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

Enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 7

All present enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 7:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 7, PDB code: 7vhz 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) 19.98 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.676, 89.219, 91.132, 114.99, 95.33, 92.02
R / Rfree (%) 19.1 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7 (pdb code 7vhz). 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 7, PDB code: 7vhz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7vhz

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


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:52.9
occ:1.00
 ND1 A:HIS1255 2.1 53.2 1.0
SG A:CYS1258 2.3 47.6 1.0
SG A:CYS1163 2.3 59.7 1.0
SG A:CYS1164 2.3 57.8 1.0
CE1 A:HIS1255 3.1 58.1 1.0
CG A:HIS1255 3.1 52.0 1.0
CB A:CYS1164 3.3 57.7 1.0
CB A:HIS1255 3.4 43.1 1.0
CB A:CYS1258 3.5 41.3 1.0
N A:CYS1164 3.6 70.2 1.0
CA A:CYS1164 4.1 58.3 1.0
CB A:CYS1163 4.1 77.0 1.0
NE2 A:HIS1255 4.2 54.6 1.0
CD2 A:HIS1255 4.2 49.5 1.0
CD1 A:LEU1168 4.3 50.6 1.0
N A:HIS1255 4.4 50.0 1.0
O A:HOH2006 4.4 55.4 1.0
CA A:HIS1255 4.5 49.7 1.0
NH2 A:ARG1645 4.6 40.0 1.0
C A:CYS1163 4.6 71.9 1.0
CA A:CYS1163 4.8 80.4 1.0
CA A:CYS1258 4.9 42.3 1.0
N A:CYS1163 4.9 84.5 1.0
C A:CYS1164 5.0 61.5 1.0

Zinc binding site 2 out of 6 in 7vhz

Go back to Zinc Binding Sites List in 7vhz
Zinc binding site 2 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:76.1
occ:1.00
 SG A:CYS1250 2.3 103.9 1.0
SG A:CYS1272 2.3 75.0 1.0
SG A:CYS1247 2.3 75.3 1.0
SG A:CYS1275 2.3 75.8 1.0
CB A:CYS1250 2.9 74.1 1.0
CB A:CYS1272 3.3 63.2 1.0
CB A:CYS1275 3.3 68.4 1.0
CB A:CYS1247 3.4 68.1 1.0
N A:CYS1250 3.5 81.8 1.0
CA A:CYS1250 3.8 78.0 1.0
N A:CYS1272 3.9 59.8 1.0
N A:CYS1275 3.9 79.1 1.0
CA A:CYS1272 4.1 65.0 1.0
CA A:CYS1275 4.2 75.2 1.0
C A:GLU1249 4.6 83.2 1.0
C A:CYS1272 4.6 70.4 1.0
O A:CYS1272 4.7 71.9 1.0
CB A:GLU1249 4.7 80.3 1.0
CA A:CYS1247 4.8 64.9 1.0
C A:CYS1250 5.0 75.1 1.0

Zinc binding site 3 out of 6 in 7vhz

Go back to Zinc Binding Sites List in 7vhz
Zinc binding site 3 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:87.8
occ:1.00
 SG A:CYS1177 2.3 99.0 1.0
SG A:CYS1201 2.3 68.9 1.0
SG A:CYS1183 2.3 97.4 1.0
SG A:CYS1204 2.4 102.2 1.0
CB A:CYS1204 3.1 79.5 1.0
CB A:CYS1177 3.3 81.3 1.0
CB A:CYS1183 3.5 90.8 1.0
CB A:CYS1201 3.5 77.9 1.0
N A:CYS1204 4.2 86.9 1.0
CA A:CYS1204 4.3 84.1 1.0
N A:CYS1201 4.3 72.8 1.0
CA A:CYS1201 4.5 72.5 1.0
CB A:LYS1180 4.6 93.0 1.0
CE A:LYS1180 4.7 94.1 1.0
CA A:CYS1177 4.7 82.7 1.0
CA A:CYS1183 4.8 92.6 1.0
O A:CYS1201 4.9 77.6 1.0
NZ A:LYS1180 4.9 97.3 1.0
C A:CYS1201 5.0 76.3 1.0

Zinc binding site 4 out of 6 in 7vhz

Go back to Zinc Binding Sites List in 7vhz
Zinc binding site 4 out of 6 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1701

b:50.7
occ:1.00
 ND1 B:HIS1255 2.1 40.2 1.0
SG B:CYS1163 2.3 47.0 1.0
SG B:CYS1258 2.3 43.8 1.0
SG B:CYS1164 2.3 56.3 1.0
CG B:HIS1255 3.0 46.3 1.0
CE1 B:HIS1255 3.1 50.8 1.0
CB B:CYS1258 3.3 39.7 1.0
CB B:HIS1255 3.3 40.7 1.0
N B:CYS1164 3.4 74.9 1.0
CB B:CYS1164 3.5 62.7 1.0
CB B:CYS1163 3.6 56.2 1.0
CA B:CYS1164 4.1 62.4 1.0
CD2 B:HIS1255 4.2 43.7 1.0
NE2 B:HIS1255 4.2 50.5 1.0
N B:HIS1255 4.2 41.7 1.0
C B:CYS1163 4.2 71.8 1.0
CA B:HIS1255 4.4 44.0 1.0
NH2 B:ARG1166 4.4 60.2 1.0
CA B:CYS1163 4.5 75.4 1.0
CD1 B:LEU1168 4.5 42.0 1.0
NH2 B:ARG1645 4.6 39.0 1.0
CA B:CYS1258 4.7 42.5 1.0
C B:CYS1164 4.9 68.0 1.0
NE B:ARG1166 5.0 64.0 1.0
N B:CYS1163 5.0 76.0 1.0

Zinc binding site 5 out of 6 in 7vhz

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


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1702

b:77.3
occ:1.00
 SG B:CYS1250 2.3 80.3 1.0
SG B:CYS1272 2.3 72.6 1.0
SG B:CYS1247 2.3 76.9 1.0
SG B:CYS1275 2.3 75.7 1.0
CB B:CYS1247 3.3 64.1 1.0
CB B:CYS1250 3.3 65.6 1.0
CB B:CYS1275 3.4 68.2 1.0
CB B:CYS1272 3.5 68.0 1.0
N B:CYS1272 3.8 63.5 1.0
N B:CYS1250 3.9 75.5 1.0
CA B:CYS1272 4.2 57.5 1.0
N B:CYS1275 4.2 78.1 1.0
CA B:CYS1250 4.2 70.0 1.0
CA B:CYS1275 4.4 79.7 1.0
O B:CYS1272 4.6 68.0 1.0
CA B:CYS1247 4.7 62.8 1.0
C B:CYS1272 4.7 71.3 1.0
CB B:ARG1252 4.8 67.8 1.0
CG1 B:VAL1271 4.8 75.2 1.0
CB B:GLU1249 4.9 77.7 1.0
C B:VAL1271 4.9 64.6 1.0
C B:GLU1249 4.9 76.5 1.0

Zinc binding site 6 out of 6 in 7vhz

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


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1703

b:85.2
occ:1.00
 SG B:CYS1201 2.3 67.1 1.0
SG B:CYS1204 2.3 96.3 1.0
SG B:CYS1177 2.3 83.2 1.0
SG B:CYS1183 2.3 86.4 1.0
CB B:CYS1204 3.1 74.0 1.0
CB B:CYS1201 3.3 73.3 1.0
CB B:CYS1177 3.3 77.2 1.0
CB B:CYS1183 3.5 80.0 1.0
N B:CYS1201 4.1 72.4 1.0
N B:CYS1204 4.1 72.2 1.0
CA B:CYS1204 4.2 76.5 1.0
CA B:CYS1201 4.2 71.1 1.0
CB B:LYS1180 4.6 89.5 1.0
O B:CYS1201 4.7 72.9 1.0
CA B:CYS1177 4.8 80.6 1.0
C B:CYS1201 4.8 71.0 1.0
CA B:CYS1183 4.8 88.3 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 12:39:35 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy