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Zinc in PDB 5lkz: Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.

Enzymatic activity of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.

All present enzymatic activity of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A., PDB code: 5lkz was solved by Z.Kaczmarska, E.Ortega, J.A.Marquez, D.Panne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.600, 155.910, 110.090, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A. (pdb code 5lkz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A., PDB code: 5lkz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5lkz

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Zinc binding site 1 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:96.6
occ:1.00
SG A:CYS1201 2.3 76.8 1.0
SG A:CYS1204 2.4 85.0 1.0
SG A:CYS1183 2.4 93.8 1.0
SG A:CYS1177 2.4 95.8 1.0
CB A:CYS1201 3.4 84.5 1.0
CB A:CYS1177 3.4 95.1 1.0
CB A:CYS1204 3.6 88.1 1.0
CB A:CYS1183 3.6 96.0 1.0
O A:GLY1179 3.9 0.6 1.0
N A:CYS1201 4.1 86.7 1.0
CA A:CYS1201 4.3 85.2 1.0
CA A:CYS1177 4.9 97.5 1.0
CA A:CYS1204 4.9 90.2 1.0
O A:CYS1201 4.9 83.6 1.0
CA A:CYS1183 5.0 0.8 1.0

Zinc binding site 2 out of 4 in 5lkz

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Zinc binding site 2 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:53.3
occ:1.00
SG A:CYS1250 2.3 50.5 1.0
SG A:CYS1247 2.3 48.5 1.0
SG A:CYS1272 2.3 53.7 1.0
SG A:CYS1275 2.3 59.4 1.0
CB A:CYS1247 3.2 49.0 1.0
CB A:CYS1250 3.3 54.5 1.0
CB A:CYS1272 3.4 54.2 1.0
CB A:CYS1275 3.4 62.1 1.0
N A:CYS1250 3.8 55.4 1.0
N A:CYS1272 4.0 48.8 1.0
CA A:CYS1250 4.1 53.8 1.0
N A:CYS1275 4.2 61.0 1.0
CA A:CYS1272 4.2 52.9 1.0
CA A:CYS1275 4.4 64.2 1.0
CA A:CYS1247 4.7 47.7 1.0
O A:CYS1272 4.8 57.4 1.0
C A:CYS1272 4.8 55.8 1.0
CB A:GLU1249 4.9 61.2 1.0
C A:CYS1250 4.9 53.0 1.0
C A:GLU1249 4.9 58.8 1.0

Zinc binding site 3 out of 4 in 5lkz

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Zinc binding site 3 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:37.6
occ:1.00
ND1 A:HIS1255 2.1 37.2 1.0
SG A:CYS1164 2.3 41.1 1.0
SG A:CYS1163 2.3 38.8 1.0
SG A:CYS1258 2.4 35.9 1.0
CE1 A:HIS1255 3.0 38.4 1.0
CG A:HIS1255 3.1 36.4 1.0
CB A:CYS1163 3.4 43.9 1.0
CB A:HIS1255 3.4 36.8 1.0
CB A:CYS1258 3.4 34.6 1.0
CB A:CYS1164 3.5 40.4 1.0
N A:CYS1164 3.6 42.7 1.0
C A:CYS1163 4.0 45.0 1.0
CA A:CYS1164 4.0 41.4 1.0
N A:HIS1255 4.2 38.7 1.0
NE2 A:HIS1255 4.2 37.8 1.0
CD2 A:HIS1255 4.2 36.7 1.0
CA A:CYS1163 4.3 45.6 1.0
O A:CYS1164 4.3 42.4 1.0
CA A:HIS1255 4.4 37.3 1.0
C A:CYS1164 4.4 42.2 1.0
NH2 A:ARG1166 4.5 45.8 1.0
CD1 A:LEU1168 4.6 36.8 1.0
O A:CYS1163 4.7 48.8 1.0
CA A:CYS1258 4.9 35.5 1.0
NH2 A:ARG1645 4.9 30.6 1.0

Zinc binding site 4 out of 4 in 5lkz

Go back to Zinc Binding Sites List in 5lkz
Zinc binding site 4 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Crotonyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1704

b:27.9
occ:0.50
NE2 A:HIS1315 2.2 27.8 1.0
SG A:CYS1408 2.3 27.2 0.5
SG A:CYS1408 2.4 27.2 0.5
CD2 A:HIS1315 3.1 28.8 1.0
CE1 A:HIS1315 3.2 27.9 1.0
CB A:CYS1408 3.3 26.5 0.5
CB A:CYS1408 3.4 26.4 0.5
ND1 A:HIS1315 4.3 29.6 1.0
CG A:HIS1315 4.3 30.1 1.0
CA A:CYS1408 4.7 26.5 0.5
CA A:CYS1408 4.8 26.4 0.5

Reference:

Z.Kaczmarska, E.Ortega, A.Goudarzi, H.Huang, S.Kim, J.A.Marquez, Y.Zhao, S.Khochbin, D.Panne. Structure of P300 in Complex with Acyl-Coa Variants. Nat. Chem. Biol. V. 13 21 2017.
ISSN: ESSN 1552-4469
PubMed: 27820805
DOI: 10.1038/NCHEMBIO.2217
Page generated: Wed Dec 16 06:29:32 2020

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