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Cadmium in PDB 1g0c: Alkaline Cellulase K Catalytic Domain-Cellobiose Complex

Enzymatic activity of Alkaline Cellulase K Catalytic Domain-Cellobiose Complex

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

Protein crystallography data

The structure of Alkaline Cellulase K Catalytic Domain-Cellobiose Complex, PDB code: 1g0c 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 (°) 97.900, 97.900, 121.600, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 20.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Alkaline Cellulase K Catalytic Domain-Cellobiose Complex (pdb code 1g0c). 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-Cellobiose Complex, PDB code: 1g0c:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd586

b:12.2
occ:1.00
 OE1 A:GLU321 2.4 15.1 1.0
OE2 A:GLU276 2.5 17.0 1.0
OE2 A:GLU321 2.5 15.5 1.0
OE1 A:GLU276 2.6 13.0 1.0
CD A:GLU321 2.8 13.6 1.0
CD A:GLU276 2.9 13.6 1.0
CD2 A:LEU318 4.2 9.3 1.0
O A:HOH948 4.3 18.0 1.0
CG A:GLU321 4.3 11.5 1.0
CG A:GLU276 4.4 12.0 1.0
CE1 A:HIS322 4.6 12.3 1.0
O A:HOH994 4.8 39.3 1.0
NE2 A:HIS322 4.9 12.3 1.0

Cadmium binding site 2 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd587

b:16.8
occ:1.00
 O A:ACY598 2.3 23.7 1.0
OXT A:ACY598 2.3 22.8 1.0
OXT A:ACY597 2.3 19.6 1.0
O A:ACY597 2.4 20.7 1.0
C A:ACY598 2.6 24.2 1.0
O A:HOH879 2.7 32.0 1.0
CD2 A:HIS322 2.7 11.8 1.0
C A:ACY597 2.8 20.7 1.0
NE2 A:HIS322 3.6 12.3 1.0
CG A:HIS322 3.8 11.8 1.0
O A:HOH817 3.9 47.2 1.0
CA A:HIS322 4.0 10.0 1.0
CH3 A:ACY598 4.1 22.5 1.0
CB A:HIS322 4.1 11.1 1.0
O A:GLU321 4.2 8.2 1.0
CH3 A:ACY597 4.3 20.3 1.0
O A:HOH939 4.4 31.0 1.0
O A:HOH940 4.4 45.3 1.0
OD1 A:ASN284 4.5 15.8 1.0
O A:HOH873 4.6 24.3 1.0
O A:HOH941 4.7 27.0 1.0
O A:HOH948 4.7 18.0 1.0
CE1 A:HIS322 4.8 12.3 1.0
CG2 A:VAL280 4.8 10.3 1.0
C A:GLU321 4.9 8.8 1.0
ND1 A:HIS322 4.9 13.9 1.0
N A:HIS322 4.9 9.3 1.0
C A:HIS322 4.9 10.1 1.0

Cadmium binding site 3 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd588

b:18.8
occ:1.00
 OD2 A:ASP359 2.4 15.2 1.0
OD1 A:ASP359 2.7 16.7 1.0
CG A:ASP359 2.8 15.8 1.0
CE A:LYS358 4.2 22.4 1.0
CB A:ASP359 4.3 14.7 1.0
O A:HOH880 4.6 20.8 1.0
CG A:LYS358 4.7 16.7 1.0
CD A:LYS358 4.8 20.7 1.0
NZ A:LYS358 4.9 24.5 1.0

Cadmium binding site 4 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd589

b:8.6
occ:1.00
 O A:ACY596 2.2 18.2 1.0
OD1 A:ASP500 2.4 12.3 1.0
OE1 A:GLU501 2.6 11.6 1.0
OD2 A:ASP500 2.7 11.0 1.0
OE2 A:GLU501 2.7 12.5 1.0
CG A:ASP500 2.8 9.5 1.0
C A:ACY596 3.0 18.7 1.0
CH3 A:ACY596 3.0 17.4 1.0
CD A:GLU501 3.0 13.5 1.0
O A:HOH707 4.1 37.2 1.0
OXT A:ACY596 4.1 21.7 1.0
CB A:ASP500 4.3 8.7 1.0
O A:HOH881 4.5 31.9 1.0
CG A:GLU501 4.6 12.7 1.0
N A:ASP500 4.7 8.9 1.0
CD2 A:TYR498 4.7 9.4 1.0
N A:GLU501 4.7 9.1 1.0
CA A:ASP500 5.0 8.8 1.0

Cadmium binding site 5 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd590

b:11.1
occ:1.00
 O A:HOH886 2.2 28.4 1.0
O A:HOH713 2.2 12.4 1.0
O A:HOH712 2.4 17.5 1.0
NE2 A:HIS452 2.9 12.7 1.0
CD2 A:HIS452 3.3 12.7 1.0
O A:HOH1018 3.9 27.1 1.0
CE1 A:HIS452 4.0 13.8 1.0
O A:HOH887 4.1 13.3 1.0
O A:HOH1016 4.5 25.4 1.0
O A:HOH970 4.5 43.3 1.0
O A:HOH1033 4.6 26.3 1.0
CG A:HIS452 4.6 12.5 1.0
O A:HOH711 4.7 9.8 1.0
ND1 A:HIS452 4.9 14.4 1.0
O A:HOH971 4.9 41.5 1.0

Cadmium binding site 6 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd591

b:31.4
occ:1.00
 OXT A:ACY599 2.3 30.0 1.0
O A:HOH1055 2.3 35.2 1.0
O A:ACY599 2.3 27.3 1.0
O A:HOH973 2.3 35.2 1.0
C A:ACY599 2.7 28.6 1.0
CE1 A:HIS512 2.7 15.1 1.0
ND1 A:HIS512 3.4 16.2 1.0
NE2 A:HIS512 3.7 16.0 1.0
O A:HOH735 4.1 18.9 1.0
NH2 A:ARG472 4.2 13.8 1.0
CH3 A:ACY599 4.2 28.0 1.0
O A:HOH1070 4.3 37.9 1.0
O A:HOH725 4.3 6.4 1.0
CG A:HIS512 4.6 14.2 1.0
CD2 A:HIS512 4.7 13.6 1.0
CE A:LYS511 5.0 27.1 1.0

Cadmium binding site 7 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd592

b:23.7
occ:1.00
 O A:HOH980 2.3 14.9 1.0
O A:HOH979 2.4 34.5 1.0
OE2 A:GLU485 2.4 9.3 1.0
OE1 A:GLU373 2.5 10.1 1.0
O A:HOH981 2.6 17.1 1.0
O A:HOH1057 2.7 37.1 1.0
OE2 A:GLU373 2.7 11.1 1.0
CD A:GLU373 2.9 10.5 1.0
CD A:GLU485 3.5 5.4 1.0
OE1 A:GLU485 3.8 5.9 1.0
OH A:TYR444 3.9 16.7 1.0
CE2 A:TYR444 4.2 15.7 1.0
O A:HOH690 4.2 13.6 1.0
CG A:GLU373 4.3 7.5 1.0
CZ A:TYR444 4.4 16.1 1.0
CD A:CD593 4.5 36.5 1.0
O A:HOH1073 4.5 20.0 1.0
ND1 A:HIS442 4.7 4.5 1.0
CG A:GLU485 4.8 7.6 1.0
ND2 A:ASN372 4.8 4.2 1.0
CD2 A:HIS333 4.9 18.2 1.0
NE2 A:HIS333 4.9 19.3 1.0
OD1 A:ASN372 4.9 8.0 1.0

Cadmium binding site 8 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd593

b:36.5
occ:1.00
 O A:HOH982 2.2 15.0 1.0
O A:HOH981 2.3 17.1 1.0
NE2 A:HIS333 2.8 19.3 1.0
CE1 A:HIS333 3.4 18.1 1.0
CD2 A:HIS333 3.8 18.2 1.0
O1' A:CBI585 3.9 30.3 1.0
O A:HOH979 4.1 34.5 1.0
O A:HOH958 4.3 24.2 1.0
O5' A:CBI585 4.4 27.9 1.0
O A:HOH1057 4.4 37.1 1.0
CD A:CD592 4.5 23.7 1.0
O A:HOH690 4.6 13.6 1.0
OE2 A:GLU373 4.6 11.1 1.0
ND1 A:HIS333 4.6 16.9 1.0
C1' A:CBI585 4.7 27.4 1.0
CG A:HIS333 4.8 15.6 1.0
C5' A:CBI585 4.9 24.8 1.0
O A:HOH983 4.9 40.7 1.0
C6' A:CBI585 4.9 23.8 1.0

Cadmium binding site 9 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd594

b:11.4
occ:1.00
 OE2 A:GLU351 2.4 18.3 1.0
OE1 A:GLU351 2.5 19.9 1.0
CD A:GLU351 2.8 16.0 1.0
O A:HOH1026 2.8 29.5 1.0
CG A:GLU351 4.4 14.4 1.0
OD1 A:ASP348 4.6 11.8 1.0
O A:HOH680 4.8 14.2 1.0
O A:HOH838 4.9 14.5 1.0

Cadmium binding site 10 out of 10 in 1g0c

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


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-Cellobiose Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd595

b:26.3
occ:1.00
 O A:HOH1042 2.2 10.9 1.0
O A:HOH1040 2.3 34.5 1.0
O A:HOH1041 2.3 25.8 1.0
O A:HOH1056 2.3 36.3 1.0
OE2 A:GLU314 2.4 13.3 1.0
O A:HOH890 2.5 42.9 1.0
CD A:GLU314 3.2 12.5 1.0
OE1 A:GLU314 3.2 12.9 1.0
O A:HOH952 4.1 18.1 1.0
O A:HOH900 4.4 30.2 1.0
CG A:GLU314 4.6 10.0 1.0
O A:HOH646 5.0 14.8 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 13:21:41 2024

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