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

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

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

Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom
Sodium	(Na)	3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 28 binding sites of Cadmium where determined in the Structure of Fungal Beta-Mannosidase (GH2) From Trichoderma Harzianum, PDB code: 4uoj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1980 b:54.3 occ:0.50 OD2 A:ASP660 2.5 66.4 1.0 OD1 A:ASP660 2.7 57.5 1.0 CG A:ASP660 3.0 56.4 1.0 O7 A:NAG1954 3.9 52.0 1.0 O3 A:NAG1954 4.3 47.6 1.0 CB A:ASP660 4.5 47.5 1.0 N2 A:NAG1954 4.5 43.4 1.0 O A:HOH2719 4.5 58.3 1.0 C7 A:NAG1954 4.6 46.9 1.0 C3 A:NAG1954 4.8 46.2 1.0

Cadmium binding site 2 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1981 b:82.8 occ:0.50 OE2 A:GLU438 2.1 53.0 1.0 OE1 A:GLU438 2.8 59.1 1.0 CD A:GLU438 2.9 57.6 1.0 O A:HOH2350 3.5 47.1 1.0 O A:HOH2161 3.7 45.8 1.0 O A:HOH2377 4.4 40.2 1.0 CG A:GLU438 4.4 50.3 1.0 O A:HOH2355 4.7 37.9 1.0

Cadmium binding site 3 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1982 b:73.5 occ:0.50 OD1 A:ASP296 2.5 88.8 1.0 CG A:ASP296 3.3 85.5 1.0 OD2 A:ASP296 3.6 86.1 1.0 O A:GLY262 4.0 81.8 1.0 O A:ASP296 4.3 68.6 1.0 OG1 A:THR263 4.4 81.8 1.0 C A:GLY262 4.6 81.2 1.0 CB A:ASP296 4.6 75.4 1.0 O A:HOH2269 4.6 51.0 1.0 C A:ASP296 4.9 70.8 1.0 CA A:ASP296 4.9 71.4 1.0

Cadmium binding site 4 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1983 b:0.3 occ:1.00 OD2 A:ASP811 2.3 95.9 1.0 CG A:ASP811 3.3 91.7 1.0 OE2 A:GLU752 3.5 99.7 1.0 OD1 A:ASP811 3.7 95.7 1.0 N A:ASN807 4.3 77.3 1.0 CD A:GLU752 4.3 99.7 1.0 OE1 A:GLU752 4.4 0.8 1.0 CB A:ASN807 4.6 79.6 1.0 CB A:ASP811 4.6 84.7 1.0 CA A:ALA806 4.8 70.5 1.0 O A:THR805 4.9 74.6 1.0 C A:ALA806 4.9 72.6 1.0

Cadmium binding site 5 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1984 b:94.3 occ:1.00 OE2 A:GLU381 1.9 49.9 1.0 O A:HOH2323 2.8 42.7 1.0 CD A:GLU381 2.8 47.1 1.0 OE1 A:GLU381 3.1 48.5 1.0 NE A:ARG699 3.6 47.2 1.0 CD1 A:ILE367 3.9 50.8 1.0 NE2 A:GLN362 4.2 56.5 1.0 CG A:GLU381 4.2 45.7 1.0 CD A:ARG699 4.3 48.3 1.0 CZ A:ARG699 4.5 52.1 1.0 NH2 A:ARG699 4.5 43.7 1.0 CG A:ARG699 4.6 49.0 1.0 CG A:GLN362 4.8 55.6 1.0 CD A:GLN362 5.0 59.9 1.0 O A:HOH2332 5.0 53.1 1.0

Cadmium binding site 6 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1985 b:41.3 occ:1.00 OD2 B:ASP611 2.2 43.5 1.0 O A:HOH2054 2.3 27.0 1.0 OD1 A:ASN72 2.4 45.6 1.0 O A:HOH2740 2.7 31.5 1.0 OD1 B:ASP611 2.7 47.0 1.0 CG B:ASP611 2.8 45.6 1.0 O A:HOH2050 3.0 28.2 1.0 CG A:ASN72 3.3 46.2 1.0 CB A:ASN72 3.5 43.0 1.0 O A:HOH2484 4.2 46.9 1.0 CB B:ASP611 4.3 42.9 1.0 O A:HOH2051 4.3 38.2 1.0 O A:HOH2055 4.3 36.1 1.0 O A:HOH2483 4.4 44.3 1.0 O A:HOH2482 4.4 33.0 1.0 ND2 A:ASN72 4.5 43.1 1.0 O B:HOH2486 4.6 33.1 1.0 O A:HOH2471 4.7 46.3 1.0 N A:GLU69 4.8 45.1 1.0 CA A:GLY68 4.9 47.8 1.0

