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Cadmium in PDB 3p5v: Actinidin From Actinidia Arguta Planch (Sarusashi)

Enzymatic activity of Actinidin From Actinidia Arguta Planch (Sarusashi)

All present enzymatic activity of Actinidin From Actinidia Arguta Planch (Sarusashi):
3.4.22.14;

Protein crystallography data

The structure of Actinidin From Actinidia Arguta Planch (Sarusashi), PDB code: 3p5v was solved by Y.Manickam, N.Nirmal, A.Suzuki, Y.Sugiyama, T.Yamane, V.Devadasan, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.64 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.269, 55.812, 70.225, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 21.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Actinidin From Actinidia Arguta Planch (Sarusashi) (pdb code 3p5v). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Actinidin From Actinidia Arguta Planch (Sarusashi), PDB code: 3p5v:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3p5v

Go back to Cadmium Binding Sites List in 3p5v
Cadmium binding site 1 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd221

b:18.9
occ:0.75
 O A:HOH241 2.2 17.9 1.0
O A:HOH400 2.2 27.2 1.0
ND1 A:HIS162 2.3 14.0 1.0
OD A:CSO25 2.7 24.8 1.0
CE1 A:HIS162 3.2 14.8 1.0
CG A:HIS162 3.4 15.6 1.0
SG A:CSO25 3.5 22.7 1.0
CB A:HIS162 3.8 16.2 1.0
O A:HOH435 4.0 32.6 1.0
O A:ASP161 4.1 18.2 1.0
CA A:HIS162 4.2 16.6 1.0
NE2 A:GLN19 4.2 18.2 1.0
NE2 A:HIS162 4.3 14.1 1.0
CB A:CSO25 4.3 20.9 1.0
CD2 A:HIS162 4.5 14.9 1.0
O A:HOH335 4.5 26.9 1.0
NE1 A:TRP184 4.6 14.6 1.0
CZ2 A:TRP184 4.7 14.5 1.0
OE1 A:GLN19 4.8 17.7 1.0
CD A:GLN19 4.9 17.8 1.0

Cadmium binding site 2 out of 9 in 3p5v

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Cadmium binding site 2 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd222

b:14.9
occ:0.60
 O A:HOH315 2.0 37.9 1.0
O A:HOH314 2.1 11.8 1.0
OD2 A:ASP176 2.2 15.5 1.0
O A:HOH290 2.3 29.8 1.0
CG A:ASP176 2.9 16.8 1.0
OD1 A:ASP176 2.9 15.8 1.0
ND2 A:ASN199 4.1 17.5 1.0
O A:HOH296 4.2 25.3 1.0
CB A:ASP176 4.4 17.2 1.0
O A:HOH442 4.4 20.1 0.5
O A:GLY174 4.7 23.5 1.0

Cadmium binding site 3 out of 9 in 3p5v

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Cadmium binding site 3 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd223

b:18.6
occ:0.57
 O A:HOH327 2.1 23.8 1.0
O A:HOH326 2.2 28.1 1.0
O A:HOH401 2.3 28.7 0.5
OE2 A:GLU191 2.4 23.2 1.0
OE1 A:GLU191 2.4 23.4 1.0
O A:HOH402 2.5 19.6 1.0
CD A:GLU191 2.7 21.9 1.0
CG A:GLU191 4.2 19.5 1.0
O A:HOH363 4.4 34.1 1.0

Cadmium binding site 4 out of 9 in 3p5v

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Cadmium binding site 4 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd224

b:16.9
occ:0.35
 O A:HOH303 2.2 24.0 1.0
O A:HOH328 2.5 39.3 1.0
OD1 A:ASP44 2.8 30.6 1.0
CD A:CD229 3.2 63.2 0.3
CG A:ASP44 3.9 28.7 1.0
O A:GLY43 4.2 26.0 1.0
O A:HOH445 4.3 44.3 1.0
OD2 A:ASP44 4.3 31.8 1.0
O A:HOH320 4.6 61.8 1.0
C A:GLY43 4.7 25.8 1.0

