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Zinc in PDB 7l92: C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate

Enzymatic activity of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate

All present enzymatic activity of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate:
2.7.11.13;

Protein crystallography data

The structure of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate, PDB code: 7l92 was solved by S.S.Katti, I.V.Krieger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.96 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.068, 89.068, 218.679, 90, 90, 120
R / Rfree (%) 21.4 / 24.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate (pdb code 7l92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate, PDB code: 7l92:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 7l92

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Zinc binding site 1 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:30.8
occ:1.00
 ND1 A:HIS231 2.1 31.2 1.0
SG A:CYS261 2.3 30.8 1.0
SG A:CYS280 2.3 35.3 1.0
SG A:CYS264 2.3 29.5 1.0
CE1 A:HIS231 2.9 34.1 1.0
CB A:CYS264 3.1 33.2 1.0
CB A:CYS280 3.2 34.0 1.0
CG A:HIS231 3.2 36.9 1.0
CB A:CYS261 3.3 24.2 1.0
N A:CYS264 3.6 32.4 1.0
CB A:HIS231 3.6 37.2 1.0
CA A:HIS231 3.9 33.3 1.0
CA A:CYS264 4.0 23.3 1.0
CA A:CYS280 4.0 38.2 1.0
NE2 A:HIS231 4.1 38.2 1.0
CD2 A:HIS231 4.2 35.2 1.0
O A:HOH412 4.4 61.0 1.0
C A:ASP263 4.6 38.8 1.0
N A:ARG232 4.7 29.3 1.0
CB A:ASP263 4.7 30.3 1.0
C A:CYS264 4.7 30.8 1.0
CA A:CYS261 4.8 27.4 1.0
N A:HIS231 4.8 36.2 1.0
C A:HIS231 4.8 34.7 1.0
C A:CYS280 4.9 49.5 1.0
N A:ASP263 4.9 31.6 1.0
N A:GLY265 4.9 24.1 1.0
CA A:ASP263 4.9 29.6 1.0

Zinc binding site 2 out of 16 in 7l92

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Zinc binding site 2 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:32.3
occ:1.00
 ND1 A:HIS269 2.1 29.8 1.0
SG A:CYS272 2.3 39.2 1.0
SG A:CYS247 2.3 36.7 1.0
SG A:CYS244 2.3 25.4 1.0
CB A:CYS244 3.0 26.1 1.0
CE1 A:HIS269 3.1 32.3 1.0
CG A:HIS269 3.2 25.3 1.0
CB A:CYS247 3.2 37.0 1.0
CB A:CYS272 3.4 34.2 1.0
CB A:HIS269 3.5 25.9 1.0
N A:CYS247 3.8 39.9 1.0
N A:HIS269 4.0 26.1 1.0
CA A:CYS247 4.1 44.3 1.0
NE2 A:HIS269 4.2 31.7 1.0
CD2 A:HIS269 4.3 27.7 1.0
CA A:HIS269 4.4 27.5 1.0
CA A:CYS244 4.5 32.4 1.0
CA A:CYS272 4.7 34.8 1.0
CB A:HIS246 4.7 41.4 1.0
C A:CYS247 4.8 43.5 1.0
CE A:LYS271 4.8 39.2 1.0
N A:CYS272 4.9 34.0 1.0
C A:HIS246 5.0 45.4 1.0
N A:GLY248 5.0 32.4 1.0

Zinc binding site 3 out of 16 in 7l92

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Zinc binding site 3 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:37.9
occ:1.00
 ND1 D:HIS231 2.0 38.3 1.0
SG D:CYS261 2.3 40.4 1.0
SG D:CYS264 2.3 37.1 1.0
SG D:CYS280 2.3 38.0 1.0
CE1 D:HIS231 2.9 43.9 1.0
CG D:HIS231 3.1 40.0 1.0
CB D:CYS261 3.2 39.9 1.0
CB D:CYS264 3.3 34.5 1.0
CB D:CYS280 3.3 49.6 1.0
CB D:HIS231 3.5 35.3 1.0
N D:CYS264 3.7 38.4 1.0
CA D:HIS231 3.8 41.0 1.0
CA D:CYS280 4.0 55.1 1.0
CA D:CYS264 4.1 36.7 1.0
NE2 D:HIS231 4.1 43.2 1.0
O D:HOH425 4.1 53.4 1.0
CD2 D:HIS231 4.2 38.3 1.0
CB D:ASP263 4.5 52.6 1.0
N D:ARG232 4.6 41.5 1.0
CA D:CYS261 4.7 33.0 1.0
C D:ASP263 4.7 49.9 1.0
N D:HIS231 4.7 47.1 1.0
C D:HIS231 4.8 41.9 1.0
C D:CYS264 4.8 32.6 1.0
C D:CYS280 4.9 60.8 1.0
O D:CYS280 4.9 65.3 1.0
N D:ASP263 4.9 50.5 1.0
CA D:ASP263 5.0 48.8 1.0

Zinc binding site 4 out of 16 in 7l92

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Zinc binding site 4 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:29.2
occ:1.00
 ND1 D:HIS269 2.2 24.5 1.0
SG D:CYS244 2.3 27.4 1.0
SG D:CYS247 2.3 28.3 1.0
SG D:CYS272 2.4 29.0 1.0
CB D:CYS244 3.0 25.1 1.0
CE1 D:HIS269 3.2 30.2 1.0
CG D:HIS269 3.2 28.7 1.0
CB D:CYS247 3.3 32.4 1.0
CB D:CYS272 3.4 30.9 1.0
CB D:HIS269 3.5 23.1 1.0
N D:CYS247 3.8 31.1 1.0
N D:HIS269 4.1 19.9 1.0
CA D:CYS247 4.1 26.7 1.0
NE2 D:HIS269 4.3 22.3 1.0
CD2 D:HIS269 4.3 22.4 1.0
CA D:HIS269 4.4 26.1 1.0
CA D:CYS244 4.5 23.5 1.0
CA D:CYS272 4.8 38.3 1.0
CB D:HIS246 4.8 31.5 1.0
C D:CYS247 4.9 36.5 1.0
C D:HIS246 4.9 36.3 1.0

Zinc binding site 5 out of 16 in 7l92

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Zinc binding site 5 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn301

b:31.6
occ:1.00
 ND1 G:HIS231 2.1 28.5 1.0
SG G:CYS261 2.3 31.0 1.0
SG G:CYS264 2.3 29.6 1.0
SG G:CYS280 2.3 35.0 1.0
CE1 G:HIS231 3.0 31.5 1.0
CB G:CYS264 3.1 35.2 1.0
CG G:HIS231 3.2 36.9 1.0
CB G:CYS280 3.2 37.0 1.0
CB G:CYS261 3.3 24.9 1.0
CB G:HIS231 3.6 33.7 1.0
N G:CYS264 3.7 32.2 1.0
CA G:HIS231 3.8 33.7 1.0
CA G:CYS264 4.0 22.4 1.0
CA G:CYS280 4.1 42.6 1.0
NE2 G:HIS231 4.1 39.4 1.0
CD2 G:HIS231 4.2 33.8 1.0
C G:ASP263 4.6 37.9 1.0
N G:ARG232 4.7 32.4 1.0
C G:CYS264 4.7 28.8 1.0
CB G:ASP263 4.7 28.1 1.0
CA G:CYS261 4.8 25.1 1.0
N G:HIS231 4.8 37.6 1.0
C G:HIS231 4.9 35.6 1.0
C G:CYS280 4.9 48.0 1.0
N G:GLY265 4.9 23.4 1.0
N G:ASP263 5.0 28.7 1.0

Zinc binding site 6 out of 16 in 7l92

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Zinc binding site 6 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:32.6
occ:1.00
 ND1 G:HIS269 2.1 30.5 1.0
SG G:CYS272 2.3 38.1 1.0
SG G:CYS247 2.3 37.9 1.0
SG G:CYS244 2.3 25.4 1.0
CE1 G:HIS269 3.0 30.6 1.0
CB G:CYS244 3.0 26.4 1.0
CG G:HIS269 3.1 26.0 1.0
CB G:CYS247 3.2 35.8 1.0
CB G:CYS272 3.4 35.9 1.0
CB G:HIS269 3.5 26.1 1.0
N G:CYS247 3.8 38.1 1.0
N G:HIS269 4.0 26.1 1.0
CA G:CYS247 4.1 44.0 1.0
NE2 G:HIS269 4.2 33.6 1.0
CD2 G:HIS269 4.2 27.4 1.0
CA G:HIS269 4.4 26.9 1.0
CA G:CYS244 4.5 29.2 1.0
CB G:HIS246 4.7 43.6 1.0
CA G:CYS272 4.7 38.1 1.0
CE G:LYS271 4.8 39.6 1.0
C G:CYS247 4.8 43.3 1.0
N G:CYS272 4.9 36.6 1.0
C G:HIS246 4.9 46.2 1.0
N G:GLY248 4.9 34.8 1.0

Zinc binding site 7 out of 16 in 7l92

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Zinc binding site 7 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn301

b:37.3
occ:1.00
 ND1 J:HIS231 1.9 34.7 1.0
SG J:CYS261 2.3 37.0 1.0
SG J:CYS280 2.3 37.7 1.0
SG J:CYS264 2.4 39.2 1.0
CE1 J:HIS231 2.7 44.8 1.0
CG J:HIS231 3.0 41.8 1.0
CB J:CYS261 3.2 39.7 1.0
CB J:CYS264 3.2 33.8 1.0
CB J:CYS280 3.3 44.4 1.0
CB J:HIS231 3.5 39.5 1.0
N J:CYS264 3.7 35.5 1.0
CA J:HIS231 3.8 43.4 1.0
NE2 J:HIS231 3.9 43.6 1.0
CD2 J:HIS231 4.0 37.4 1.0
CA J:CYS264 4.0 31.8 1.0
CA J:CYS280 4.0 54.6 1.0
CB J:ASP263 4.5 54.4 1.0
C J:ASP263 4.6 46.2 1.0
CA J:CYS261 4.6 38.3 1.0
N J:HIS231 4.7 46.1 1.0
C J:CYS264 4.8 34.1 1.0
N J:ARG232 4.8 43.2 1.0
C J:HIS231 4.9 43.1 1.0
CA J:ASP263 4.9 51.2 1.0
N J:ASP263 4.9 49.8 1.0
N J:GLY265 5.0 37.6 1.0

Zinc binding site 8 out of 16 in 7l92

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Zinc binding site 8 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn302

b:29.7
occ:1.00
 ND1 J:HIS269 2.2 24.2 1.0
SG J:CYS244 2.3 27.4 1.0
SG J:CYS247 2.3 29.0 1.0
SG J:CYS272 2.3 30.4 1.0
CB J:CYS244 3.0 23.9 1.0
CE1 J:HIS269 3.1 30.3 1.0
CG J:HIS269 3.2 29.3 1.0
CB J:CYS247 3.4 30.0 1.0
CB J:CYS272 3.4 30.0 1.0
CB J:HIS269 3.5 23.1 1.0
N J:CYS247 3.8 32.3 1.0
N J:HIS269 4.0 19.9 1.0
CA J:CYS247 4.2 26.2 1.0
NE2 J:HIS269 4.3 23.9 1.0
CD2 J:HIS269 4.3 21.9 1.0
CA J:HIS269 4.4 24.3 1.0
CA J:CYS244 4.4 22.9 1.0
CB J:HIS246 4.8 27.9 1.0
CA J:CYS272 4.8 39.0 1.0
NZ J:LYS271 4.8 55.8 1.0
C J:HIS246 4.9 40.2 1.0
C J:CYS247 4.9 36.3 1.0

Zinc binding site 9 out of 16 in 7l92

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Zinc binding site 9 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn301

b:37.2
occ:1.00
 ND1 M:HIS231 2.1 38.3 1.0
SG M:CYS261 2.3 40.2 1.0
SG M:CYS264 2.3 40.5 1.0
SG M:CYS280 2.4 36.8 1.0
CE1 M:HIS231 3.0 45.4 1.0
CG M:HIS231 3.1 42.1 1.0
CB M:CYS280 3.1 47.1 1.0
CB M:CYS261 3.2 40.9 1.0
CB M:CYS264 3.3 37.3 1.0
CB M:HIS231 3.5 38.3 1.0
CA M:HIS231 3.7 41.5 1.0
N M:CYS264 3.8 38.1 1.0
CA M:CYS280 3.9 57.4 1.0
CA M:CYS264 4.1 39.1 1.0
NE2 M:HIS231 4.1 44.0 1.0
O M:HOH432 4.1 54.0 1.0
CD2 M:HIS231 4.2 39.5 1.0
N M:HIS231 4.6 47.5 1.0
N M:ARG232 4.7 47.6 1.0
CA M:CYS261 4.7 34.4 1.0
C M:ASP263 4.8 45.8 1.0
CB M:ASP263 4.8 50.5 1.0
C M:HIS231 4.8 47.4 1.0
C M:CYS264 4.8 36.5 1.0
C M:CYS280 4.8 63.3 1.0
N M:CYS280 4.9 55.0 1.0
N M:GLY265 5.0 39.9 1.0

Zinc binding site 10 out of 16 in 7l92

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Zinc binding site 10 out of 16 in the C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of C1B Domain of Protein Kinase C in Complex with Diacylglycerol and Dodecyl 2-(Trimethylammonio)Ethyl Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn302

b:30.3
occ:1.00
 ND1 M:HIS269 2.2 24.4 1.0
SG M:CYS244 2.3 27.9 1.0
SG M:CYS272 2.3 29.2 1.0
SG M:CYS247 2.3 28.1 1.0
CB M:CYS244 3.0 23.8 1.0
CE1 M:HIS269 3.1 31.2 1.0
CG M:HIS269 3.2 29.7 1.0
CB M:CYS247 3.3 37.2 1.0
CB M:CYS272 3.4 25.8 1.0
CB M:HIS269 3.5 25.1 1.0
N M:CYS247 3.8 30.4 1.0
N M:HIS269 4.1 21.8 1.0
CA M:CYS247 4.1 24.6 1.0
NE2 M:HIS269 4.3 24.0 1.0
CD2 M:HIS269 4.3 22.4 1.0
CA M:HIS269 4.4 24.6 1.0
CA M:CYS244 4.4 24.8 1.0
O P:HOH415 4.7 47.1 1.0
CA M:CYS272 4.8 37.7 1.0
CB M:HIS246 4.8 33.6 1.0
C M:CYS247 4.9 36.5 1.0
C M:HIS246 4.9 36.5 1.0

Reference:

S.S.Katti, I.V.Krieger, J.Ann, J.Lee, J.C.Sacchettini, T.I.Igumenova. Structural Anatomy of Protein Kinase C C1 Domain Interactions with Diacylglycerol and Other Agonists. Nat Commun V. 13 2695 2022.
ISSN: ESSN 2041-1723
PubMed: 35577811
DOI: 10.1038/S41467-022-30389-2
Page generated: Tue Oct 29 22:42:43 2024

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