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Cadmium in PDB 1g01: Alkaline Cellulase K Catalytic Domain

Enzymatic activity of Alkaline Cellulase K Catalytic Domain

All present enzymatic activity of Alkaline Cellulase K Catalytic Domain:
3.2.1.4;

Protein crystallography data

The structure of Alkaline Cellulase K Catalytic Domain, PDB code: 1g01 was solved by T.Shirai, H.Ishida, J.Noda, T.Yamane, K.Ozaki, Y.Hakamada, S.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 98.200, 98.200, 122.000, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 22.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Alkaline Cellulase K Catalytic Domain (pdb code 1g01). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Alkaline Cellulase K Catalytic Domain, PDB code: 1g01:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 1g01

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Cadmium binding site 1 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd585

b:16.3
occ:1.00
 OE1 A:GLU463 2.3 17.9 1.0
OE2 A:GLU463 2.4 22.8 1.0
CD A:GLU463 2.7 18.1 1.0
CG A:GLU463 4.2 15.0 1.0
CD A:PRO460 4.4 13.1 1.0
O A:HOH808 4.5 67.3 1.0
OG1 A:THR459 4.6 11.6 1.0
O A:HOH810 4.7 42.8 1.0
CG2 A:THR459 4.7 10.0 1.0
CG A:PRO460 4.9 16.9 1.0
CA A:THR459 4.9 11.5 1.0
CB A:GLU463 5.0 11.2 1.0

Cadmium binding site 2 out of 10 in 1g01

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Cadmium binding site 2 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd586

b:18.3
occ:1.00
 O A:ACY597 2.4 17.5 1.0
OXT A:ACY597 2.4 18.0 1.0
OXT A:ACY596 2.5 26.7 1.0
O A:HOH803 2.5 28.8 1.0
O A:HOH850 2.6 27.5 1.0
O A:ACY596 2.7 26.3 1.0
C A:ACY597 2.7 16.3 1.0
ND1 A:HIS322 2.9 16.5 1.0
C A:ACY596 2.9 27.7 1.0
CE1 A:HIS322 3.7 12.0 1.0
CG A:HIS322 3.9 14.8 1.0
O A:HOH804 4.0 39.7 1.0
O A:GLU321 4.1 11.4 1.0
CH3 A:ACY597 4.1 11.8 1.0
CA A:HIS322 4.1 10.6 1.0
O A:HOH776 4.2 22.2 1.0
CB A:HIS322 4.3 12.1 1.0
CH3 A:ACY596 4.4 27.7 1.0
OD1 A:ASN284 4.4 19.6 1.0
O A:HOH916 4.4 40.4 1.0
O A:HOH917 4.5 34.2 1.0
O A:HOH922 4.8 34.2 1.0
NE2 A:HIS322 4.8 17.1 1.0
C A:GLU321 4.9 8.3 1.0
C A:HIS322 4.9 10.8 1.0
N A:HIS322 4.9 9.0 1.0
CG2 A:VAL280 5.0 8.7 1.0
O A:HOH924 5.0 24.6 1.0
CD2 A:HIS322 5.0 18.3 1.0

Cadmium binding site 3 out of 10 in 1g01

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Cadmium binding site 3 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd587

b:23.3
occ:1.00
 O A:HOH1037 2.6 35.1 1.0
OE1 A:GLU403 2.7 24.2 1.0
O A:HOH985 2.8 46.4 1.0
OE2 A:GLU403 2.9 27.0 1.0
CD A:GLU403 3.1 24.9 1.0
O A:HOH728 4.1 51.4 1.0
CG A:GLU403 4.6 19.0 1.0
O A:HOH731 5.0 22.3 1.0

Cadmium binding site 4 out of 10 in 1g01

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Cadmium binding site 4 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd588

b:9.7
occ:1.00
 OE2 A:GLU396 2.2 7.1 1.0
OXT A:ACY595 2.4 19.0 1.0
O A:ACY595 3.0 14.3 1.0
CD A:GLU396 3.0 14.2 1.0
C A:ACY595 3.2 15.8 1.0
OE1 A:GLU396 3.2 10.7 1.0
O A:HOH984 4.4 45.9 1.0
CG A:GLU396 4.4 7.8 1.0
NH1 A:ARG339 4.5 10.7 1.0
O A:HOH867 4.6 40.4 1.0
CH3 A:ACY595 4.6 14.0 1.0
O A:HOH711 4.8 11.5 1.0
O A:HOH641 4.8 10.0 1.0
O A:HOH745 4.9 17.9 1.0

Cadmium binding site 5 out of 10 in 1g01

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Cadmium binding site 5 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd589

b:15.6
occ:1.00
 ND1 A:HIS356 2.7 14.7 1.0
O A:HOH716 2.7 10.6 1.0
O A:HOH1064 2.9 26.6 1.0
O A:HOH1036 2.9 34.6 1.0
CG A:HIS356 3.4 10.3 1.0
CE1 A:HIS356 3.6 12.4 1.0
CB A:HIS356 3.9 9.5 1.0
O A:HOH805 4.0 27.5 1.0
O A:HOH715 4.4 10.5 1.0
CD2 A:HIS356 4.5 11.1 1.0
NE2 A:HIS356 4.6 11.8 1.0
OH A:TYR313 4.6 9.1 1.0
CA A:HIS356 4.7 12.3 1.0
CE2 A:TYR313 5.0 9.2 1.0

