Atomistry » Cadmium » PDB 1dpe-1gwg » 1g0c
Atomistry »
  Cadmium »
    PDB 1dpe-1gwg »
      1g0c »

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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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

Go back to Cadmium Binding Sites List in 1g0c
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: Thu Jul 10 10:41:53 2025

Last articles

Cl in 2V1Q
Cl in 2V1P
Cl in 2UZC
Cl in 2V0Y
Cl in 2V0N
Cl in 2UXP
Cl in 2V08
Cl in 2V0D
Cl in 2V06
Cl in 2UYA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy