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Cadmium in PDB 4l1l: Rat Pkc C2 Domain Bound to Cd

Enzymatic activity of Rat Pkc C2 Domain Bound to Cd

All present enzymatic activity of Rat Pkc C2 Domain Bound to Cd:
2.7.11.13;

Protein crystallography data

The structure of Rat Pkc C2 Domain Bound to Cd, PDB code: 4l1l was solved by K.M.Morales, Y.Yang, Z.Long, P.Li, A.B.Taylor, P.J.Hart, T.I.Igumenova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.82 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.224, 58.224, 88.539, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 19.5

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Rat Pkc C2 Domain Bound to Cd (pdb code 4l1l). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Rat Pkc C2 Domain Bound to Cd, PDB code: 4l1l:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4l1l

Go back to Cadmium Binding Sites List in 4l1l
Cadmium binding site 1 out of 6 in the Rat Pkc C2 Domain Bound to Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Rat Pkc C2 Domain Bound to Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:18.9
occ:1.00
 OD1 A:ASP246 2.3 18.9 1.0
OD2 A:ASP193 2.3 17.8 1.0
O A:TRP247 2.4 18.5 1.0
OD1 A:ASP248 2.4 25.5 1.0
O A:HOH410 2.5 30.1 1.0
OD2 A:ASP187 2.5 24.4 1.0
OD1 A:ASP187 2.6 26.6 1.0
CG A:ASP187 2.9 25.0 1.0
CG A:ASP246 3.2 20.5 1.0
CG A:ASP193 3.3 18.6 1.0
C A:TRP247 3.4 17.5 1.0
OD2 A:ASP246 3.4 22.8 1.0
CG A:ASP248 3.6 22.2 1.0
CD A:CD307 3.7 23.1 0.7
CB A:ASP193 3.8 17.9 1.0
CA A:ASP248 3.8 21.3 1.0
N A:ASP193 3.9 17.0 1.0
N A:ASP248 4.0 18.0 1.0
O4 A:SO4305 4.2 27.6 0.5
CB A:ASP248 4.3 22.2 1.0
N A:TRP247 4.3 16.5 1.0
OD1 A:ASP193 4.3 18.7 1.0
CB A:ASP187 4.4 25.1 1.0
CD A:CD309 4.4 27.4 0.3
C A:ASP246 4.4 18.2 1.0
CA A:ASP193 4.4 16.4 1.0
CA A:TRP247 4.5 16.7 1.0
OD2 A:ASP248 4.5 22.7 1.0
O A:HOH408 4.5 28.9 1.0
O A:HOH419 4.5 33.3 1.0
C A:SER192 4.6 18.7 1.0
CB A:ASP246 4.6 19.1 1.0
O A:ASP246 4.6 19.5 1.0
CA A:SER192 4.7 19.1 0.5
CA A:SER192 4.7 19.1 0.5
CA A:ASP246 4.9 16.0 1.0

Cadmium binding site 2 out of 6 in 4l1l

Go back to Cadmium Binding Sites List in 4l1l
Cadmium binding site 2 out of 6 in the Rat Pkc C2 Domain Bound to Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Rat Pkc C2 Domain Bound to Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:23.1
occ:0.74
 OD2 A:ASP246 2.3 22.8 1.0
OD2 A:ASP254 2.4 28.3 1.0
OD1 A:ASP187 2.5 26.6 1.0
O A:MET186 2.5 25.0 0.6
O A:MET186 2.5 26.1 0.4
O A:HOH443 2.5 32.5 1.0
OD1 A:ASP248 2.5 25.5 1.0
OD2 A:ASP248 2.7 22.7 1.0
CG A:ASP248 3.0 22.2 1.0
C A:MET186 3.4 26.2 0.6
C A:MET186 3.4 26.1 0.4
CG A:ASP246 3.4 20.5 1.0
CG A:ASP254 3.5 28.5 1.0
CG A:ASP187 3.6 25.0 1.0
CD A:CD306 3.7 18.9 1.0
OD1 A:ASP246 3.9 18.9 1.0
CB A:MET186 4.0 26.6 0.4
CB A:MET186 4.0 28.3 0.6
N A:ASP187 4.1 24.4 1.0
CA A:ASP187 4.1 24.5 1.0
CB A:ASP254 4.1 26.4 1.0
O A:HOH518 4.2 40.2 1.0
O4 A:SO4305 4.3 27.6 0.5
CA A:MET186 4.3 26.1 0.6
CA A:MET186 4.3 25.8 0.4
CD A:CD308 4.3 61.1 0.3
OD2 A:ASP187 4.3 24.4 1.0
OD1 A:ASP254 4.4 30.2 1.0
CB A:ASP187 4.4 25.1 1.0
CB A:ASP248 4.4 22.2 1.0
O A:HOH524 4.5 41.1 1.0
CB A:ASP246 4.5 19.1 1.0
O1 A:SO4305 4.5 31.4 0.5
O A:HOH410 4.7 30.1 1.0
O A:ASP246 4.9 19.5 1.0
OG1 A:THR251 5.0 26.2 1.0

