Atomistry » Cadmium » PDB 4qe1-5ai3 » 4uoj
Atomistry »
  Cadmium »
    PDB 4qe1-5ai3 »
      4uoj »

Cadmium 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:

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

Cadmium Binding Sites:

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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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 4uoj

Go back to Cadmium Binding Sites List in 4uoj
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

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: Sat Dec 12 08:25:52 2020

Last articles

Zn in 7RE3
Zn in 7RDX
Zn in 7RDZ
Zn in 7RWM
Zn in 7PGU
Zn in 7PGR
Zn in 7PGT
Zn in 7PGS
Zn in 7SQE
Zn in 7RWK
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy