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Zinc in PDB 7vi0: Crystal Structure of EP300 Hat Domain in Complex with Compound 11

Enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 11

All present enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 11:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 11, PDB code: 7vi0 was solved by M.Takahashi, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.555, 88.361, 90.655, 116.52, 94.38, 91.36
R / Rfree (%) 19.9 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11 (pdb code 7vi0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11, PDB code: 7vi0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7vi0

Go back to Zinc Binding Sites List in 7vi0
Zinc binding site 1 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11


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 EP300 Hat Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:51.6
occ:1.00
 ND1 A:HIS1255 2.1 44.7 1.0
SG A:CYS1163 2.3 55.3 1.0
SG A:CYS1258 2.3 41.8 1.0
SG A:CYS1164 2.3 48.7 1.0
CG A:HIS1255 3.1 42.9 1.0
CE1 A:HIS1255 3.1 44.9 1.0
CB A:HIS1255 3.4 33.9 1.0
CB A:CYS1258 3.4 31.8 1.0
N A:CYS1164 3.5 71.8 1.0
CB A:CYS1164 3.7 56.0 1.0
CB A:CYS1163 3.9 86.2 1.0
CA A:CYS1164 4.2 57.0 1.0
NE2 A:HIS1255 4.2 50.1 1.0
CD2 A:HIS1255 4.2 44.4 1.0
N A:HIS1255 4.3 46.7 1.0
NH2 A:ARG1645 4.4 45.8 1.0
CA A:HIS1255 4.4 44.4 1.0
C A:CYS1163 4.5 77.0 1.0
CD1 A:LEU1168 4.5 34.8 1.0
N A:CYS1163 4.5 85.1 1.0
CA A:CYS1163 4.6 86.8 1.0
CA A:CYS1258 4.8 38.2 1.0
O A:CYS1164 4.8 75.5 1.0
C A:CYS1164 4.9 73.4 1.0

Zinc binding site 2 out of 6 in 7vi0

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Zinc binding site 2 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11


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 EP300 Hat Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:72.3
occ:1.00
 SG A:CYS1247 2.3 63.8 1.0
SG A:CYS1272 2.3 71.0 1.0
SG A:CYS1275 2.3 71.5 1.0
SG A:CYS1250 2.3 63.6 1.0
CB A:CYS1247 3.3 56.4 1.0
CB A:CYS1272 3.3 64.0 1.0
CB A:CYS1275 3.3 64.7 1.0
CB A:CYS1250 3.5 69.7 1.0
N A:CYS1250 3.7 76.8 1.0
N A:CYS1272 3.9 55.4 1.0
N A:CYS1275 4.0 74.3 1.0
CA A:CYS1272 4.1 60.6 1.0
CA A:CYS1250 4.2 74.0 1.0
CA A:CYS1275 4.3 78.1 1.0
CB A:GLU1249 4.5 77.2 1.0
O A:CYS1272 4.6 59.2 1.0
C A:CYS1272 4.6 63.5 1.0
CA A:CYS1247 4.7 59.3 1.0
C A:GLU1249 4.7 75.8 1.0
N A:GLU1249 4.9 78.5 1.0
CA A:GLU1249 5.0 73.1 1.0

Zinc binding site 3 out of 6 in 7vi0

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Zinc binding site 3 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11


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 EP300 Hat Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:108.5
occ:1.00
 CB A:CYS1177 2.0 94.7 1.0
SG A:CYS1204 2.3 98.5 1.0
SG A:CYS1177 2.3 118.1 1.0
SG A:CYS1183 2.3 106.1 1.0
SG A:CYS1201 2.3 96.6 1.0
CB A:CYS1204 3.2 76.4 1.0
CB A:CYS1183 3.3 88.1 1.0
CA A:CYS1177 3.5 93.0 1.0
CB A:CYS1201 3.6 88.1 1.0
N A:CYS1177 4.1 94.1 1.0
N A:CYS1201 4.3 86.9 1.0
CA A:CYS1204 4.4 96.1 1.0
N A:CYS1204 4.5 87.3 1.0
C A:CYS1177 4.5 101.7 1.0
CA A:CYS1201 4.5 92.5 1.0
O A:CYS1177 4.6 118.9 1.0
CA A:CYS1183 4.7 96.2 1.0
C A:CYS1183 4.9 92.5 1.0
CB A:LYS1180 5.0 71.4 1.0

Zinc binding site 4 out of 6 in 7vi0

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Zinc binding site 4 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11


