Zinc in PDB 6gyt: Transcription Factor Dimerization Activates the P300 Acetyltransferase
Enzymatic activity of Transcription Factor Dimerization Activates the P300 Acetyltransferase
All present enzymatic activity of Transcription Factor Dimerization Activates the P300 Acetyltransferase:
2.3.1.48;
Protein crystallography data
The structure of Transcription Factor Dimerization Activates the P300 Acetyltransferase, PDB code: 6gyt
was solved by
D.Panne,
E.Ortega,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.09 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.640,
83.710,
165.620,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.1 /
28.8
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Transcription Factor Dimerization Activates the P300 Acetyltransferase
(pdb code 6gyt). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Transcription Factor Dimerization Activates the P300 Acetyltransferase, PDB code: 6gyt:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6gyt
Go back to
Zinc Binding Sites List in 6gyt
Zinc binding site 1 out
of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1301
b:70.8
occ:1.00
|
ND1
|
A:HIS1255
|
2.1
|
64.8
|
1.0
|
SG
|
A:CYS1163
|
2.3
|
61.6
|
1.0
|
SG
|
A:CYS1258
|
2.3
|
45.8
|
1.0
|
SG
|
A:CYS1164
|
2.4
|
60.8
|
1.0
|
HB2
|
A:HIS1255
|
2.9
|
57.6
|
1.0
|
HB2
|
A:CYS1163
|
2.9
|
60.1
|
1.0
|
CE1
|
A:HIS1255
|
3.1
|
65.0
|
1.0
|
CG
|
A:HIS1255
|
3.2
|
61.1
|
1.0
|
HB2
|
A:CYS1258
|
3.2
|
47.6
|
1.0
|
H
|
A:CYS1164
|
3.2
|
61.2
|
1.0
|
HE1
|
A:HIS1255
|
3.2
|
65.0
|
1.0
|
CB
|
A:CYS1163
|
3.2
|
60.1
|
1.0
|
CB
|
A:CYS1258
|
3.3
|
47.6
|
1.0
|
H
|
A:HIS1255
|
3.4
|
53.9
|
1.0
|
CB
|
A:CYS1164
|
3.5
|
63.2
|
1.0
|
HB3
|
A:CYS1164
|
3.5
|
63.2
|
1.0
|
N
|
A:CYS1164
|
3.5
|
61.2
|
1.0
|
CB
|
A:HIS1255
|
3.5
|
57.6
|
1.0
|
HB3
|
A:CYS1258
|
3.6
|
47.6
|
1.0
|
HB3
|
A:CYS1163
|
3.9
|
60.1
|
1.0
|
CA
|
A:CYS1164
|
4.0
|
62.6
|
1.0
|
C
|
A:CYS1163
|
4.0
|
58.9
|
1.0
|
N
|
A:HIS1255
|
4.2
|
53.9
|
1.0
|
HB3
|
A:HIS1255
|
4.2
|
57.6
|
1.0
|
NE2
|
A:HIS1255
|
4.2
|
65.2
|
1.0
|
CA
|
A:CYS1163
|
4.2
|
58.1
|
1.0
|
CD2
|
A:HIS1255
|
4.3
|
63.6
|
1.0
|
HB2
|
A:CYS1164
|
4.3
|
63.2
|
1.0
|
HH2
|
A:TRP1115
|
4.4
|
58.0
|
1.0
|
CA
|
A:HIS1255
|
4.5
|
54.6
|
1.0
|
C
|
A:CYS1164
|
4.5
|
64.6
|
1.0
|
HZ2
|
B:LYS1284
|
4.5
|
67.6
|
1.0
|
HZ2
|
A:TRP1115
|
4.6
|
56.9
|
1.0
|
O
|
A:CYS1164
|
4.6
|
64.5
|
1.0
|
H
|
A:CYS1163
|
4.7
|
56.3
|
1.0
|
HD23
|
A:LEU1168
|
4.7
|
93.3
|
1.0
|
H
|
A:CYS1258
|
4.7
|
46.6
|
1.0
|
CA
|
A:CYS1258
|
4.8
|
46.6
|
1.0
|
O
|
A:CYS1163
|
4.8
|
58.8
|
1.0
|
HA
|
A:CYS1164
|
4.8
|
62.6
|
1.0
|
N
|
A:CYS1163
|
4.9
|
56.3
|
1.0
|
HE2
|
A:HIS1255
|
5.0
|
65.2
|
1.0
|
HA
|
A:CYS1163
|
5.0
|
58.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6gyt
Go back to
Zinc Binding Sites List in 6gyt
Zinc binding site 2 out
of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1302
b:82.5
occ:1.00
|
SG
|
A:CYS1272
|
2.3
|
56.0
|
1.0
|
SG
|
A:CYS1247
|
2.3
|
59.4
|
1.0
|
SG
|
A:CYS1250
|
2.4
|
69.5
|
1.0
|
SG
|
A:CYS1275
|
2.4
|
69.9
|
1.0
|
H
|
A:CYS1250
|
2.8
|
67.3
|
1.0
|
HB2
|
A:CYS1275
|
3.1
|
67.5
|
1.0
|
HB3
|
A:CYS1247
|
3.2
|
62.1
|
1.0
|
HB3
|
A:CYS1250
|
3.3
|
69.7
|
1.0
|
CB
|
A:CYS1247
|
3.3
|
62.1
|
1.0
|
CB
|
A:CYS1275
|
3.4
|
67.5
|
1.0
|
CB
|
A:CYS1250
|
3.4
|
69.7
|
1.0
|
H
|
A:CYS1272
|
3.4
|
56.9
|
1.0
|
HB3
|
A:CYS1272
|
3.5
|
57.9
|
1.0
|
HB2
|
A:CYS1247
|
3.5
|
62.1
|
1.0
|
CB
|
A:CYS1272
|
3.6
|
57.9
|
1.0
|
HB2
|
A:GLU1249
|
3.6
|
62.8
|
1.0
|
O
|
A:CYS1250
|
3.6
|
75.3
|
1.0
|
N
|
A:CYS1250
|
3.6
|
67.3
|
1.0
|
H
|
A:CYS1275
|
3.6
|
64.2
|
1.0
|
O
|
A:HOH1410
|
4.0
|
60.2
|
1.0
|
HB3
|
A:CYS1275
|
4.0
|
67.5
|
1.0
|
CA
|
A:CYS1250
|
4.0
|
68.9
|
1.0
|
HD2
|
A:ARG1252
|
4.1
|
57.1
|
1.0
|
N
|
A:CYS1272
|
4.2
|
56.9
|
1.0
|
C
|
A:CYS1250
|
4.2
|
69.6
|
1.0
|
HB2
|
A:CYS1250
|
4.2
|
69.7
|
1.0
|
HB2
|
A:CYS1272
|
4.3
|
57.9
|
1.0
|
N
|
A:CYS1275
|
4.3
|
64.2
|
1.0
|
H
|
A:GLU1249
|
4.3
|
60.2
|
1.0
|
HH11
|
A:ARG1252
|
4.3
|
55.4
|
1.0
|
HB2
|
A:ARG1252
|
4.4
|
58.9
|
1.0
|
CA
|
A:CYS1272
|
4.4
|
56.9
|
1.0
|
CA
|
A:CYS1275
|
4.4
|
65.9
|
1.0
|
CB
|
A:GLU1249
|
4.5
|
62.8
|
1.0
|
HG13
|
A:VAL1271
|
4.5
|
51.9
|
1.0
|
H
|
A:ARG1252
|
4.6
|
61.1
|
1.0
|
CA
|
A:CYS1247
|
4.7
|
59.6
|
1.0
|
C
|
A:GLU1249
|
4.7
|
64.9
|
1.0
|
HA
|
A:CYS1275
|
4.8
|
65.9
|
1.0
|
HB3
|
A:GLU1249
|
4.8
|
62.8
|
1.0
|
O
|
A:CYS1272
|
4.8
|
58.1
|
1.0
|
HA
|
A:VAL1271
|
4.8
|
53.7
|
1.0
|
HG12
|
A:VAL1271
|
4.8
|
51.9
|
1.0
|
HE2
|
A:MET1254
|
4.8
|
55.6
