Zinc in PDB 9gbf: X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
Enzymatic activity of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
All present enzymatic activity of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2:
2.1.1.357;
Protein crystallography data
The structure of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2, PDB code: 9gbf
was solved by
G.Musco,
P.Cocomazzi,
A.Berardi,
S.Knapp,
A.Kramer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
4.97 /
1.76
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
36.131,
45.249,
60.646,
90,
99.65,
90
|
|
R / Rfree (%)
|
18.8 /
22.8
|
Other elements in 9gbf:
The structure of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
(pdb code 9gbf). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2, PDB code: 9gbf:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 1 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1401
b:16.1
occ:1.00
|
NE2
|
A:HIS1283
|
2.0
|
16.6
|
1.0
|
|
SG
|
A:CYS1259
|
2.3
|
15.2
|
1.0
|
|
SG
|
A:CYS1280
|
2.3
|
16.1
|
1.0
|
|
SG
|
A:CYS1254
|
2.3
|
17.8
|
1.0
|
|
CD2
|
A:HIS1283
|
2.8
|
14.4
|
1.0
|
|
HD2
|
A:HIS1283
|
2.8
|
17.6
|
1.0
|
|
CE1
|
A:HIS1283
|
3.1
|
15.7
|
1.0
|
|
CB
|
A:CYS1259
|
3.1
|
18.2
|
1.0
|
|
HB2
|
A:CYS1259
|
3.1
|
22.2
|
1.0
|
|
HB3
|
A:CYS1259
|
3.2
|
22.2
|
1.0
|
|
HB2
|
A:CYS1254
|
3.2
|
19.2
|
1.0
|
|
CB
|
A:CYS1254
|
3.2
|
15.7
|
1.0
|
|
H
|
A:CYS1280
|
3.2
|
24.8
|
1.0
|
|
HB3
|
A:CYS1254
|
3.3
|
19.2
|
1.0
|
|
HB3
|
A:CYS1280
|
3.3
|
20.4
|
1.0
|
|
HE1
|
A:HIS1283
|
3.4
|
19.2
|
1.0
|
|
CB
|
A:CYS1280
|
3.5
|
16.7
|
1.0
|
|
HB3
|
A:ARG1256
|
3.5
|
21.4
|
1.0
|
|
HB2
|
A:LYS1261
|
3.7
|
15.4
|
1.0
|
|
CG
|
A:HIS1283
|
4.0
|
14.3
|
1.0
|
|
N
|
A:CYS1280
|
4.0
|
20.4
|
1.0
|
|
ND1
|
A:HIS1283
|
4.1
|
17.1
|
1.0
|
|
HB2
|
A:CYS1280
|
4.2
|
20.4
|
1.0
|
|
HB3
|
A:TRP1282
|
4.2
|
25.4
|
1.0
|
|
HE3
|
A:TRP1282
|
4.3
|
17.4
|
1.0
|
|
CA
|
A:CYS1280
|
4.3
|
14.3
|
1.0
|
|
CB
|
A:ARG1256
|
4.4
|
17.5
|
1.0
|
|
HB2
|
A:ARG1256
|
4.4
|
21.4
|
1.0
|
|
H
|
A:ARG1256
|
4.4
|
18.4
|
1.0
|
|
HH
|
A:TYR1263
|
4.4
|
22.7
|
1.0
|
|
H
|
A:LYS1261
|
4.4
|
19.9
|
1.0
|
|
HE1
|
A:TYR1263
|
4.5
|
20.9
|
1.0
|
|
HB2
|
A:TRP1282
|
4.5
|
25.4
|
1.0
|
|
CA
|
A:CYS1259
|
4.6
|
18.1
|
1.0
|
|
CA
|
A:CYS1254
|
4.6
|
20.6
|
1.0
|
|
CB
|
A:LYS1261
|
4.6
|
13.5
|
1.0
|
|
HG2
|
A:ARG1256
|
4.7
|
19.9
|
1.0
|
|
C
|
A:CYS1280
|
4.7
|
17.4
|
1.0
|
|
O
|
A:CYS1280
|
4.7
|
15.1
|
1.0
|
|
H
|
A:TRP1282
|
4.8
|
17.7
|
1.0
|
|
HG2
|
A:LYS1261
|
4.8
|
22.4
|
1.0
|
|
HA
|
A:CYS1259
|
4.8
|
22.1
|
1.0
|
|
HA
|
A:GLU1279
|
4.8
|
31.4
|
1.0
|
|
CB
|
A:TRP1282
|
4.8
|
20.8
|
1.0
|
|
HA
|
A:CYS1254
|
4.9
|
25.1
|
1.0
|
|
HD1
|
A:HIS1283
|
4.9
|
20.9
|
1.0
|
|
HG3
|
A:LYS1261
|
4.9
|
22.4
|
1.0
|
|
Zinc binding site 2 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 2 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1402
b:25.1
occ:1.00
|
NE2
|
A:HIS1326
|
2.1
|
34.5
|
1.0
|
|
SG
|
A:CYS1323
|
2.3
|
31.6
|
1.0
|
|
SG
|
A:CYS1296
|
2.3
|
22.0
|
1.0
|
|
SG
|
A:CYS1299
|
2.3
|
22.0
|
1.0
|
|
CD2
|
A:HIS1326
|
3.0
|
39.9
|
1.0
|
|
CE1
|
A:HIS1326
|
3.1
|
38.4
|
1.0
|
|
HD2
|
A:HIS1326
|
3.1
|
48.3
|
1.0
|
|
H
|
A:CYS1323
|
3.2
|
49.6
|
1.0
|
|
HB3
|
A:CYS1299
|
3.3
|
26.4
|
1.0
|
|
CB
|
A:CYS1296
|
3.3
|
19.8
|
1.0
|
|
HE1
|
A:HIS1326
|
3.3
|
46.5
|
1.0
|
|
CB
|
A:CYS1299
|
3.4
|
21.7
|
1.0
|
|
HB3
|
A:CYS1296
|
3.4
|
24.2
|
1.0
|
|
HB2
|
A:CYS1296
|
3.4
|
24.2
|
1.0
|
|
HB2
|
A:ASN1301
|
3.4
|
26.1
|
1.0
|
|
HD21
|
A:ASN1301
|
3.5
|
46.0
|
1.0
|
|
HB3
|
A:CYS1323
|
3.5
|
42.6
|
1.0
|
|
CB
|
A:CYS1323
|
3.6
|
35.2
|
1.0
|
|
H
|
A:CYS1299
|
3.6
|
28.1
|
1.0
|
|
HB2
|
A:LEU1298
|
3.6
|
38.7
|
1.0
|
|
N
|
A:CYS1299
|
3.8
|
23.1
|
1.0
|
|
HB2
|
A:GLU1325
|
3.8
|
60.9
|
1.0
|
|
N
|
A:CYS1323
|
4.0
|
41.0
|
1.0
|
|
CA
|
A:CYS1299
|
4.0
|
21.8
|
1.0
|
|
ND2
|
A:ASN1301
|
4.1
|
38.0
|
1.0
|
|
H
|
A:ASN1301
|
4.1
|
24.8
|
1.0
|
|
CG
|
A:HIS1326
|
4.1
|
45.3
|
1.0
|
|
ND1
|
A:HIS1326
|
4.2
|
43.3
|
1.0
|
|
HB2
|
A:CYS1299
|
4.2
|
26.4
|
1.0
|
|
H
|
A:LEU1298
|
4.2
|
33.3
|
1.0
|
|
CA
|
A:CYS1323
|
4.3
|
38.5
|
1.0
|
|
CB
|
A:ASN1301
|
4.3
|
21.4
|
1.0
|
|
HB2
|
A:CYS1323
|
4.3
|
42.6
|
1.0
|
|
C
|
A:LEU1298
|
4.4
|
26.3
|
1.0
|
|
C
|
A:CYS1299
|
4.4
|
20.1
|
1.0
|
|
HD22
|
A:ASN1301
|
4.5
|
46.0
|
1.0
|
|
CB
|
A:LEU1298
|
4.5
|
31.9
|
1.0
|
|
O
|
A:CYS1299
|
4.5
|
18.7
|
1.0
|
|
H
|
A:GLU1325
|
4.5
|
64.5
|
1.0
|
|
HG3
|
A:GLU1325
|
4.5
|
48.7
|
1.0
|
|
CG
|
A:ASN1301
|
4.6
|
33.5
|
1.0
|
|
HB2
|
A:TYR1322
|
4.6
|
50.5
|
1.0
|
|
CA
|
A:CYS1296
|
4.7
|
20.0
|
1.0
|
|
HA
|
A:TYR1322
|
4.7
|
46.3
|
1.0
|
|
CB
|
A:GLU1325
|
4.7
|
50.4
|
1.0
|
|
C
|
A:CYS1323
|
4.8
|
40.7
|
1.0
|
|
HB3
|
A:LEU1298
|
4.8
|
38.7
|
1.0
|
|
CA
|
A:LEU1298
|
4.8
|
28.7
|
1.0
|
|
HB3
|
A:ASN1301
|
4.8
|
26.1
|
1.0
|
|
N
|
A:LEU1298
|
4.9
|
27.4
|
1.0
|
|
N
|
A:ASN1301
|
4.9
|
20.3
|
1.0
|
|
HA
|
A:CYS1299
|
4.9
|
26.6
|
1.0
|
|
HA
|
A:CYS1296
|
4.9
|
24.4
|
1.0
|
|
HD1
|
A:HIS1326
|
4.9
|
52.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 3 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1403
b:25.8
occ:1.00
|
ND1
|
A:HIS1307
|
2.0
|
36.3
|
1.0
|
|
SG
|
A:CYS1304
|
2.2
|
26.9
|
1.0
|
|
SG
|
A:CYS1288
|
2.2
|
26.6
|
1.0
|
|
SG
|
A:CYS1285
|
2.3
|
25.6
|
1.0
|
|
CE1
|
A:HIS1307
|
2.9
|
28.9
|
1.0
|
|
HE1
|
A:HIS1307
|
2.9
|
35.1
|
1.0
|
|
HB2
|
A:CYS1285
|
3.0
|
24.0
|
1.0
|
|
CB
|
A:CYS1285
|
3.1
|
19.7
|
1.0
|
|
HB2
|
A:HIS1307
|
3.1
|
28.8
|
1.0
|
|
HB3
|
A:CYS1285
|
3.1
|
24.0
|
1.0
|
|
CG
|
A:HIS1307
|
3.2
|
32.3
|
1.0
|
|
H
|
A:CYS1304
|
3.3
|
25.9
|
1.0
|
|
H
|
A:CYS1288
|
3.3
|
33.4
|
1.0
|
|
HB3
|
A:CYS1304
|
3.4
|
27.2
|
1.0
|
|
HB
|
A:VAL1287
|
3.4
|
36.5
|
1.0
|
|
HB3
|
A:CYS1288
|
3.4
|
39.3
|
1.0
|
|
CB
|
A:CYS1304
|
3.5
|
22.4
|
1.0
|
|
CB
|
A:CYS1288
|
3.5
|
32.4
|
1.0
|
|
CB
|
A:HIS1307
|
3.6
|
25.7
|
1.0
|
|
N
|
A:CYS1288
|
3.9
|
27.5
|
1.0
|
|
HB2
|
A:LYS1290
|
4.0
|
33.6
|
1.0
|
|
NE2
|
A:HIS1307
|
4.0
|
42.8
|
1.0
|
|
N
|
A:CYS1304
|
4.1
|
21.2
|
1.0
|
|
H
|
A:HIS1307
|
4.1
|
46.0
|
1.0
|
|
HB2
|
A:CYS1304
|
4.2
|
27.2
|
1.0
|
|
HB2
|
A:GLU1306
|
4.2
|
55.5
|
1.0
|
|
CD2
|
A:HIS1307
|
4.2
|
38.2
|
1.0
|
|
H
|
A:VAL1287
|
4.2
|
27.8
|
1.0
|
|
HB2
|
A:CYS1288
|
4.2
|
39.3
|
1.0
|
|
HB3
|
A:HIS1307
|
4.2
|
28.8
|
1.0
|
|
CA
|
A:CYS1288
|
4.3
|
30.9
|
1.0
|
|
CB
|
A:VAL1287
|
4.3
|
30.1
|
1.0
|
|
CA
|
A:CYS1304
|
4.3
|
21.0
|
1.0
|
|
H
|
A:LYS1290
|
4.4
|
26.2
|
1.0
|
|
N
|
A:HIS1307
|
4.5
|
38.0
|
1.0
|
|
CA
|
A:CYS1285
|
4.5
|
17.6
|
1.0
|
|
HG12
|
A:VAL1287
|
4.5
|
38.6
|
1.0
|
|
H
|
A:GLY1289
|
4.6
|
31.8
|
1.0
|
|
HA
|
A:PHE1303
|
4.7
|
25.3
|
1.0
|
|
CA
|
A:HIS1307
|
4.7
|
38.0
|
1.0
|
|
HE2
|
A:HIS1307
|
4.8
|
51.7
|
1.0
|
|
HG2
|
A:LYS1290
|
4.8
|
37.1
|
1.0
|
|
C
|
A:VAL1287
|
4.8
|
28.7
|
1.0
|
|
HA
|
A:CYS1285
|
4.8
|
21.5
|
1.0
|
|
H
|
A:GLU1306
|
4.9
|
48.8
|
1.0
|
|
C
|
A:CYS1304
|
4.9
|
28.6
|
1.0
|
|
N
|
A:VAL1287
|
4.9
|
22.9
|
1.0
|
|
CB
|
A:LYS1290
|
4.9
|
27.6
|
1.0
|
|
HB3
|
A:PHE1303
|
4.9
|
22.7
|
1.0
|
|
CG1
|
A:VAL1287
|
4.9
|
31.8
|
1.0
|
|
CA
|
A:VAL1287
|
4.9
|
31.1
|
1.0
|
|
C
|
A:CYS1288
|
5.0
|
26.8
|
1.0
|
|
