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Nickel in PDB 8fvf: Bromodomain of EP300 Liganded with Ccs-1477

Enzymatic activity of Bromodomain of EP300 Liganded with Ccs-1477

All present enzymatic activity of Bromodomain of EP300 Liganded with Ccs-1477:
2.3.1.48;

Protein crystallography data

The structure of Bromodomain of EP300 Liganded with Ccs-1477, PDB code: 8fvf was solved by E.Schonbrunn, M.Bikowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.74 / 2.10
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.15, 103.15, 59.22, 90, 90, 90
R / Rfree (%) 18.1 / 23.9

Other elements in 8fvf:

The structure of Bromodomain of EP300 Liganded with Ccs-1477 also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Bromodomain of EP300 Liganded with Ccs-1477 (pdb code 8fvf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Bromodomain of EP300 Liganded with Ccs-1477, PDB code: 8fvf:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 8fvf

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Nickel binding site 1 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1203

b:20.1
occ:1.00
 O A:HOH1363 1.9 20.9 1.0
OD2 A:ASP1119 2.2 24.9 1.0
O A:HOH1377 2.3 23.8 1.0
O A:HOH1392 2.4 27.0 1.0
OD1 A:ASP1119 2.7 18.0 1.0
O A:HOH1342 2.7 24.4 1.0
CG A:ASP1119 2.7 15.5 1.0
O A:HOH1378 3.7 27.3 1.0
CB A:ASP1119 4.2 16.8 1.0
O A:HOH1396 4.4 31.6 1.0
O A:ASP1119 4.4 17.3 1.0
C A:ASP1119 4.8 14.7 1.0
CA A:ASP1119 4.9 18.6 1.0

Nickel binding site 2 out of 9 in 8fvf

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Nickel binding site 2 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1204

b:30.6
occ:1.00
 O B:HOH1303 1.9 35.9 1.0
O A:HOH1325 2.1 15.8 1.0
OE2 B:GLU1152 2.4 30.3 1.0
OE1 A:GLU1152 2.5 26.5 1.0
OE2 A:GLU1152 2.6 32.1 1.0
O A:HOH1380 2.7 31.4 1.0
CD A:GLU1152 2.9 28.7 1.0
OE1 B:GLU1152 2.9 26.4 1.0
CD B:GLU1152 3.0 28.3 1.0
O B:HOH1328 4.0 39.2 1.0
O A:HOH1304 4.3 30.0 1.0
CG A:GLU1152 4.4 27.7 1.0
CG B:GLU1152 4.5 24.1 1.0
O A:HOH1347 4.5 27.8 1.0
O A:HOH1338 4.5 29.1 1.0
O B:HOH1323 4.7 30.2 1.0
O B:HOH1352 4.9 27.3 1.0
O B:HOH1387 5.0 32.3 1.0

Nickel binding site 3 out of 9 in 8fvf

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Nickel binding site 3 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1205

b:26.1
occ:1.00
 OE2 B:GLU1063 2.0 45.1 1.0
O B:HOH1320 2.1 33.8 1.0
O A:HOH1381 2.3 20.8 1.0
OE1 A:GLU1063 2.4 26.5 1.0
OE2 A:GLU1063 2.5 26.6 1.0
CD A:GLU1063 2.8 27.1 1.0
CD B:GLU1063 2.8 41.4 1.0
OE1 B:GLU1063 3.0 41.5 1.0
O B:HOH1381 3.6 33.5 1.0
O A:HOH1402 3.6 38.2 1.0
O A:HOH1387 4.0 31.4 1.0
CG B:GLU1063 4.2 32.0 1.0
CG A:GLU1063 4.3 23.1 1.0
O A:HOH1316 4.3 24.1 1.0
O A:HOH1373 4.4 37.2 1.0
CG A:PRO1060 4.9 29.9 1.0
CB B:GLU1063 5.0 19.1 1.0

Nickel binding site 4 out of 9 in 8fvf

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Nickel binding site 4 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1206

b:58.0
occ:1.00
 OE1 A:GLU1071 2.6 25.4 1.0
O A:HOH1370 2.9 37.5 1.0
OE2 A:GLU1071 3.0 30.7 1.0
CD A:GLU1071 3.1 27.3 1.0
O A:ASP1069 3.4 31.3 1.0
OE1 A:GLN1068 3.7 34.1 1.0
N A:ASP1069 4.0 26.3 1.0
C A:ASP1069 4.1 32.3 1.0
CA A:GLN1068 4.5 23.6 1.0
CG A:GLU1071 4.6 26.5 1.0
C A:GLN1068 4.6 23.9 1.0
CB A:GLN1068 4.6 25.1 1.0
CD A:GLN1068 4.6 29.3 1.0
CD A:PRO1070 4.7 25.9 1.0
NZ A:LYS1144 4.7 38.2 1.0
CA A:ASP1069 4.7 28.4 1.0
N A:PRO1070 4.7 31.2 1.0
CE A:LYS1144 4.9 37.2 1.0