|
1.0
|
N
|
A:GLU1249
|
4.9
|
60.2
|
1.0
|
CA
|
A:GLU1249
|
4.9
|
62.8
|
1.0
|
C
|
A:CYS1272
|
4.9
|
57.7
|
1.0
|
HA
|
A:CYS1250
|
5.0
|
68.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6gyt
Go back to
Zinc Binding Sites List in 6gyt
Zinc binding site 3 out
of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1301
b:76.3
occ:1.00
|
ND1
|
B:HIS1255
|
2.1
|
70.7
|
1.0
|
SG
|
B:CYS1163
|
2.3
|
67.4
|
1.0
|
SG
|
B:CYS1258
|
2.3
|
61.0
|
1.0
|
SG
|
B:CYS1164
|
2.3
|
68.1
|
1.0
|
HB2
|
B:HIS1255
|
2.8
|
64.5
|
1.0
|
HB2
|
B:CYS1163
|
2.9
|
64.2
|
1.0
|
CE1
|
B:HIS1255
|
3.0
|
70.7
|
1.0
|
CG
|
B:HIS1255
|
3.1
|
67.1
|
1.0
|
H
|
B:CYS1164
|
3.1
|
64.7
|
1.0
|
HE1
|
B:HIS1255
|
3.2
|
70.7
|
1.0
|
CB
|
B:CYS1163
|
3.2
|
64.2
|
1.0
|
HB2
|
B:CYS1258
|
3.2
|
60.9
|
1.0
|
N
|
B:CYS1164
|
3.4
|
64.7
|
1.0
|
H
|
B:HIS1255
|
3.4
|
62.5
|
1.0
|
CB
|
B:CYS1258
|
3.4
|
60.9
|
1.0
|
CB
|
B:HIS1255
|
3.4
|
64.5
|
1.0
|
CB
|
B:CYS1164
|
3.4
|
67.4
|
1.0
|
HB3
|
B:CYS1164
|
3.5
|
67.4
|
1.0
|
HB3
|
B:CYS1258
|
3.7
|
60.9
|
1.0
|
C
|
B:CYS1163
|
3.9
|
62.3
|
1.0
|
CA
|
B:CYS1164
|
3.9
|
66.6
|
1.0
|
HB3
|
B:CYS1163
|
3.9
|
64.2
|
1.0
|
HB3
|
B:HIS1255
|
4.1
|
64.5
|
1.0
|
CA
|
B:CYS1163
|
4.1
|
62.2
|
1.0
|
NE2
|
B:HIS1255
|
4.1
|
69.0
|
1.0
|
N
|
B:HIS1255
|
4.1
|
62.5
|
1.0
|
CD2
|
B:HIS1255
|
4.2
|
67.4
|
1.0
|
HB2
|
B:CYS1164
|
4.3
|
67.4
|
1.0
|
C
|
B:CYS1164
|
4.4
|
66.6
|
1.0
|
CA
|
B:HIS1255
|
4.4
|
62.9
|
1.0
|
HH2
|
B:TRP1115
|
4.6
|
58.4
|
1.0
|
O
|
B:CYS1164
|
4.6
|
65.2
|
1.0
|
O
|
B:CYS1163
|
4.6
|
61.5
|
1.0
|
H
|
B:CYS1163
|
4.6
|
59.9
|
1.0
|
HH22
|
B:ARG1166
|
4.7
|
92.1
|
1.0
|
HZ2
|
B:TRP1115
|
4.7
|
57.6
|
1.0
|
H
|
B:CYS1258
|
4.7
|
58.5
|
1.0
|
HA
|
B:CYS1164
|
4.8
|
66.6
|
1.0
|
HB2
|
B:ARG1166
|
4.8
|
74.1
|
1.0
|
CA
|
B:CYS1258
|
4.8
|
59.5
|
1.0
|
N
|
B:CYS1163
|
4.8
|
59.9
|
1.0
|
HA
|
B:CYS1163
|
4.9
|
62.2
|
1.0
|
HE2
|
B:HIS1255
|
4.9
|
69.0
|
1.0
|
NH2
|
B:ARG1166
|
4.9
|
92.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6gyt
Go back to
Zinc Binding Sites List in 6gyt
Zinc binding site 4 out
of 4 in the Transcription Factor Dimerization Activates the P300 Acetyltransferase
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Transcription Factor Dimerization Activates the P300 Acetyltransferase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1302
