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Cadmium in PDB 1kuf: High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu

Enzymatic activity of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu

All present enzymatic activity of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu:
3.4.24.44;

Protein crystallography data

The structure of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu, PDB code: 1kuf was solved by K.F.Huang, S.H.Chiou, T.P.Ko, J.M.Yuann, 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 / 1.35
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.991, 60.991, 128.398, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.4

Cadmium Binding Sites:

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

Cadmium binding site 1 out of 10 in 1kuf

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Cadmium binding site 1 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd701

b:9.2
occ:1.00
 O A:HOH416 2.2 19.3 1.0
NE2 A:HIS154 2.2 8.6 1.0
NE2 A:HIS144 2.3 6.8 1.0
NE2 A:HIS148 2.3 7.8 1.0
O A:HOH359 2.3 13.3 1.0
O A:HOH418 2.3 15.2 1.0
CD2 A:HIS154 3.2 9.5 1.0
CE1 A:HIS154 3.2 10.6 1.0
CE1 A:HIS144 3.2 6.6 1.0
CD2 A:HIS144 3.2 7.0 1.0
CD2 A:HIS148 3.3 7.4 1.0
CE1 A:HIS148 3.3 7.2 1.0
O A:HOH417 4.1 23.7 1.0
O A:HOH663 4.3 34.6 1.0
ND1 A:HIS154 4.3 10.7 1.0
CG A:HIS154 4.4 9.2 1.0
ND1 A:HIS144 4.4 6.2 1.0
CG A:HIS144 4.4 7.0 1.0
ND1 A:HIS148 4.4 7.2 1.0
CG A:HIS148 4.4 6.8 1.0
O A:HOH681 4.4 35.1 1.0
O A:HOH518 4.6 39.0 1.0
OE1 A:GLU145 4.7 12.0 1.0
O A:ALA169 4.8 18.2 1.0
OE2 A:GLU145 4.8 10.4 1.0
CE A:MET167 4.9 7.7 1.0
O A:HOH682 5.0 33.8 1.0

Cadmium binding site 2 out of 10 in 1kuf

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Cadmium binding site 2 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd702

b:8.6
occ:1.00
 ND1 A:HIS36 2.3 8.7 1.0
O A:HOH350 2.5 1.9 1.0
CE1 A:HIS36 3.2 7.8 1.0
CG A:HIS36 3.3 7.2 1.0
CB A:HIS36 3.6 7.2 1.0
NE2 A:HIS36 4.3 7.9 1.0
CD2 A:HIS36 4.4 8.7 1.0
O A:HOH695 4.6 34.9 1.0
CA A:HIS36 4.7 6.3 1.0

Cadmium binding site 3 out of 10 in 1kuf

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Cadmium binding site 3 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd703

b:14.7
occ:1.00
 O A:HOH437 2.2 22.8 1.0
OD2 A:ASP181 2.2 15.0 1.0
O A:HOH435 2.3 19.6 1.0
OD2 A:ASP185 2.3 12.0 1.0
OD1 A:ASP185 2.4 12.0 1.0
CG A:ASP185 2.7 11.9 1.0
OD1 A:ASP181 2.8 17.9 1.0
CG A:ASP181 2.9 14.9 1.0
CB A:ASP185 4.3 9.5 1.0
O A:ASP181 4.3 8.2 1.0
CB A:ASP181 4.4 10.8 1.0
O A:HOH394 4.4 21.2 1.0
NH2 A:ARG4 4.4 20.1 1.0
O A:HOH598 4.4 37.9 1.0
NH1 A:ARG4 4.6 19.8 1.0
O A:HOH436 4.7 14.8 1.0
C A:ASP181 5.0 8.3 1.0
CZ A:ARG4 5.0 19.1 1.0

Cadmium binding site 4 out of 10 in 1kuf

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Cadmium binding site 4 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd704

b:28.7
occ:1.00
 NE2 A:HIS18 2.3 13.3 1.0
O A:HOH602 2.3 25.9 1.0
O A:HOH634 2.3 35.2 1.0
O A:HOH632 2.5 26.6 1.0
O A:HOH600 2.6 32.9 1.0
O A:HOH601 2.8 32.4 1.0
CE1 A:HIS18 3.1 13.5 1.0
CD2 A:HIS18 3.3 12.8 1.0
O A:HOH633 3.7 29.4 1.0
O A:HOH429 4.0 19.2 1.0
O A:HOH329 4.3 28.3 1.0
OG1 A:THR22 4.3 15.0 1.0
ND1 A:HIS18 4.3 12.7 1.0
CG A:HIS18 4.4 11.8 1.0
O A:GLU63 4.5 17.5 1.0
O A:HOH471 4.7 34.6 1.0

Cadmium binding site 5 out of 10 in 1kuf

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Cadmium binding site 5 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd705

b:22.4
occ:1.00
 OE1 A:GLN7 2.2 18.2 1.0
OD1 A:ASN50 2.2 11.7 1.0
O A:HOH442 2.3 22.2 1.0
O A:HOH321 2.4 18.5 1.0
O A:HOH404 2.5 28.9 1.0
O A:HOH320 2.6 20.8 1.0
CD A:GLN7 3.2 17.0 1.0
CG A:ASN50 3.3 12.0 1.0
NE2 A:GLN7 3.6 15.2 1.0
O A:HOH444 3.7 39.6 1.0
ND2 A:ASN50 3.7 12.2 1.0
O A:HOH324 4.0 37.5 1.0
O A:HOH582 4.1 39.0 1.0
O A:HOH630 4.3 30.8 1.0
OE1 A:GLN3 4.4 32.7 1.0
CG A:GLN7 4.5 15.2 1.0
O A:HOH618 4.6 38.0 1.0
CB A:ASN50 4.6 10.0 1.0
CB A:GLN7 4.7 13.6 1.0
CA A:ASN50 4.8 10.5 1.0
O A:ASN50 4.9 10.8 1.0
CD A:GLN3 4.9 31.2 1.0