Cadmium binding site 6 out of 10 in 1g01

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Cadmium binding site 6 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd590

b:37.1
occ:1.00
 O A:HOH919 2.3 36.3 1.0
O A:ACY598 2.7 34.5 1.0
OXT A:ACY598 2.7 39.8 1.0
C A:ACY598 3.0 39.0 1.0
NE2 A:HIS512 3.1 18.7 1.0
CD2 A:HIS512 3.7 21.1 1.0
O A:HOH692 3.9 19.1 1.0
NZ A:LYS511 4.0 40.3 1.0
CE1 A:HIS512 4.0 20.4 1.0
NH2 A:ARG472 4.2 12.4 1.0
CH3 A:ACY598 4.4 36.4 1.0
CE A:LYS511 4.6 35.5 1.0
CG A:HIS512 4.8 18.0 1.0
ND1 A:HIS512 4.9 20.6 1.0

Cadmium binding site 7 out of 10 in 1g01

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Cadmium binding site 7 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd591

b:19.4
occ:1.00
 OE2 A:GLU485 2.2 7.1 1.0
OE1 A:GLU373 2.2 7.2 1.0
O A:HOH717 2.4 40.9 1.0
O A:HOH699 2.6 13.7 1.0
CD A:GLU373 2.7 9.5 1.0
OE2 A:GLU373 2.8 15.2 1.0
CD A:GLU485 3.3 10.0 1.0
OH A:TYR444 3.4 22.0 1.0
OE1 A:GLU485 3.7 7.6 1.0
O A:HOH1026 3.7 25.2 1.0
CE2 A:TYR444 3.9 17.0 1.0
CG A:GLU373 4.1 9.2 1.0
CZ A:TYR444 4.1 19.4 1.0
O A:HOH918 4.2 23.9 1.0
CD A:CD592 4.5 22.5 1.0
CG A:GLU485 4.5 7.6 1.0
ND1 A:HIS442 4.5 6.7 1.0
O A:HOH807 4.6 42.0 1.0
O A:HOH1063 4.7 34.7 1.0
OD1 A:ASN372 4.9 9.6 1.0
O A:ALA491 4.9 29.6 1.0

Cadmium binding site 8 out of 10 in 1g01

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Cadmium binding site 8 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd592

b:22.5
occ:1.00
 O A:HOH1026 2.3 25.2 1.0
O A:HOH1063 2.6 34.7 1.0
O A:ACY599 2.7 39.9 1.0
OXT A:ACY599 2.8 37.3 1.0
NE2 A:HIS333 3.0 17.3 1.0
C A:ACY599 3.1 39.4 1.0
CD2 A:HIS333 3.7 16.8 1.0
CE1 A:HIS333 3.8 16.0 1.0
O A:HOH989 4.0 55.4 1.0
O A:HOH619 4.0 16.4 1.0
O A:HOH918 4.2 23.9 1.0
OE2 A:GLU373 4.3 15.2 1.0
O A:HOH717 4.4 40.9 1.0
CD A:CD591 4.5 19.4 1.0
CH3 A:ACY599 4.5 39.2 1.0
O A:ALA491 4.7 29.6 1.0
CG A:HIS333 4.8 14.8 1.0
ND1 A:HIS333 4.8 19.6 1.0
O A:HOH699 4.9 13.7 1.0

Cadmium binding site 9 out of 10 in 1g01

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Cadmium binding site 9 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd593

b:11.7
occ:0.50
 OE2 A:GLU351 2.3 26.4 1.0
OE1 A:GLU351 2.5 27.8 1.0
CD A:GLU351 2.7 19.2 1.0
CG A:GLU351 4.2 19.2 1.0
OD1 A:ASP348 4.5 14.4 1.0
O A:HOH714 4.6 6.8 1.0
O A:HOH713 4.7 14.6 1.0

Cadmium binding site 10 out of 10 in 1g01

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Cadmium binding site 10 out of 10 in the Alkaline Cellulase K Catalytic Domain


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Alkaline Cellulase K Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd594

b:35.8
occ:1.00
 O A:HOH920 2.0 10.8 1.0
O A:HOH811 2.4 30.1 1.0
OE2 A:GLU314 2.5 14.7 1.0
CD A:GLU314 3.3 13.2 1.0
OE1 A:GLU314 3.4 14.6 1.0
O A:HOH704 3.7 17.1 1.0
O A:HOH1062 4.3 41.5 1.0
CG A:GLU314 4.6 7.7 1.0
O A:HOH612 4.9 11.0 1.0

Reference:

T.Shirai, H.Ishida, J.Noda, T.Yamane, K.Ozaki, Y.Hakamada, S.Ito. Crystal Structure of Alkaline Cellulase K: Insight Into the Alkaline Adaptation of An Industrial Enzyme. J.Mol.Biol. V. 310 1079 2001.
ISSN: ISSN 0022-2836
PubMed: 11501997
DOI: 10.1006/JMBI.2001.4835
Page generated: Fri Jul 19 13:21:26 2024

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