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Cadmium in PDB 4iug: Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose

Enzymatic activity of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose

All present enzymatic activity of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose, PDB code: 4iug was solved by M.Maksimainen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.380, 146.380, 136.330, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 21.4

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose (pdb code 4iug). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 29 binding sites of Cadmium where determined in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose, PDB code: 4iug:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 29 in 4iug

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Cadmium binding site 1 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1101

b:0.0
occ:1.00
OE1 A:GLU126 2.6 51.8 1.0
OE2 A:GLU126 3.2 50.1 1.0
CD A:GLU126 3.3 48.8 1.0
CD A:CD1128 3.3 73.9 1.0
C6 A:BMA1165 3.5 53.0 1.0
O4 A:NAG1164 3.6 55.1 1.0
O5 A:BMA1165 4.1 54.2 1.0
O6 A:BMA1165 4.2 53.1 1.0
C5 A:BMA1165 4.4 53.5 1.0
CB A:SER584 4.7 41.3 1.0
C4 A:NAG1164 4.7 53.3 1.0
CG A:GLU126 4.7 39.3 1.0

Cadmium binding site 2 out of 29 in 4iug

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Cadmium binding site 2 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1102

b:49.8
occ:1.00
O6 A:BMA1160 2.5 44.4 1.0
OE2 A:GLU112 2.6 40.9 1.0
O A:HOH3080 2.6 34.1 1.0
OE1 A:GLU112 2.7 41.1 1.0
CD A:GLU112 2.9 39.3 1.0
C6 A:BMA1160 2.9 42.5 1.0
C1 A:NAG1158 4.4 41.2 1.0
C5 A:BMA1160 4.4 44.9 1.0
CG A:GLU112 4.4 34.2 1.0
N2 A:NAG1158 4.4 41.3 1.0
O4 A:BMA1160 4.8 43.3 1.0
C2 A:NAG1158 4.8 40.7 1.0
O A:HOH3241 4.9 37.8 1.0
C4 A:BMA1160 4.9 42.8 1.0

Cadmium binding site 3 out of 29 in 4iug

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Cadmium binding site 3 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1103

b:47.4
occ:1.00
OD2 A:ASP803 2.6 31.4 1.0
O A:HOH3075 2.6 23.3 1.0
O A:HOH3074 2.6 27.4 1.0
OD1 A:ASP803 2.6 31.1 1.0
O A:HOH3224 2.7 30.9 1.0
CG A:ASP803 2.9 30.6 1.0
ND2 A:ASN815 3.9 28.0 1.0
CB A:MET774 3.9 31.5 1.0
CG A:MET774 4.2 35.6 1.0
O A:HOH3235 4.3 24.4 1.0
NH2 A:ARG817 4.3 25.5 1.0
CB A:ASP803 4.4 28.0 1.0
CG A:ASN815 4.6 31.2 1.0
CB A:ASN815 4.6 28.6 1.0
SD A:MET774 4.8 49.0 1.0
CA A:GLY750 4.8 27.6 1.0
NH1 A:ARG817 4.9 25.5 1.0

Cadmium binding site 4 out of 29 in 4iug

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Cadmium binding site 4 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1104

b:42.5
occ:1.00
OE1 A:GLU460 2.4 37.2 1.0
O A:HOH3076 2.5 29.2 1.0
OE2 A:GLU460 2.5 36.2 1.0
O A:HOH3079 2.7 27.7 1.0
CD A:GLU460 2.8 37.0 1.0
CG1 A:VAL534 3.8 38.4 1.0
O A:HOH3250 4.0 34.5 1.0
CD A:CD1105 4.3 42.5 1.0
CG A:GLU460 4.3 36.4 1.0
O A:GLY532 4.6 37.8 1.0
C A:GLY532 4.9 38.3 1.0
CG2 A:VAL534 4.9 38.1 1.0

Cadmium binding site 5 out of 29 in 4iug

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Cadmium binding site 5 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1105

b:42.5
occ:1.00
O A:HOH3077 2.5 26.2 1.0
OD2 A:ASP547 2.6 34.0 1.0
O A:HOH3078 2.7 25.6 1.0
O A:HOH3250 2.7 34.5 1.0
OD1 A:ASP547 2.7 31.8 1.0
O A:HOH3079 2.8 27.7 1.0
CG A:ASP547 3.0 32.6 1.0
ND1 A:HIS512 3.9 32.8 1.0
OE1 A:GLU460 4.0 37.2 1.0
CE1 A:HIS512 4.3 33.0 1.0
CD A:CD1104 4.3 42.5 1.0
O A:GLY532 4.4 37.8 1.0
CB A:ASP547 4.5 31.9 1.0
CD A:GLU460 4.5 37.0 1.0
O A:HOH3131 4.8 37.6 1.0
CG A:HIS512 4.8 32.2 1.0
OE2 A:GLU460 4.9 36.2 1.0
CA A:GLY532 5.0 38.9 1.0