Cadmium binding site 6 out of 10 in 1kuf

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Cadmium binding site 6 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd706

b:29.4
occ:1.00
 O A:HOH586 2.1 12.4 1.0
OD1 A:ASP194 2.3 23.0 1.0
OD2 A:ASP194 2.4 21.5 1.0
O A:HOH533 2.4 30.3 1.0
O A:HOH447 2.5 30.1 1.0
O A:HOH448 2.7 32.1 1.0
CG A:ASP194 2.7 20.6 1.0
O A:HOH608 3.5 34.5 1.0
O A:GLY116 4.0 12.3 1.0
CB A:ASP194 4.2 18.1 1.0
O A:MET118 4.3 10.5 1.0
CB A:PRO196 4.5 16.0 1.0
O A:HOH524 4.7 34.1 1.0
CE1 A:PHE190 4.9 12.6 1.0
CG A:PRO196 5.0 14.9 1.0
CD A:PRO196 5.0 15.0 1.0
CZ A:PHE190 5.0 11.5 1.0

Cadmium binding site 7 out of 10 in 1kuf

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Cadmium binding site 7 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd707

b:34.8
occ:1.00
 O A:PRO203 2.3 17.4 1.0
OXT A:PRO203 2.3 17.3 1.0
C A:PRO203 2.7 17.9 1.0
CA A:PRO203 4.2 17.3 1.0
O A:ALA202 4.7 18.5 1.0
CB A:PRO203 4.9 17.2 1.0

Cadmium binding site 8 out of 10 in 1kuf

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Cadmium binding site 8 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd708

b:12.9
occ:1.00
 O A:HOH356 2.2 14.2 1.0
ND1 A:HIS131 2.3 9.4 1.0
O A:HOH428 2.3 18.3 1.0
O A:HOH357 2.5 9.9 1.0
O A:HOH358 2.5 24.2 1.0
O A:HIS131 2.6 9.9 1.0
CE1 A:HIS131 3.2 8.8 1.0
CG A:HIS131 3.3 8.5 1.0
C A:HIS131 3.4 9.0 1.0
CB A:HIS131 3.6 8.9 1.0
O A:HOH355 3.9 18.7 1.0
CA A:HIS131 4.1 8.2 1.0
CB A:SER132 4.2 9.5 1.0
O A:HOH490 4.3 38.1 1.0
N A:SER132 4.3 8.9 1.0
NE2 A:HIS131 4.4 9.5 1.0
CD2 A:HIS131 4.4 9.0 1.0
CA A:SER132 4.5 9.5 1.0
O A:HOH488 4.5 25.1 1.0
O A:HOH637 4.6 32.5 1.0
O A:HOH491 4.7 43.4 1.0
O A:HOH642 4.7 29.6 1.0
O A:HOH547 4.9 37.0 1.0

Cadmium binding site 9 out of 10 in 1kuf

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Cadmium binding site 9 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd709

b:27.8
occ:1.00
 O A:HOH564 2.0 25.9 1.0
O A:HOH562 2.4 29.5 1.0
O A:HOH389 2.4 1.0 1.0
O A:HOH563 2.5 28.7 1.0
O A:HOH383 2.7 8.4 1.0
CB A:ASP181 4.0 10.8 1.0
N A:ASP181 4.5 7.9 1.0
N A:LYS161 4.6 9.1 1.0
O A:HOH391 4.7 24.0 1.0
CA A:ASP181 4.9 8.7 1.0
CB A:CYS160 4.9 7.8 1.0
N A:CYS162 5.0 10.5 1.0

Cadmium binding site 10 out of 10 in 1kuf

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Cadmium binding site 10 out of 10 in the High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of High-Resolution Crystal Structure of A Snake Venom Metalloproteinase From Taiwan Habu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd710

b:27.9
occ:1.00
 OE2 A:GLU85 2.1 16.3 1.0
O A:HOH460 2.3 29.5 1.0
O A:HOH595 2.4 29.0 1.0
O A:HOH459 2.5 8.6 1.0
O A:HOH458 2.7 28.1 1.0
CD A:GLU85 2.9 16.4 1.0
OE1 A:GLU85 2.9 18.4 1.0
CG A:GLU85 4.3 14.3 1.0
O A:HOH653 4.5 25.3 0.5
OE1 A:GLU121 4.6 24.8 1.0
O A:HOH609 4.6 31.5 1.0

Reference:

K.F.Huang, S.H.Chiou, T.P.Ko, J.M.Yuann, A.H.Wang. The 1.35 A Structure of Cadmium-Substituted Tm-3, A Snake-Venom Metalloproteinase From Taiwan Habu: Elucidation of A Tnfalpha-Converting Enzyme-Like Active-Site Structure with A Distorted Octahedral Geometry of Cadmium. Acta Crystallogr.,Sect.D V. 58 1118 2002.
ISSN: ISSN 0907-4449
PubMed: 12077431
DOI: 10.1107/S090744490200656X
Page generated: Fri Jul 19 13:45:23 2024

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