Cadmium binding site 5 out of 9 in 3p5v

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Cadmium binding site 5 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd225

b:31.6
occ:0.50
 OD2 A:ASP111 2.3 20.3 1.0
OD1 A:ASP111 2.3 20.1 1.0
O A:HOH403 2.5 22.6 0.5
CG A:ASP111 2.6 19.4 1.0
O A:HOH278 2.6 36.7 1.0
CB A:ASP111 4.1 18.3 1.0
O A:HOH403 4.3 16.9 0.5
NZ A:LYS217 4.5 20.9 1.0
CD2 A:TYR218 4.7 21.2 1.0
CA A:ASP111 4.8 18.1 1.0
N A:TYR218 4.8 20.1 1.0
N A:ASP111 4.9 17.3 1.0
OG A:SER109 4.9 16.1 0.5

Cadmium binding site 6 out of 9 in 3p5v

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Cadmium binding site 6 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd226

b:35.0
occ:0.47
 O A:HOH329 2.3 43.9 1.0
OD1 A:ASP72 2.3 17.9 1.0
O A:HOH269 2.6 26.2 1.0
O A:HOH405 2.9 16.4 0.4
OD2 A:ASP72 3.0 20.2 1.0
CG A:ASP72 3.0 17.5 1.0
O A:HOH404 3.2 34.0 0.5
OD1 A:ASN61 4.4 27.7 1.0
O A:HOH432 4.4 38.9 1.0
OG1 A:THR59 4.5 23.1 1.0
CB A:ASP72 4.5 16.4 1.0
NE2 A:GLN75 4.6 17.8 0.5
CB A:ASN61 4.9 24.1 1.0

Cadmium binding site 7 out of 9 in 3p5v

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Cadmium binding site 7 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd227

b:36.4
occ:0.44
 O A:HOH307 2.1 35.8 1.0
O A:HOH309 2.2 30.9 1.0
O A:HOH306 2.4 23.2 1.0
O A:HOH308 2.5 24.2 1.0
O A:HOH305 2.7 17.6 0.5
O A:HOH305 2.8 2.0 0.5
CG2 A:THR186 3.2 16.8 1.0
OG1 A:THR186 3.4 17.9 1.0
CB A:THR186 3.9 16.9 1.0
O A:ILE16 4.1 16.3 1.0
O A:HOH310 4.3 42.9 1.0
N A:THR186 4.3 15.7 1.0
CA A:THR186 4.7 16.5 1.0
O A:HOH337 4.9 44.0 1.0

Cadmium binding site 8 out of 9 in 3p5v

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Cadmium binding site 8 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd228

b:55.2
occ:0.30
 OD2 A:ASP15 2.6 23.6 1.0
OD1 A:ASP15 2.7 19.5 1.0
CG A:ASP15 3.0 19.1 1.0
O A:HOH407 3.1 21.2 0.3
O A:HOH406 3.8 10.7 0.2
CB A:ASP15 4.5 17.2 1.0
O A:HOH295 4.7 25.2 1.0
O A:HOH321 4.9 44.5 1.0
O A:HOH423 4.9 39.0 1.0

Cadmium binding site 9 out of 9 in 3p5v

Go back to Cadmium Binding Sites List in 3p5v
Cadmium binding site 9 out of 9 in the Actinidin From Actinidia Arguta Planch (Sarusashi)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Actinidin From Actinidia Arguta Planch (Sarusashi) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd229

b:63.2
occ:0.30
 O A:HOH445 2.5 44.3 1.0
OD1 A:ASP44 2.8 30.6 1.0
O A:HOH320 2.9 61.8 1.0
CD A:CD224 3.2 16.9 0.3
CG A:ASP44 3.8 28.7 1.0
O A:HOH328 4.0 39.3 1.0
OD2 A:ASP44 4.4 31.8 1.0
CB A:ASP44 4.7 26.0 1.0
O A:HOH438 5.0 51.7 1.0

Reference:

M.Yogavel, N.Nithya, A.Suzuki, Y.Sugiyama, T.Yamane, D.Velmurugan, A.Sharma. Structural Analysis of Actinidin and A Comparison of Cadmium and Sulfur Anomalous Signals From Actinidin Crystals Measured Using in-House Copper- and Chromium-Anode X-Ray Sources Acta Crystallogr.,Sect.D V. 66 1323 2010.
ISSN: ISSN 0907-4449
PubMed: 21123873
DOI: 10.1107/S0907444910040394
Page generated: Fri Jul 19 16:21:32 2024

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