Cadmium binding site 7 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1986 b:40.3 occ:1.00 OD2 A:ASP611 2.2 43.1 1.0 O A:HOH2482 2.3 33.0 1.0 OD1 B:ASN72 2.4 42.7 1.0 O A:HOH2481 2.6 27.4 1.0 OD1 A:ASP611 2.7 48.4 1.0 CG A:ASP611 2.8 47.3 1.0 O A:HOH2741 2.9 31.3 1.0 CG B:ASN72 3.3 44.2 1.0 CB B:ASN72 3.5 38.8 1.0 O A:HOH2479 4.2 34.7 1.0 O A:HOH2485 4.2 35.7 1.0 O A:HOH2483 4.2 44.3 1.0 CB A:ASP611 4.3 43.3 1.0 O A:HOH2484 4.4 46.9 1.0 O B:HOH2053 4.4 48.9 1.0 O A:HOH2478 4.5 34.8 1.0 O A:HOH2054 4.5 27.0 1.0 ND2 B:ASN72 4.5 42.3 1.0 N B:GLU69 4.8 42.7 1.0 O A:HOH2480 4.8 47.5 1.0 O A:HOH2058 4.9 46.4 1.0 CA B:GLY68 4.9 46.4 1.0

Cadmium binding site 8 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1987 b:39.9 occ:1.00 O A:HOH2043 2.2 33.5 1.0 OE2 B:GLU613 2.3 55.9 1.0 OE1 B:GLU613 2.4 60.9 1.0 O A:HOH2742 2.4 19.5 1.0 NE2 A:HIS62 2.4 44.5 1.0 O A:HOH2042 2.4 35.0 1.0 CD B:GLU613 2.7 59.5 1.0 CD2 A:HIS62 3.3 45.0 1.0 CE1 A:HIS62 3.3 45.1 1.0 OE1 A:GLU69 4.1 46.5 1.0 CG B:GLU613 4.2 48.4 1.0 O B:HOH2491 4.3 37.9 1.0 O A:HOH2027 4.3 41.1 1.0 CG A:HIS62 4.4 45.3 1.0 ND1 A:HIS62 4.4 45.7 1.0 O A:HOH2041 4.5 52.8 1.0 O A:HOH2051 4.6 38.2 1.0 CB A:GLU69 4.7 43.5 1.0 O B:HOH2490 4.7 57.3 1.0 O A:HOH2345 4.7 42.0 1.0

Cadmium binding site 9 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1988 b:55.4 occ:1.00 OE1 A:GLU412 2.5 51.0 1.0 O A:HOH2362 2.7 41.0 1.0 O A:HOH2285 2.8 38.4 1.0 O A:HOH2743 3.0 44.6 1.0 CD A:GLU412 3.3 46.2 1.0 OE2 A:GLU412 3.4 43.6 1.0 O A:HOH2297 4.3 38.3 1.0 NE A:ARG316 4.3 38.6 1.0 O A:ARG439 4.4 42.3 1.0 CG A:GLU412 4.6 43.0 1.0 NH2 A:ARG316 4.7 36.8 1.0 O A:HOH2288 4.7 39.1 1.0 CB A:GLU412 5.0 39.1 1.0

Cadmium binding site 10 out of 28 in the Structure of Fungal Beta-Mannosidase (GH2) From 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 (GH2) From Trichoderma Harzianum within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1989 b:47.5 occ:0.72 OD1 A:ASP430 2.3 53.8 1.0 OD2 A:ASP434 2.5 54.5 1.0 OD2 A:ASP430 2.5 61.4 1.0 OD1 A:ASP434 2.6 51.7 1.0 O A:HOH2376 2.6 47.0 1.0 O A:HOH2301 2.7 39.7 1.0 CG A:ASP430 2.8 55.9 1.0 CG A:ASP434 2.9 50.9 1.0 O A:HOH2300 4.2 50.8 1.0 CB A:ASP430 4.3 46.5 1.0 CB A:ASP434 4.4 44.4 1.0 O6 A:NAG1979 4.4 26.3 0.5 CE1 A:HIS478 4.4 47.1 1.0 O A:HOH2303 4.5 43.6 1.0 O A:ASP430 4.5 44.1 1.0 CE1 A:HIS477 4.6 49.8 1.0 O A:HOH2378 4.6 50.9 1.0 CD A:CD1990 4.6 58.0 0.5 C A:ASP430 4.7 46.0 1.0 NE2 A:HIS478 5.0 47.3 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