Cadmium binding site 6 out of 29 in 4iug

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Cadmium binding site 6 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1106

b:85.1
occ:1.00
OD1 A:ASP40 2.9 46.2 1.0
CG A:ASP40 3.3 46.8 1.0
OD2 A:ASP40 3.6 42.7 1.0
O A:ALA251 4.2 32.7 1.0
CB A:ASP40 4.3 41.7 1.0
NE2 A:GLN217 4.4 36.2 1.0
OE1 A:GLN217 4.6 38.9 1.0
O A:HOH3094 4.9 31.9 1.0
CD A:GLN217 5.0 38.1 1.0

Cadmium binding site 7 out of 29 in 4iug

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Cadmium binding site 7 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1107

b:97.7
occ:1.00
OD1 A:ASP122 2.6 40.5 1.0
OD2 A:ASP122 2.8 44.6 1.0
CG A:ASP122 3.1 41.1 1.0
CB A:ASP122 4.6 35.9 1.0

Cadmium binding site 8 out of 29 in 4iug

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Cadmium binding site 8 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1108

b:70.1
occ:1.00
OE1 A:GLU804 2.6 35.1 1.0
OE2 A:GLU142 2.6 28.7 1.0
OE2 A:GLU804 2.7 31.7 1.0
CD A:GLU804 2.9 32.1 1.0
ND2 A:ASN140 3.1 33.4 1.0
CD A:GLU142 3.5 29.4 1.0
CG A:GLU142 3.5 28.8 1.0
CG A:ASN140 3.6 32.2 1.0
O4 A:GAL1130 3.7 31.1 1.0
OD1 A:ASN140 3.7 33.9 1.0
N A:GLU142 4.0 27.9 1.0
CA A:GLU142 4.2 28.2 1.0
CG A:GLU804 4.4 30.1 1.0
CB A:GLU142 4.5 28.2 1.0
NE2 A:HIS355 4.5 29.8 1.0
OE1 A:GLU142 4.6 29.1 1.0
CB A:ASN140 4.8 30.6 1.0
CD A:CD1125 4.8 89.6 1.0
CD2 A:HIS355 4.8 29.2 1.0
N A:ALA141 4.9 28.3 1.0
CB A:GLU804 5.0 30.4 1.0

Cadmium binding site 9 out of 29 in 4iug

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Cadmium binding site 9 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1109

b:95.7
occ:1.00
OD2 A:ASP163 2.6 46.0 1.0
OD1 A:ASP163 2.9 42.3 1.0
CG A:ASP163 3.1 43.3 1.0
OG1 A:THR158 3.3 44.0 1.0
CB A:THR158 4.0 40.6 1.0
N A:THR158 4.4 39.1 1.0
CB A:ASP163 4.6 40.2 1.0
OG A:SER161 4.9 39.0 1.0
CA A:THR158 4.9 39.2 1.0

Cadmium binding site 10 out of 29 in 4iug

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Cadmium binding site 10 out of 29 in the Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Beta-Galactosidase From Aspergillus Oryzae in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1110

b:91.5
occ:1.00
OD1 A:ASP214 2.7 53.0 1.0
OD2 A:ASP214 3.0 57.3 1.0
CG A:ASP214 3.1 54.0 1.0
CD A:CD1111 4.2 0.2 1.0
CB A:ASP214 4.6 48.4 1.0
OG1 A:THR249 4.8 42.2 1.0
OD1 A:ASP212 4.9 53.2 1.0

Reference:

M.M.Maksimainen, A.Lampio, M.Mertanen, O.Turunen, J.Rouvinen. The Crystal Structure of Acidic Beta-Galactosidase From Aspergillus Oryzae. Int.J.Biol.Macromol. V. 60C 109 2013.
ISSN: ISSN 0141-8130
PubMed: 23688418
DOI: 10.1016/J.IJBIOMAC.2013.05.003
Page generated: Sat Dec 12 08:24:51 2020

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