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Cadmium in PDB 1kuk: Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.

Enzymatic activity of Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.

All present enzymatic activity of Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.:
3.4.24.44;

Protein crystallography data

The structure of Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw., PDB code: 1kuk was solved by K.F.Huang, S.H.Chiou, T.P.Ko, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.220, 61.220, 128.086, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.7

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. (pdb code 1kuk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw., PDB code: 1kuk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 1kuk

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Cadmium binding site 1 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd801

b:9.1
occ:1.00
 OXT B:TRP253 2.1 8.4 1.0
NE2 A:HIS154 2.2 8.1 1.0
NE2 A:HIS148 2.2 7.3 1.0
NE2 A:HIS144 2.3 5.0 1.0
O B:HOH414 2.4 17.6 1.0
O B:TRP253 2.5 8.0 1.0
C B:TRP253 2.6 8.4 1.0
CD2 A:HIS154 3.2 8.8 1.0
CE1 A:HIS154 3.2 8.7 1.0
CE1 A:HIS148 3.2 7.1 1.0
CD2 A:HIS148 3.2 6.5 1.0
CD2 A:HIS144 3.3 5.9 1.0
CE1 A:HIS144 3.3 5.2 1.0
CD1 B:TRP253 4.0 6.6 1.0
CA B:TRP253 4.1 8.2 1.0
O A:HOH417 4.2 23.4 1.0
O B:HOH511 4.2 36.2 1.0
O A:HOH637 4.3 21.5 1.0
ND1 A:HIS154 4.3 9.0 1.0
CG A:HIS154 4.3 8.3 1.0
ND1 A:HIS148 4.3 7.2 1.0
CG A:HIS148 4.4 6.4 1.0
O B:HOH413 4.4 19.6 1.0
ND1 A:HIS144 4.4 6.1 1.0
CG A:HIS144 4.4 5.3 1.0
CG B:TRP253 4.5 7.1 1.0
CB B:TRP253 4.7 7.2 1.0
NE1 B:TRP253 4.8 7.4 1.0
N B:TRP253 4.8 8.7 1.0
OE1 A:GLU145 4.8 6.6 1.0
OE2 A:GLU145 4.9 7.5 1.0
O A:HOH687 4.9 30.6 1.0
CE A:MET167 4.9 7.8 1.0

Cadmium binding site 2 out of 10 in 1kuk

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Cadmium binding site 2 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd802

b:10.2
occ:1.00
 ND1 A:HIS36 2.3 8.9 1.0
CE1 A:HIS36 3.2 9.4 1.0
CG A:HIS36 3.3 8.0 1.0
CB A:HIS36 3.6 7.3 1.0
NE2 A:HIS36 4.3 10.3 1.0
CD2 A:HIS36 4.4 9.3 1.0
O A:HOH430 4.7 39.5 1.0
CA A:HIS36 4.8 7.6 1.0

Cadmium binding site 3 out of 10 in 1kuk

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Cadmium binding site 3 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd803

b:16.1
occ:1.00
 O A:HOH434 2.2 26.7 1.0
O A:HOH432 2.3 21.6 1.0
OD2 A:ASP181 2.3 16.6 1.0
OD2 A:ASP185 2.3 12.3 1.0
OD1 A:ASP185 2.5 14.0 1.0
OD1 A:ASP181 2.7 17.6 1.0
CG A:ASP185 2.7 11.7 1.0
CG A:ASP181 2.8 15.0 1.0
O A:ASP181 4.3 9.2 1.0
CB A:ASP185 4.3 10.0 1.0
CB A:ASP181 4.4 11.0 1.0
O A:HOH392 4.4 23.4 1.0
NH2 A:ARG4 4.6 23.0 1.0
O A:HOH433 4.7 19.2 1.0
NH1 A:ARG4 4.7 23.6 1.0
C A:ASP181 4.9 8.6 1.0

Cadmium binding site 4 out of 10 in 1kuk

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Cadmium binding site 4 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd804

b:34.7
occ:1.00
 O A:HOH468 2.1 40.6 1.0
NE2 A:HIS18 2.3 16.3 1.0
O A:HOH626 2.4 34.4 1.0
O A:HOH592 3.0 42.0 1.0
CE1 A:HIS18 3.2 17.7 1.0
CD2 A:HIS18 3.3 17.1 1.0
O A:HOH426 3.9 28.8 1.0
O A:HOH594 4.1 41.7 1.0
O A:HOH328 4.3 35.1 1.0
OG1 A:THR22 4.3 17.8 1.0
ND1 A:HIS18 4.3 17.5 1.0
CG A:HIS18 4.4 15.4 1.0
O A:GLU63 4.5 20.9 1.0

Cadmium binding site 5 out of 10 in 1kuk

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Cadmium binding site 5 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd805

b:30.2
occ:1.00
 OD1 A:ASN50 2.2 12.9 1.0
OE1 A:GLN7 2.2 21.8 1.0
O A:HOH439 2.3 30.2 1.0
O A:HOH641 2.4 31.1 1.0
O A:HOH321 2.4 21.7 1.0
O A:HOH320 2.5 29.2 1.0
CD A:GLN7 3.2 18.8 1.0
CG A:ASN50 3.3 13.4 1.0
NE2 A:GLN7 3.6 19.2 1.0
ND2 A:ASN50 3.7 12.4 1.0
O A:HOH742 3.7 35.2 1.0
O A:HOH383 4.1 35.0 1.0
OE1 A:GLN3 4.3 37.3 1.0
CG A:GLN7 4.5 17.2 1.0
CB A:ASN50 4.6 11.5 1.0
O A:HOH642 4.6 35.9 1.0
CB A:GLN7 4.7 13.5 1.0
O A:ASN50 4.8 10.8 1.0
CA A:ASN50 4.8 10.9 1.0
CD A:GLN3 4.9 36.2 1.0