Nickel binding site 5 out of 9 in 8fvf

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Nickel binding site 5 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1207

b:47.2
occ:1.00
 O A:HOH1397 2.4 44.3 1.0
NE2 A:GLN1112 2.4 32.6 1.0
O A:HOH1384 2.8 40.3 1.0
CD A:GLN1112 3.7 32.4 1.0
O A:HOH1311 4.3 29.6 1.0
OE1 A:GLN1112 4.5 36.0 1.0
CG A:GLN1112 4.7 29.1 1.0
CB A:GLN1112 4.8 27.5 1.0

Nickel binding site 6 out of 9 in 8fvf

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Nickel binding site 6 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1208

b:75.3
occ:1.00
 OD2 A:ASP1154 2.4 43.9 1.0
OD1 A:ASP1154 2.7 41.0 1.0
OE1 A:GLU1150 2.7 51.6 1.0
CG A:ASP1154 2.9 43.9 1.0
CD A:GLU1150 3.4 56.6 1.0
OE2 A:GLU1150 3.5 53.6 1.0
CB A:ASP1154 4.4 33.6 1.0
O A:HOH1388 4.5 37.5 1.0
CG A:GLU1150 4.7 41.8 1.0
CB A:GLU1150 4.9 29.8 1.0

Nickel binding site 7 out of 9 in 8fvf

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Nickel binding site 7 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1205

b:27.0
occ:1.00
 O B:HOH1370 2.1 33.2 1.0
O B:HOH1301 2.2 30.9 1.0
O B:HOH1379 2.4 39.2 1.0
O B:HOH1359 2.5 25.7 1.0
OE1 B:GLU1071 2.6 20.9 1.0
OE2 B:GLU1071 2.7 32.8 1.0
O B:HOH1394 2.7 32.5 1.0
CD B:GLU1071 3.0 24.8 1.0
NZ B:LYS1144 3.8 35.3 1.0
NE2 B:GLN1068 3.8 20.0 1.0
O B:ASP1069 3.9 26.4 1.0
N B:ASP1069 4.2 24.4 1.0
C B:ASP1069 4.4 25.4 1.0
CG B:GLU1071 4.4 22.1 1.0
CA B:GLN1068 4.6 21.9 1.0
CB B:GLN1068 4.6 24.4 1.0
O A:HOH1395 4.7 35.6 1.0
C B:GLN1068 4.8 23.8 1.0
O B:HOH1306 4.9 34.4 1.0
CD B:PRO1070 4.9 22.0 1.0
CD B:GLN1068 4.9 32.9 1.0
N B:PRO1070 5.0 19.8 1.0

Nickel binding site 8 out of 9 in 8fvf

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Nickel binding site 8 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1206

b:57.3
occ:1.00
 OE2 B:GLU1113 2.1 48.4 1.0
CD B:GLU1113 2.8 37.6 1.0
OE1 B:GLU1113 2.9 34.8 1.0
CG B:GLU1113 4.2 28.4 1.0

Nickel binding site 9 out of 9 in 8fvf

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Nickel binding site 9 out of 9 in the Bromodomain of EP300 Liganded with Ccs-1477


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Bromodomain of EP300 Liganded with Ccs-1477 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1207

b:65.7
occ:1.00
 OE1 B:GLU1150 2.5 33.8 1.0
CD B:GLU1150 3.6 36.8 1.0
O B:HOH1324 4.2 31.9 1.0
OE2 B:GLU1150 4.2 35.8 1.0
O B:HOH1373 4.3 29.9 1.0
CG B:GLU1150 4.7 32.7 1.0
CG B:GLU1147 4.9 31.5 1.0
O B:HOH1388 5.0 35.4 1.0

Reference:

E.Schonbrunn, M.Bikowitz. Group 3 Medulloblastoma Transcriptional Networks Are Sensitive to EP300/Cbp Bromodomain Inhibition To Be Published.
Page generated: Thu Oct 10 09:41:57 2024

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