5 1.0 CD A:GLU438 2.9 42.0 1.0 O A:HOH3356 4.2 42.3 1.0 CG A:GLU438 4.4 40.0 1.0 O A:HOH3381 4.6 39.7 1.0 NH2 A:ARG345 4.8 45.2 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