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

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

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

Protein crystallography data

The structure of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Butyryl-Coenzyme A., PDB code: 5lkt 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) 50.01 / 2.04
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 92.480, 154.690, 109.230, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 5lkt:

The structure of Crystal Structure of the P300 Acetyltransferase Catalytic Core with Butyryl-Coenzyme A. also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5lkt

Go back to Zinc Binding Sites List in 5lkt
Zinc binding site 1 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Butyryl-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 Butyryl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:97.5
occ:1.00
 SG A:CYS1183 2.1 86.8 1.0
SG A:CYS1201 2.2 72.6 1.0
SG A:CYS1204 2.3 0.4 1.0
SG A:CYS1177 2.8 79.8 1.0
CB A:CYS1201 3.1 83.7 1.0
CB A:CYS1183 3.4 77.0 1.0
CB A:CYS1204 3.4 98.7 1.0
CB A:CYS1177 3.5 81.5 1.0
N A:CYS1201 3.9 86.1 1.0
CA A:CYS1201 4.1 83.3 1.0
N A:CYS1204 4.5 0.5 1.0
CA A:CYS1204 4.5 0.1 1.0
CA A:CYS1183 4.7 81.2 1.0
O A:CYS1201 4.7 84.5 1.0
C A:CYS1201 4.8 83.7 1.0
N A:THR1184 4.9 91.1 1.0
C A:CYS1183 4.9 88.5 1.0

Zinc binding site 2 out of 4 in 5lkt

Go back to Zinc Binding Sites List in 5lkt
Zinc binding site 2 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Butyryl-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 Butyryl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:46.5
occ:1.00
 SG A:CYS1250 2.3 44.0 1.0
SG A:CYS1275 2.3 47.2 1.0
SG A:CYS1272 2.4 44.6 1.0
SG A:CYS1247 2.4 41.0 1.0
CB A:CYS1247 3.2 41.3 1.0
CB A:CYS1250 3.2 44.9 1.0
CB A:CYS1275 3.4 49.4 1.0
CB A:CYS1272 3.4 45.3 1.0
N A:CYS1250 3.7 46.9 1.0
N A:CYS1272 4.0 39.6 1.0
CA A:CYS1250 4.1 43.9 1.0
N A:CYS1275 4.2 51.7 1.0
CA A:CYS1272 4.2 42.7 1.0
CA A:CYS1275 4.4 52.8 1.0
O A:HOH2112 4.4 57.1 1.0
O A:HOH1822 4.6 43.6 1.0
CA A:CYS1247 4.6 39.1 1.0
O A:CYS1272 4.7 43.5 1.0
CB A:GLU1249 4.8 54.7 1.0
C A:CYS1272 4.8 46.0 1.0
C A:CYS1250 4.9 43.2 1.0
C A:GLU1249 4.9 53.6 1.0
NH1 A:ARG1252 4.9 48.5 1.0
N A:GLY1251 5.0 41.3 1.0

Zinc binding site 3 out of 4 in 5lkt

Go back to Zinc Binding Sites List in 5lkt
Zinc binding site 3 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Butyryl-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 Butyryl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:33.8
occ:1.00
 ND1 A:HIS1255 2.1 30.6 1.0
SG A:CYS1164 2.2 35.2 1.0
SG A:CYS1163 2.3 34.3 1.0
SG A:CYS1258 2.4 32.0 1.0
CG A:HIS1255 3.1 31.9 1.0
CE1 A:HIS1255 3.1 31.9 1.0
CB A:CYS1163 3.3 38.0 1.0
CB A:CYS1164 3.4 38.3 1.0
CB A:HIS1255 3.4 30.4 1.0
CB A:CYS1258 3.4 27.2 1.0
N A:CYS1164 3.5 36.5 1.0
CA A:CYS1164 3.9 37.3 1.0
C A:CYS1163 4.0 36.5 1.0
N A:HIS1255 4.1 30.9 1.0
O A:CYS1164 4.2 36.9 1.0
NE2 A:HIS1255 4.2 31.1 1.0
CD2 A:HIS1255 4.2 30.6 1.0
CA A:CYS1163 4.3 37.1 1.0
C A:CYS1164 4.3 37.9 1.0
CA A:HIS1255 4.4 30.8 1.0
NH2 A:ARG1166 4.5 45.7 1.0
CD1 A:LEU1168 4.6 31.0 1.0
O A:CYS1163 4.7 37.3 1.0
CA A:CYS1258 4.8 29.4 1.0
NH2 A:ARG1645 4.9 29.1 1.0

Zinc binding site 4 out of 4 in 5lkt

Go back to Zinc Binding Sites List in 5lkt
Zinc binding site 4 out of 4 in the Crystal Structure of the P300 Acetyltransferase Catalytic Core with Butyryl-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 Butyryl-Coenzyme A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1704

b:29.2
occ:0.60
 SG A:CYS1408 2.3 28.9 0.5
NE2 A:HIS1315 2.5 29.8 1.0
SG A:CYS1408 2.9 23.0 0.5
CD2 A:HIS1315 3.2 29.1 1.0
CB A:CYS1408 3.3 26.0 0.5
CB A:CYS1408 3.4 23.7 0.5
CE1 A:HIS1315 3.7 29.6 1.0
O A:HOH2131 4.3 41.2 1.0
CG A:HIS1315 4.5 30.6 1.0
ND1 A:HIS1315 4.7 33.0 1.0
CA A:CYS1408 4.7 25.1 0.5
CA A:CYS1408 4.8 24.0 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: Sun Oct 27 21:03:01 2024

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