b:72.8
occ:1.00
|
SG
|
B:CYS1247
|
2.3
|
61.6
|
1.0
|
SG
|
B:CYS1250
|
2.3
|
66.7
|
1.0
|
SG
|
B:CYS1272
|
2.3
|
50.2
|
1.0
|
SG
|
B:CYS1275
|
2.4
|
63.3
|
1.0
|
H
|
B:CYS1250
|
2.8
|
63.5
|
1.0
|
HB2
|
B:CYS1275
|
3.2
|
60.6
|
1.0
|
HB3
|
B:CYS1247
|
3.2
|
64.0
|
1.0
|
H
|
B:CYS1272
|
3.3
|
54.9
|
1.0
|
CB
|
B:CYS1247
|
3.3
|
64.0
|
1.0
|
HB3
|
B:CYS1272
|
3.3
|
55.3
|
1.0
|
HB3
|
B:CYS1250
|
3.3
|
66.0
|
1.0
|
CB
|
B:CYS1275
|
3.4
|
60.6
|
1.0
|
CB
|
B:CYS1250
|
3.4
|
66.0
|
1.0
|
HB2
|
B:CYS1247
|
3.4
|
64.0
|
1.0
|
CB
|
B:CYS1272
|
3.5
|
55.3
|
1.0
|
HB2
|
B:GLU1249
|
3.6
|
69.0
|
1.0
|
N
|
B:CYS1250
|
3.6
|
63.5
|
1.0
|
H
|
B:CYS1275
|
3.6
|
57.3
|
1.0
|
N
|
B:CYS1272
|
4.0
|
54.9
|
1.0
|
CA
|
B:CYS1250
|
4.0
|
64.0
|
1.0
|
HB3
|
B:CYS1275
|
4.1
|
60.6
|
1.0
|
HB2
|
B:CYS1272
|
4.2
|
55.3
|
1.0
|
HB2
|
B:CYS1250
|
4.2
|
66.0
|
1.0
|
N
|
B:CYS1275
|
4.3
|
57.3
|
1.0
|
HB2
|
B:ARG1252
|
4.3
|
58.2
|
1.0
|
HG13
|
B:VAL1271
|
4.3
|
53.5
|
1.0
|
HH11
|
B:ARG1252
|
4.3
|
58.5
|
1.0
|
CA
|
B:CYS1272
|
4.3
|
55.8
|
1.0
|
HB3
|
B:GLU1249
|
4.4
|
69.0
|
1.0
|
H
|
B:GLU1249
|
4.4
|
63.9
|
1.0
|
CB
|
B:GLU1249
|
4.4
|
69.0
|
1.0
|
CA
|
B:CYS1275
|
4.4
|
59.2
|
1.0
|
HD2
|
B:ARG1252
|
4.4
|
59.6
|
1.0
|
H
|
B:GLY1251
|
4.5
|
60.6
|
1.0
|
H
|
B:ARG1252
|
4.5
|
57.9
|
1.0
|
HA
|
B:VAL1271
|
4.7
|
52.8
|
1.0
|
C
|
B:GLU1249
|
4.7
|
66.0
|
1.0
|
HE2
|
B:MET1254
|
4.7
|
64.3
|
1.0
|
CA
|
B:CYS1247
|
4.7
|
63.2
|
1.0
|
O
|
B:CYS1272
|
4.8
|
56.8
|
1.0
|
HA
|
B:CYS1275
|
4.8
|
59.2
|
1.0
|
HA
|
B:CYS1250
|
4.8
|
64.0
|
1.0
|
C
|
B:CYS1272
|
4.9
|
57.2
|
1.0
|
C
|
B:CYS1250
|
4.9
|
62.6
|
1.0
|
N
|
B:GLY1251
|
4.9
|
60.6
|
1.0
|
HG12
|
B:VAL1271
|
4.9
|
53.5
|
1.0
|
CA
|
B:GLU1249
|
5.0
|
66.1
|
1.0
|
N
|
B:GLU1249
|
5.0
|
63.9
|
1.0
|
NH1
|
B:ARG1252
|
5.0
|
58.5
|
1.0
|
|
Reference:
E.Ortega,
S.Rengachari,
Z.Ibrahim,
N.Hoghoughi,
J.Gaucher,
A.S.Holehouse,
S.Khochbin,
D.Panne.
Transcription Factor Dimerization Activates the P300 Acetyltransferase. Nature V. 562 538 2018.
ISSN: ESSN 1476-4687
PubMed: 30323286
DOI: 10.1038/S41586-018-0621-1
Page generated: Mon Oct 28 22:06:48 2024
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