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

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

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

Protein crystallography data

The structure of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Propionyl-Coenzyme A., PDB code: 5lkx 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 / 2.52
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.810, 155.260, 109.790, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Propionyl-Coenzyme A. (pdb code 5lkx). 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 Propionyl-Coenzyme A., PDB code: 5lkx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5lkx

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Zinc binding site 1 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Propionyl-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 Propionyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:0.5
occ:1.00
SG A:CYS1201 2.0 72.6 1.0
SG A:CYS1183 2.2 95.1 1.0
SG A:CYS1204 2.3 0.3 1.0
SG A:CYS1177 2.8 0.5 1.0
CB A:CYS1204 3.1 0.3 1.0
CB A:CYS1201 3.4 87.7 1.0
CB A:CYS1183 3.4 94.7 1.0
CB A:CYS1177 3.6 0.5 1.0
N A:CYS1201 4.1 91.0 1.0
CA A:CYS1201 4.3 90.8 1.0
CA A:CYS1204 4.4 0.9 1.0
CE A:LYS1180 4.5 0.9 1.0
N A:CYS1204 4.5 0.8 1.0
NZ A:LYS1180 4.6 0.3 1.0
CA A:CYS1183 4.7 0.7 1.0
O A:CYS1201 4.8 90.2 1.0

Zinc binding site 2 out of 4 in 5lkx

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Zinc binding site 2 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Propionyl-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 Propionyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:59.0
occ:1.00
SG A:CYS1250 2.2 67.5 1.0
SG A:CYS1275 2.3 76.2 1.0
SG A:CYS1247 2.4 56.0 1.0
SG A:CYS1272 2.5 67.3 1.0
CB A:CYS1250 3.2 63.8 1.0
CB A:CYS1247 3.2 53.2 1.0
CB A:CYS1275 3.4 72.5 1.0
CB A:CYS1272 3.6 68.8 1.0
N A:CYS1250 3.6 66.4 1.0
CA A:CYS1250 4.0 64.9 1.0
N A:CYS1272 4.1 56.4 1.0
N A:CYS1275 4.2 62.4 1.0
CA A:CYS1272 4.4 61.9 1.0
CA A:CYS1275 4.4 70.4 1.0
CB A:GLU1249 4.7 78.1 1.0
CA A:CYS1247 4.7 53.6 1.0
C A:GLU1249 4.8 72.0 1.0
C A:CYS1250 4.8 65.2 1.0
O A:CYS1272 4.8 66.1 1.0
NH1 A:ARG1252 4.8 70.4 1.0
C A:CYS1272 4.9 61.8 1.0
N A:GLY1251 4.9 64.8 1.0

Zinc binding site 3 out of 4 in 5lkx

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Zinc binding site 3 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Propionyl-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 Propionyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:42.3
occ:1.00
ND1 A:HIS1255 2.1 41.5 1.0
SG A:CYS1164 2.2 43.6 1.0
SG A:CYS1163 2.3 43.7 1.0
SG A:CYS1258 2.5 40.3 1.0
CE1 A:HIS1255 3.1 44.1 1.0
CG A:HIS1255 3.1 38.8 1.0
CB A:CYS1163 3.3 53.8 1.0
CB A:CYS1164 3.3 43.2 1.0
CB A:HIS1255 3.4 43.0 1.0
N A:CYS1164 3.5 48.0 1.0
CB A:CYS1258 3.5 35.5 1.0
CA A:CYS1164 3.9 46.8 1.0
C A:CYS1163 4.0 51.5 1.0
N A:HIS1255 4.2 41.0 1.0
NE2 A:HIS1255 4.2 43.6 1.0
O A:CYS1164 4.2 51.1 1.0
CD2 A:HIS1255 4.2 39.8 1.0
CA A:CYS1163 4.2 55.0 1.0
C A:CYS1164 4.3 48.6 1.0
CA A:HIS1255 4.4 43.3 1.0
NH2 A:ARG1166 4.5 52.6 1.0
O A:CYS1163 4.6 52.6 1.0
CD1 A:LEU1168 4.6 45.7 1.0
CA A:CYS1258 4.9 38.1 1.0
N A:CYS1163 5.0 60.0 1.0
NH2 A:ARG1645 5.0 42.4 1.0

Zinc binding site 4 out of 4 in 5lkx

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Zinc binding site 4 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Propionyl-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 Propionyl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1704

b:39.8
occ:0.60
NE2 A:HIS1315 2.0 28.1 1.0
SG A:CYS1408 2.3 28.1 0.6
SG A:CYS1408 2.5 26.7 0.4
CD2 A:HIS1315 2.7 30.8 1.0
CE1 A:HIS1315 3.1 31.4 1.0
CB A:CYS1408 3.2 27.1 0.4
CB A:CYS1408 3.4 28.0 0.6
CG A:HIS1315 3.9 34.6 1.0
ND1 A:HIS1315 4.1 35.6 1.0
CA A:CYS1408 4.5 27.4 0.4
CA A:CYS1408 4.6 27.6 0.6
CB A:PRO1406 4.7 29.1 1.0
N A:CYS1408 4.7 27.4 1.0

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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