Cadmium binding site 3 out of 6 in 4l1l

Go back to Cadmium Binding Sites List in 4l1l
Cadmium binding site 3 out of 6 in the Rat Pkc C2 Domain Bound to Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Rat Pkc C2 Domain Bound to Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:61.1
occ:0.35
 OD1 A:ASP254 2.7 30.2 1.0
OG1 A:THR251 2.8 26.2 1.0
OD2 A:ASP248 2.8 22.7 1.0
O A:ARG252 2.9 24.5 1.0
CG A:ASP254 3.3 28.5 1.0
OD2 A:ASP254 3.3 28.3 1.0
CB A:THR251 3.4 27.2 1.0
O A:HOH443 4.0 32.5 1.0
CG A:ASP248 4.0 22.2 1.0
C A:ARG252 4.0 24.4 1.0
O A:HOH518 4.3 40.2 1.0
N A:ARG252 4.3 25.6 1.0
CG2 A:THR251 4.3 27.3 1.0
CD A:CD307 4.3 23.1 0.7
O1 A:SO4305 4.3 31.4 0.5
C A:THR251 4.5 25.2 1.0
CA A:THR251 4.6 26.2 1.0
CB A:ASP254 4.7 26.4 1.0
CB A:ASP248 4.7 22.2 1.0
CA A:ARG252 4.7 25.2 1.0
N A:ASP254 4.9 25.2 1.0
C A:ASN253 4.9 25.4 1.0
OD1 A:ASP248 4.9 25.5 1.0

Cadmium binding site 4 out of 6 in 4l1l

Go back to Cadmium Binding Sites List in 4l1l
Cadmium binding site 4 out of 6 in the Rat Pkc C2 Domain Bound to Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Rat Pkc C2 Domain Bound to Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd309

b:27.4
occ:0.29
 O A:HOH408 2.4 28.9 1.0
O A:HOH419 2.4 33.3 1.0
OD1 A:ASP193 2.5 18.7 1.0
OD2 A:ASP193 2.6 17.8 1.0
O A:HOH522 2.7 42.3 1.0
CG A:ASP193 2.9 18.6 1.0
OD2 A:ASP187 3.6 24.4 1.0
OG A:SER217 3.7 29.4 1.0
ND2 A:ASN189 4.1 25.7 1.0
O A:HOH410 4.1 30.1 1.0
N A:SER217 4.3 17.8 1.0
CD A:CD306 4.4 18.9 1.0
CB A:ASP193 4.4 17.9 1.0
CG A:ASP187 4.5 25.0 1.0
CA A:SER217 4.6 19.0 1.0
O A:HOH411 4.8 28.9 1.0
CB A:SER217 4.8 21.5 1.0
O A:HOH447 4.8 37.5 1.0
CG A:ASN189 4.8 25.9 1.0
O A:SER192 4.8 18.6 1.0
OD1 A:ASN189 4.9 26.5 1.0
C A:SER192 4.9 18.7 1.0
CB A:ARG216 4.9 19.8 1.0

Cadmium binding site 5 out of 6 in 4l1l

Go back to Cadmium Binding Sites List in 4l1l
Cadmium binding site 5 out of 6 in the Rat Pkc C2 Domain Bound to Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Rat Pkc C2 Domain Bound to Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd310

b:45.9
occ:0.41
 O A:HOH541 2.2 44.0 1.0
OE1 A:GLU282 2.6 32.9 1.0
OE2 A:GLU157 2.6 47.3 1.0
OE2 A:GLU282 2.7 38.9 1.0
O A:HOH540 2.8 48.4 1.0
CD A:GLU282 2.9 35.6 1.0
OD1 A:ASN279 3.0 44.1 1.0
CD A:GLU157 3.2 48.0 1.0
N A:THR156 3.4 48.0 1.0
OE1 A:GLU157 3.7 50.8 1.0
CG A:ASN279 3.8 36.9 1.0
CG A:GLU157 3.9 44.7 1.0
CB A:ASN279 3.9 31.4 1.0
N A:ASN279 4.2 26.5 1.0
O A:HOH482 4.4 38.3 1.0
CG A:GLU282 4.4 34.5 1.0
N A:GLU157 4.7 47.4 1.0
CA A:ASN279 4.7 28.0 1.0
CA A:THR156 4.8 46.3 1.0
ND2 A:ASN279 4.9 35.9 1.0

Cadmium binding site 6 out of 6 in 4l1l

Go back to Cadmium Binding Sites List in 4l1l
Cadmium binding site 6 out of 6 in the Rat Pkc C2 Domain Bound to Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Rat Pkc C2 Domain Bound to Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd311

b:72.0
occ:0.27
 O A:HOH511 2.2 39.6 1.0
OE2 A:GLU265 2.4 45.4 1.0
O A:HOH501 2.6 43.1 1.0
O A:HOH420 2.6 30.2 1.0
OE1 A:GLU265 2.9 42.2 1.0
CD A:GLU265 3.0 42.3 1.0
NH1 A:ARG239 4.1 22.0 1.0
O3 A:SO4301 4.1 33.9 0.9
O A:HOH478 4.1 39.3 0.5
OG A:SER264 4.3 35.7 1.0
CG A:GLU265 4.5 38.1 1.0
CA A:GLY262 4.6 20.5 1.0
O A:HOH409 4.8 29.1 1.0
O A:HOH525 4.9 44.0 1.0

Reference:

K.A.Morales, Y.Yang, Z.Long, P.Li, A.B.Taylor, P.J.Hart, T.I.Igumenova. Cd(2+) As A Ca(2+) Surrogate in Protein-Membrane Interactions: Isostructural But Not Isofunctional. J.Am.Chem.Soc. V. 135 12980 2013.
ISSN: ISSN 0002-7863
PubMed: 23937054
DOI: 10.1021/JA406958K
Page generated: Sat Dec 12 08:25:04 2020

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