Zinc in PDB 5szc: Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14
Protein crystallography data
The structure of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14, PDB code: 5szc
was solved by
N.Singh,
A.Local,
A.Shiau,
B.Ren,
K.D.Corbett,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.00 /
1.19
|
|
Space group
|
P 43 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.321,
39.321,
147.571,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.7 /
16.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14
(pdb code 5szc). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14, PDB code: 5szc:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5szc
Go back to
Zinc Binding Sites List in 5szc
Zinc binding site 1 out
of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:9.4
occ:1.00
|
ND1
|
A:HIS292
|
2.1
|
9.3
|
1.0
|
|
SG
|
A:CYS295
|
2.3
|
9.9
|
1.0
|
|
SG
|
A:CYS265
|
2.3
|
9.5
|
1.0
|
|
SG
|
A:CYS262
|
2.3
|
9.0
|
1.0
|
|
HB2
|
A:HIS292
|
2.9
|
11.4
|
1.0
|
|
HB3
|
A:CYS262
|
3.0
|
11.1
|
1.0
|
|
CE1
|
A:HIS292
|
3.0
|
8.5
|
1.0
|
|
CB
|
A:CYS262
|
3.1
|
9.2
|
1.0
|
|
HB3
|
A:CYS265
|
3.1
|
11.9
|
1.0
|
|
CG
|
A:HIS292
|
3.1
|
9.0
|
1.0
|
|
H
|
A:CYS265
|
3.1
|
13.2
|
1.0
|
|
HB2
|
A:CYS262
|
3.1
|
11.1
|
1.0
|
|
HE1
|
A:HIS292
|
3.2
|
10.2
|
1.0
|
|
HB2
|
A:CYS295
|
3.2
|
12.6
|
1.0
|
|
H
|
A:HIS292
|
3.2
|
10.8
|
1.0
|
|
CB
|
A:CYS265
|
3.3
|
9.9
|
1.0
|
|
CB
|
A:CYS295
|
3.3
|
10.5
|
1.0
|
|
CB
|
A:HIS292
|
3.5
|
9.5
|
1.0
|
|
HB2
|
A:PHE264
|
3.5
|
16.2
|
1.0
|
|
HB3
|
A:CYS295
|
3.5
|
12.6
|
1.0
|
|
N
|
A:CYS265
|
3.7
|
11.0
|
1.0
|
|
HD21
|
A:ASN272
|
3.8
|
12.7
|
1.0
|
|
OD1
|
A:ASN272
|
3.9
|
11.2
|
1.0
|
|
ND2
|
A:ASN272
|
3.9
|
10.6
|
1.0
|
|
CG
|
A:ASN272
|
4.0
|
10.2
|
1.0
|
|
N
|
A:HIS292
|
4.0
|
9.0
|
1.0
|
|
HB2
|
A:CYS265
|
4.1
|
11.9
|
1.0
|
|
CA
|
A:CYS265
|
4.1
|
10.9
|
1.0
|
|
NE2
|
A:HIS292
|
4.2
|
9.5
|
1.0
|
|
HA
|
A:ASN272
|
4.2
|
11.3
|
1.0
|
|
HB3
|
A:HIS292
|
4.2
|
11.4
|
1.0
|
|
CD2
|
A:HIS292
|
4.2
|
8.9
|
1.0
|
|
H
|
A:GLY267
|
4.3
|
12.4
|
1.0
|
|
HD22
|
A:ASN272
|
4.4
|
12.7
|
1.0
|
|
CA
|
A:HIS292
|
4.4
|
8.9
|
1.0
|
|
H
|
A:PHE264
|
4.4
|
12.8
|
1.0
|
|
H
|
A:LYS273
|
4.4
|
11.2
|
1.0
|
|
CB
|
A:PHE264
|
4.5
|
13.5
|
1.0
|
|
H
|
A:CYS295
|
4.5
|
12.4
|
1.0
|
|
O
|
A:HOH620
|
4.5
|
21.3
|
1.0
|
|
CA
|
A:CYS262
|
4.6
|
9.2
|
1.0
|
|
HD1
|
A:PHE264
|
4.6
|
19.4
|
1.0
|
|
H
|
A:LEU266
|
4.6
|
12.2
|
1.0
|
|
H
|
A:LYS274
|
4.7
|
14.2
|
1.0
|
|
CA
|
A:CYS295
|
4.7
|
10.6
|
1.0
|
|
C
|
A:PHE264
|
4.8
|
12.6
|
1.0
|
|
HB2
|
A:ASN272
|
4.8
|
11.8
|
1.0
|
|
HA2
|
A:GLY291
|
4.8
|
11.4
|
1.0
|
|
CB
|
A:ASN272
|
4.8
|
9.8
|
1.0
|
|
C
|
A:CYS265
|
4.8
|
10.6
|
1.0
|
|
HB3
|
A:PHE264
|
4.8
|
16.2
|
1.0
|
|
HB3
|
A:LYS274
|
4.9
|
18.0
|
1.0
|
|
HA
|
A:CYS265
|
4.9
|
13.0
|
1.0
|
|
CA
|
A:ASN272
|
4.9
|
9.4
|
1.0
|
|
HE2
|
A:HIS292
|
4.9
|
11.4
|
1.0
|
|
HA
|
A:CYS262
|
4.9
|
11.1
|
1.0
|
|
N
|
A:LEU266
|
4.9
|
10.1
|
1.0
|
|
HA
|
A:CYS295
|
5.0
|
12.7
|
1.0
|
|
N
|
A:CYS295
|
5.0
|
10.3
|
1.0
|
|
N
|
A:PHE264
|
5.0
|
10.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5szc
Go back to
Zinc Binding Sites List in 5szc
Zinc binding site 2 out
of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:11.4
occ:1.00
|
SG
|
A:CYS287
|
2.3
|
12.5
|
1.0
|
|
SG
|
A:CYS316
|
2.3
|
13.4
|
1.0
|
|
SG
|
A:CYS313
|
2.3
|
12.3
|
1.0
|
|
SG
|
A:CYS284
|
2.3
|
9.9
|
1.0
|
|
HB2
|
A:CYS316
|
2.8
|
15.1
|
1.0
|
|
HB3
|
A:CYS287
|
3.1
|
16.7
|
1.0
|
|
CB
|
A:CYS316
|
3.2
|
12.6
|
1.0
|
|
CB
|
A:CYS284
|
3.2
|
9.2
|
1.0
|
|
HB3
|
A:CYS284
|
3.2
|
11.0
|
1.0
|
|
HB2
|
A:CYS284
|
3.2
|
11.0
|
1.0
|
|
H
|
A:CYS313
|
3.2
|
11.2
|
1.0
|
|
H
|
A:CYS287
|
3.2
|
14.4
|
1.0
|
|
CB
|
A:CYS287
|
3.3
|
13.9
|
1.0
|
|
HB3
|
A:CYS313
|
3.3
|
13.3
|
1.0
|
|
CB
|
A:CYS313
|
3.4
|
11.1
|
1.0
|
|
H
|
A:CYS316
|
3.5
|
16.2
|
1.0
|
|
N
|
A:CYS287
|
3.8
|
12.0
|
1.0
|
|
HB3
|
A:CYS316
|
3.8
|
15.1
|
1.0
|
|
HD2
|
A:ARG289
|
3.8
|
26.9
|
1.0
|
|
HB2
|
A:ASP286
|
3.9
|
17.7
|
1.0
|
|
N
|
A:CYS313
|
3.9
|
9.3
|
1.0
|
|
HB2
|
A:CYS287
|
4.0
|
16.7
|
1.0
|
|
CA
|
A:CYS287
|
4.1
|
13.7
|
1.0
|
|
N
|
A:CYS316
|
4.1
|
13.5
|
1.0
|
|
HB2
|
A:ARG289
|
4.1
|
17.1
|
1.0
|
|
O
|
A:HOH553
|
4.1
|
31.8
|
1.0
|
|
HB2
|
A:CYS313
|
4.2
|
13.3
|
1.0
|
|
CA
|
A:CYS313
|
4.2
|
10.3
|
1.0
|
|
CA
|
A:CYS316
|
4.2
|
12.7
|
1.0
|
|
H
|
A:ARG289
|
4.3
|
12.8
|
1.0
|
|
H
|
A:ASP286
|
4.4
|
13.4
|
1.0
|
|
O
|
A:HOH624
|
4.4
|
28.3
|
1.0
|
|
HB2
|
A:GLU315
|
4.5
|
22.0
|
1.0
|
|
H
|
A:GLY288
|
4.6
|
12.9
|
1.0
|
|
CA
|
A:CYS284
|
4.6
|
8.6
|
1.0
|
|
HA
|
A:GLN312
|
4.7
|
10.2
|
1.0
|
|
HA
|
A:CYS316
|
4.7
|
15.3
|
1.0
|
|
CD
|
A:ARG289
|
4.7
|
22.4
|
1.0
|
|
C
|
A:CYS287
|
4.8
|
13.4
|
1.0
|
|
CB
|
A:ASP286
|
4.8
|
14.7
|
1.0
|
|
C
|
A:ASP286
|
4.8
|
12.9
|
1.0
|
|
C
|
A:CYS313
|
4.8
|
10.1
|
1.0
|
|
HB3
|
A:GLN312
|
4.8
|
11.0
|
1.0
|
|
O
|
A:CYS313
|
4.8
|
10.9
|
1.0
|
|
HG3
|
A:ARG289
|
4.8
|
22.0
|
1.0
|
|
HA
|
A:CYS287
|
4.9
|
16.5
|
1.0
|
|
N
|
A:GLY288
|
4.9
|
10.8
|
1.0
|
|
HA
|
A:CYS284
|
4.9
|
10.3
|
1.0
|
|
H
|
A:GLU315
|
5.0
|
16.3
|
1.0
|
|
CB
|
A:ARG289
|
5.0
|
14.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5szc
Go back to
Zinc Binding Sites List in 5szc
Zinc binding site 3 out
of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:15.1
occ:1.00
|
ND1
|
A:HIS342
|
2.1
|
12.9
|
1.0
|
|
SG
|
A:CYS345
|
2.3
|
17.5
|
1.0
|
|
SG
|
A:CYS322
|
2.3
|
17.9
|
1.0
|
|
SG
|
A:CYS319
|
2.3
|
12.6
|
1.0
|
|
HB2
|
A:HIS342
|
2.7
|
16.4
|
1.0
|
|
HB3
|
A:CYS319
|
2.9
|
14.5
|
1.0
|
|
HB3
|
A:CYS322
|
3.0
|
23.7
|
1.0
|
|
CB
|
A:CYS319
|
3.0
|
12.1
|
1.0
|
|
HB2
|
A:CYS319
|
3.1
|
14.5
|
1.0
|
|
H
|
A:CYS322
|
3.1
|
24.0
|
1.0
|
|
CG
|
A:HIS342
|
3.1
|
12.7
|
1.0
|
|
CE1
|
A:HIS342
|
3.1
|
13.7
|
1.0
|
|
HB2
|
A:CYS345
|
3.2
|
21.8
|
1.0
|
|
CB
|
A:CYS322
|
3.2
|
19.8
|
1.0
|
|
H
|
A:HIS342
|
3.3
|
13.6
|
1.0
|
|
HE1
|
A:HIS342
|
3.3
|
16.4
|
1.0
|
|
CB
|
A:CYS345
|
3.3
|
18.2
|
1.0
|
|
CB
|
A:HIS342
|
3.4
|
13.6
|
1.0
|
|
HB3
|
A:CYS345
|
3.6
|
21.8
|
1.0
|
|
N
|
A:CYS322
|
3.7
|
20.0
|
1.0
|
|
HB2
|
A:LEU321
|
3.7
|
24.6
|
1.0
|
|
HE1
|
A:TYR344
|
4.0
|
21.5
|
1.0
|
|
HB2
|
A:CYS322
|
4.0
|
23.7
|
1.0
|
|
CA
|
A:CYS322
|
4.0
|
19.8
|
1.0
|
|
N
|
A:HIS342
|
4.0
|
11.4
|
1.0
|
|
HB3
|
A:HIS342
|
4.0
|
16.4
|
1.0
|
|
NE2
|
A:HIS342
|
4.2
|
13.8
|
1.0
|
|
CD2
|
A:HIS342
|
4.2
|
12.9
|
1.0
|
|
CA
|
A:HIS342
|
4.3
|
11.3
|
1.0
|
|
H
|
A:LEU321
|
4.4
|
21.7
|
1.0
|
|
CE1
|
A:TYR344
|
4.4
|
17.9
|
1.0
|
|
H
|
A:GLY323
|
4.5
|
23.8
|
1.0
|
|
CA
|
A:CYS319
|
4.5
|
12.8
|
1.0
|
|
O
|
A:HOH511
|
4.5
|
19.2
|
1.0
|
|
H
|
A:THR324
|
4.5
|
21.3
|
1.0
|
|
HH
|
A:TYR344
|
4.6
|
21.5
|
1.0
|
|
CB
|
A:LEU321
|
4.7
|
20.5
|
1.0
|
|
CA
|
A:CYS345
|
4.7
|
20.5
|
1.0
|
|
O
|
A:HOH636
|
4.7
|
31.1
|
1.0
|
|
H
|
A:CYS345
|
4.7
|
23.8
|
1.0
|
|
C
|
A:LEU321
|
4.7
|
21.6
|
1.0
|
|
C
|
A:CYS322
|
4.8
|
20.6
|
1.0
|
|
HA
|
A:CYS322
|
4.8
|
23.8
|
1.0
|
|
N
|
A:GLY323
|
4.9
|
19.8
|
1.0
|
|
HA
|
A:TYR341
|
4.9
|
12.7
|
1.0
|
|
HA
|
A:CYS319
|
4.9
|
15.4
|
1.0
|
|
OG1
|
A:THR324
|
4.9
|
19.6
|
1.0
|
|
HA
|
A:CYS345
|
4.9
|
24.6
|
1.0
|
|
HA
|
A:HIS342
|
5.0
|
13.6
|
1.0
|
|
N
|
A:LEU321
|
5.0
|
18.1
|
1.0
|
|
CZ
|
A:TYR344
|
5.0
|
17.2
|
1.0
|
|
N
|
A:CYS345
|
5.0
|
19.8
|
1.0
|
|
H
|
A:CYS319
|
5.0
|
14.7
|
1.0
|
|
HD1
|
A:TYR344
|
5.0
|
22.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5szc
Go back to
Zinc Binding Sites List in 5szc
Zinc binding site 4 out
of 4 in the Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Human DPF3 Double-Phd Domain Bound to Histone H3 Tail Peptide with Monomethylated K4 and Acetylated K14 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn404
b:9.9
occ:1.00
|
SG
|
A:CYS363
|
2.3
|
10.7
|
1.0
|
|
SG
|
A:CYS337
|
2.3
|
10.3
|
1.0
|
|
SG
|
A:CYS334
|
2.3
|
9.0
|
1.0
|
|
SG
|
A:CYS360
|
2.3
|
11.2
|
1.0
|
|
HB3
|
A:CYS337
|
3.1
|
12.4
|
1.0
|
|
H
|
A:CYS360
|
3.1
|
12.3
|
1.0
|
|
HB2
|
A:CYS363
|
3.1
|
13.3
|
1.0
|
|
CB
|
A:CYS334
|
3.2
|
9.2
|
1.0
|
|
HB3
|
A:CYS334
|
3.2
|
11.0
|
1.0
|
|
HB2
|
A:CYS334
|
3.3
|
11.0
|
1.0
|
|
CB
|
A:CYS337
|
3.3
|
10.3
|
1.0
|
|
H
|
A:CYS337
|
3.3
|
11.8
|
1.0
|
|
CB
|
A:CYS363