Cadmium binding site 6 out of 10 in 1kuk

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Cadmium binding site 6 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd806

b:30.2
occ:1.00
 O A:HOH578 2.2 17.5 1.0
OD1 A:ASP194 2.2 24.6 1.0
OD2 A:ASP194 2.3 24.2 1.0
CG A:ASP194 2.6 23.5 1.0
O A:HOH443 2.8 41.3 1.0
O A:HOH600 3.5 43.0 1.0
CB A:ASP194 4.1 21.3 1.0
O A:GLY116 4.1 13.2 1.0
O A:MET118 4.3 10.8 1.0
O A:HOH517 4.3 36.2 1.0
CB A:PRO196 4.6 18.2 1.0
CE1 A:PHE190 4.9 14.0 1.0
CA A:ASP194 4.9 20.0 1.0
CZ A:PHE190 5.0 14.3 1.0

Cadmium binding site 7 out of 10 in 1kuk

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Cadmium binding site 7 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd807

b:41.2
occ:1.00
 OXT A:PRO203 2.3 20.9 1.0
O A:PRO203 2.4 22.1 1.0
C A:PRO203 2.7 22.6 1.0
CA A:PRO203 4.2 22.7 1.0
O A:ALA202 4.8 23.8 1.0
CB A:PRO203 4.9 23.1 1.0

Cadmium binding site 8 out of 10 in 1kuk

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Cadmium binding site 8 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd808

b:14.9
occ:1.00
 O A:HOH355 2.2 22.2 1.0
ND1 A:HIS131 2.2 8.5 1.0
O A:HOH425 2.3 22.1 1.0
O A:HOH357 2.4 25.5 1.0
O A:HOH356 2.5 11.0 1.0
O A:HIS131 2.6 11.4 1.0
CE1 A:HIS131 3.2 10.0 1.0
CG A:HIS131 3.3 8.6 1.0
C A:HIS131 3.5 10.4 1.0
CB A:HIS131 3.6 8.8 1.0
O A:HOH354 3.7 19.8 1.0
O A:HOH708 4.0 30.5 1.0
CA A:HIS131 4.2 9.5 1.0
CB A:SER132 4.3 11.5 1.0
O A:HOH735 4.3 33.9 1.0
NE2 A:HIS131 4.3 10.2 1.0
N A:SER132 4.4 10.1 1.0
O A:HOH487 4.4 45.7 1.0
CD2 A:HIS131 4.4 10.3 1.0
O A:HOH634 4.5 33.7 1.0
CA A:SER132 4.6 11.6 1.0
O A:HOH484 4.8 31.0 1.0
O A:HOH624 4.8 35.3 1.0
CG2 A:ILE110 4.9 9.3 1.0

Cadmium binding site 9 out of 10 in 1kuk

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Cadmium binding site 9 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd809

b:31.6
occ:1.00
 O A:HOH557 2.2 29.5 1.0
O A:HOH387 2.3 1.3 1.0
O A:HOH381 2.5 9.0 1.0
O A:HOH556 2.7 32.0 1.0
O A:HOH555 2.9 30.0 1.0
CB A:ASP181 4.1 11.0 1.0
N A:ASP181 4.5 7.8 1.0
O A:HOH741 4.6 26.1 1.0
N A:LYS161 4.6 10.4 1.0
CB A:CYS160 4.9 8.8 1.0
CA A:ASP181 4.9 9.3 1.0
N A:CYS162 5.0 11.2 1.0

Cadmium binding site 10 out of 10 in 1kuk

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Cadmium binding site 10 out of 10 in the Crystal Structure of A Taiwan Habu Venom Metalloproteinase Complexed with Pekw.


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 A Taiwan Habu Venom Metalloproteinase Complexed with Pekw. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd810

b:31.6
occ:1.00
 O A:HOH456 2.1 29.0 1.0
OE2 A:GLU85 2.2 20.8 1.0
O A:HOH454 2.4 33.1 1.0
O A:HOH455 2.4 11.5 1.0
CD A:GLU85 2.9 19.8 1.0
OE1 A:GLU85 3.0 21.5 1.0
O A:HOH703 3.5 32.4 1.0
CG A:GLU85 4.3 18.0 1.0
OE1 A:GLU121 4.6 26.4 1.0
O A:HOH583 4.7 45.3 1.0

Reference:

K.F.Huang, S.H.Chiou, T.P.Ko, A.H.Wang. Determinants of the Inhibition of A Taiwan Habu Venom Metalloproteinase By Its Endogenous Inhibitors Revealed By X-Ray Crystallography and Synthetic Inhibitor Analogues. Eur.J.Biochem. V. 269 3047 2002.
ISSN: ISSN 0014-2956
PubMed: 12071970
DOI: 10.1046/J.1432-1033.2002.02982.X
Page generated: Sat Dec 12 08:10:45 2020

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