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 EP300 Hat Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1701

b:45.3
occ:1.00
 ND1 B:HIS1255 2.1 40.1 1.0
SG B:CYS1164 2.3 48.6 1.0
SG B:CYS1163 2.3 47.5 1.0
SG B:CYS1258 2.3 47.2 1.0
CG B:HIS1255 3.0 44.9 1.0
CE1 B:HIS1255 3.1 49.2 1.0
CB B:CYS1258 3.3 39.0 1.0
CB B:HIS1255 3.3 33.6 1.0
CB B:CYS1164 3.4 60.8 1.0
N B:CYS1164 3.5 72.3 1.0
CB B:CYS1163 4.0 74.2 1.0
CA B:CYS1164 4.1 61.1 1.0
NE2 B:HIS1255 4.1 41.7 1.0
CD2 B:HIS1255 4.1 43.4 1.0
N B:HIS1255 4.3 42.3 1.0
CD1 B:LEU1168 4.4 34.2 1.0
CA B:HIS1255 4.4 40.2 1.0
C B:CYS1163 4.5 72.4 1.0
N B:CYS1163 4.6 77.0 1.0
NH2 B:ARG1645 4.6 38.0 1.0
CA B:CYS1163 4.6 61.1 1.0
NH2 B:ARG1166 4.7 47.7 1.0
CA B:CYS1258 4.7 40.1 1.0
C B:CYS1164 4.9 70.3 1.0
O B:CYS1164 4.9 78.1 1.0

Zinc binding site 5 out of 6 in 7vi0

Go back to Zinc Binding Sites List in 7vi0
Zinc binding site 5 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of EP300 Hat Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1702

b:70.9
occ:1.00
 SG B:CYS1275 2.3 70.8 1.0
SG B:CYS1272 2.3 65.3 1.0
SG B:CYS1250 2.3 71.8 1.0
SG B:CYS1247 2.3 62.8 1.0
CB B:CYS1275 3.3 60.5 1.0
CB B:CYS1272 3.4 61.3 1.0
CB B:CYS1247 3.4 57.6 1.0
N B:CYS1250 3.7 77.5 1.0
CB B:CYS1250 3.8 67.9 1.0
N B:CYS1272 3.8 45.2 1.0
N B:CYS1275 3.9 64.5 1.0
CA B:CYS1272 4.1 49.7 1.0
CA B:CYS1275 4.2 75.6 1.0
CA B:CYS1250 4.4 70.8 1.0
CB B:GLU1249 4.4 72.9 1.0
O B:CYS1272 4.6 57.0 1.0
C B:CYS1272 4.6 59.9 1.0
C B:GLU1249 4.7 75.2 1.0
CA B:CYS1247 4.8 59.0 1.0
CA B:GLU1249 4.9 74.0 1.0
N B:GLU1249 4.9 66.8 1.0
C B:VAL1271 5.0 51.0 1.0

Zinc binding site 6 out of 6 in 7vi0

Go back to Zinc Binding Sites List in 7vi0
Zinc binding site 6 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 11


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of EP300 Hat Domain in Complex with Compound 11 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1703

b:112.7
occ:1.00
 CB B:CYS1177 2.3 90.1 1.0
SG B:CYS1204 2.3 114.1 1.0
SG B:CYS1201 2.3 94.4 1.0
SG B:CYS1177 2.3 104.7 1.0
SG B:CYS1183 2.3 94.4 1.0
CB B:CYS1201 3.0 99.7 1.0
CB B:CYS1183 3.5 84.6 1.0
CB B:CYS1204 3.6 86.0 1.0
N B:CYS1201 3.6 85.5 1.0
CA B:CYS1177 3.8 89.5 1.0
CA B:CYS1201 3.9 86.3 1.0
O B:THR1184 4.4 91.4 1.0
N B:CYS1177 4.5 91.2 1.0
CA B:CYS1183 4.6 101.1 1.0
C B:CYS1183 4.6 96.2 1.0
C B:CYS1177 4.6 88.7 1.0
N B:THR1184 4.6 102.9 1.0
C B:CYS1201 4.7 82.8 1.0
CG1 B:ILE1185 4.7 95.8 1.0
O B:CYS1177 4.7 100.0 1.0
N B:CYS1204 4.8 86.7 1.0
O B:CYS1201 4.8 86.5 1.0
CA B:CYS1204 4.8 90.6 1.0
C B:PHE1200 4.9 73.0 1.0
C B:THR1184 4.9 101.9 1.0

Reference:

R.Kanada, Y.Kagoshima, M.Asano, T.Suzuki, T.Murata, M.Haruta, M.Takahashi, O.Ubukata, K.Hashimoto, K.Obata, K.Kihara, M.Kuroha, T.Banjo, N.Togashi, K.Sato, Y.Yamamoto, K.Suzuki, T.Isoyama, Y.Tominaga, S.Higuchi, H.Naito. Discovery of EP300/Cbp Histone Acetyltransferase Inhibitors Through Scaffold Hopping of 1,4-Oxazepane Ring. Bioorg.Med.Chem.Lett. V. 66 28726 2022.
ISSN: ESSN 1464-3405
PubMed: 35413416
DOI: 10.1016/J.BMCL.2022.128726
Page generated: Wed Oct 30 12:40:11 2024

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