|
3.3
|
11.1
|
1.0
|
|
HB3
|
A:CYS360
|
3.4
|
13.8
|
1.0
|
|
H
|
A:CYS363
|
3.4
|
15.1
|
1.0
|
|
CB
|
A:CYS360
|
3.5
|
11.5
|
1.0
|
|
N
|
A:CYS337
|
3.7
|
9.8
|
1.0
|
|
HB2
|
A:ASP336
|
3.9
|
11.8
|
1.0
|
|
N
|
A:CYS360
|
3.9
|
10.3
|
1.0
|
|
HH11
|
A:ARG339
|
3.9
|
16.9
|
1.0
|
|
HB3
|
A:CYS363
|
4.0
|
13.3
|
1.0
|
|
N
|
A:CYS363
|
4.0
|
12.6
|
1.0
|
|
HB2
|
A:CYS337
|
4.1
|
12.4
|
1.0
|
|
CA
|
A:CYS337
|
4.1
|
10.4
|
1.0
|
|
HB2
|
A:ARG339
|
4.1
|
12.4
|
1.0
|
|
HB2
|
A:LEU362
|
4.1
|
18.1
|
1.0
|
|
CA
|
A:CYS360
|
4.2
|
10.9
|
1.0
|
|
H
|
A:ASP336
|
4.2
|
12.2
|
1.0
|
|
HD2
|
A:ARG339
|
4.2
|
14.1
|
1.0
|
|
HH
|
A:TYR341
|
4.3
|
17.0
|
1.0
|
|
HE1
|
A:TYR341
|
4.3
|
15.1
|
1.0
|
|
HB2
|
A:CYS360
|
4.3
|
13.8
|
1.0
|
|
H
|
A:ARG339
|
4.3
|
11.3
|
1.0
|
|
CA
|
A:CYS363
|
4.3
|
12.4
|
1.0
|
|
HB3
|
A:SER359
|
4.4
|
16.2
|
1.0
|
|
O
|
A:HOH607
|
4.5
|
24.6
|
1.0
|
|
C
|
A:ASP336
|
4.6
|
10.8
|
1.0
|
|
O
|
A:CYS360
|
4.6
|
12.2
|
1.0
|
|
CB
|
A:ASP336
|
4.6
|
9.8
|
1.0
|
|
H
|
A:ASP338
|
4.6
|
11.1
|
1.0
|
|
CA
|
A:CYS334
|
4.6
|
9.0
|
1.0
|
|
NH1
|
A:ARG339
|
4.6
|
14.1
|
1.0
|
|
HA
|
A:CYS363
|
4.7
|
14.8
|
1.0
|
|
C
|
A:CYS360
|
4.7
|
12.2
|
1.0
|
|
HB3
|
A:ASP336
|
4.7
|
11.8
|
1.0
|
|
HA
|
A:SER359
|
4.7
|
14.4
|
1.0
|
|
C
|
A:CYS337
|
4.8
|
9.4
|
1.0
|
|
HH12
|
A:ARG339
|
4.8
|
16.9
|
1.0
|
|
HA
|
A:CYS337
|
4.9
|
12.5
|
1.0
|
|
N
|
A:ASP336
|
4.9
|
10.1
|
1.0
|
|
CA
|
A:ASP336
|
4.9
|
10.2
|
1.0
|
|
N
|
A:ASP338
|
4.9
|
9.3
|
1.0
|
|
HA
|
A:CYS334
|
4.9
|
10.8
|
1.0
|
|
H
|
A:LEU362
|
5.0
|
17.6
|
1.0
|
|
CB
|
A:ARG339
|
5.0
|
10.4
|
1.0
|
|
OH
|
A:TYR341
|
5.0
|
14.2
|
1.0
|
|
Reference:
A.Local,
H.Huang,
C.P.Albuquerque,
N.Singh,
A.Y.Lee,
W.Wang,
C.Wang,
J.E.Hsia,
A.K.Shiau,
K.Ge,
K.D.Corbett,
D.Wang,
H.Zhou,
B.Ren.
Identification of H3K4ME1-Associated Proteins at Mammalian Enhancers. Nat. Genet. V. 50 73 2018.
ISSN: ISSN 1546-1718
PubMed: 29255264
DOI: 10.1038/S41588-017-0015-6
Page generated: Mon Oct 28 08:11:13 2024
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