Zinc binding site 4 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 4 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1404
b:18.8
occ:1.00
|
ND1
|
A:HIS1264
|
2.1
|
19.4
|
1.0
|
|
SG
|
A:CYS1267
|
2.3
|
23.1
|
1.0
|
|
SG
|
A:CYS1245
|
2.3
|
17.9
|
1.0
|
|
SG
|
A:CYS1242
|
2.3
|
15.4
|
1.0
|
|
HB2
|
A:HIS1264
|
2.9
|
24.3
|
1.0
|
|
HB3
|
A:CYS1242
|
2.9
|
20.5
|
1.0
|
|
HB3
|
A:CYS1245
|
3.0
|
22.4
|
1.0
|
|
CB
|
A:CYS1242
|
3.0
|
16.7
|
1.0
|
|
CE1
|
A:HIS1264
|
3.0
|
17.4
|
1.0
|
|
HB2
|
A:CYS1242
|
3.0
|
20.5
|
1.0
|
|
H
|
A:HIS1264
|
3.2
|
23.3
|
1.0
|
|
HE1
|
A:HIS1264
|
3.2
|
18.9
|
1.0
|
|
CG
|
A:HIS1264
|
3.2
|
23.3
|
1.0
|
|
CB
|
A:CYS1245
|
3.2
|
18.3
|
1.0
|
|
HB2
|
A:CYS1267
|
3.2
|
26.2
|
1.0
|
|
H
|
A:CYS1245
|
3.2
|
21.1
|
1.0
|
|
CB
|
A:CYS1267
|
3.3
|
21.5
|
1.0
|
|
CB
|
A:HIS1264
|
3.5
|
19.9
|
1.0
|
|
HB3
|
A:CYS1267
|
3.6
|
26.2
|
1.0
|
|
N
|
A:CYS1245
|
3.9
|
17.3
|
1.0
|
|
HB3
|
A:ARG1244
|
3.9
|
23.0
|
1.0
|
|
N
|
A:HIS1264
|
4.0
|
19.1
|
1.0
|
|
HB2
|
A:CYS1245
|
4.0
|
22.4
|
1.0
|
|
CA
|
A:CYS1245
|
4.1
|
18.1
|
1.0
|
|
NE2
|
A:HIS1264
|
4.2
|
19.1
|
1.0
|
|
HB3
|
A:HIS1264
|
4.2
|
24.3
|
1.0
|
|
CD2
|
A:HIS1264
|
4.3
|
20.1
|
1.0
|
|
CA
|
A:HIS1264
|
4.4
|
24.2
|
1.0
|
|
CA
|
A:CYS1242
|
4.5
|
19.6
|
1.0
|
|
H
|
A:ASP1247
|
4.5
|
20.3
|
1.0
|
|
H
|
A:CYS1267
|
4.6
|
34.1
|
1.0
|
|
H
|
A:ARG1244
|
4.7
|
16.8
|
1.0
|
|
HA
|
A:TYR1263
|
4.7
|
22.0
|
1.0
|
|
H
|
A:GLY1246
|
4.7
|
21.9
|
1.0
|
|
CA
|
A:CYS1267
|
4.7
|
22.9
|
1.0
|
|
CB
|
A:ARG1244
|
4.8
|
18.8
|
1.0
|
|
HB2
|
A:ASP1247
|
4.8
|
29.6
|
1.0
|
|
C
|
A:CYS1245
|
4.9
|
20.2
|
1.0
|
|
HA
|
A:CYS1242
|
4.9
|
23.9
|
1.0
|
|
HA
|
A:CYS1245
|
4.9
|
22.1
|
1.0
|
|
O
|
A:ASP1247
|
4.9
|
20.5
|
1.0
|
|
C
|
A:ARG1244
|
4.9
|
14.9
|
1.0
|
|
HE2
|
A:HIS1264
|
4.9
|
23.3
|
1.0
|
|
HA
|
A:CYS1267
|
5.0
|
27.9
|
1.0
|
|
HD21
|
A:LEU1251
|
5.0
|
22.0
|
1.0
|
|
Zinc binding site 5 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 5 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1401
b:17.0
occ:1.00
|
ND1
|
B:HIS1264
|
2.0
|
14.7
|
1.0
|
|
SG
|
B:CYS1245
|
2.3
|
16.3
|
1.0
|
|
SG
|
B:CYS1242
|
2.3
|
15.8
|
1.0
|
|
SG
|
B:CYS1267
|
2.3
|
22.4
|
1.0
|
|
HB3
|
B:CYS1242
|
2.8
|
19.9
|
1.0
|
|
HB3
|
B:CYS1245
|
2.9
|
22.2
|
1.0
|
|
CE1
|
B:HIS1264
|
2.9
|
16.7
|
1.0
|
|
CB
|
B:CYS1242
|
3.0
|
16.3
|
1.0
|
|
HB2
|
B:CYS1242
|
3.0
|
19.9
|
1.0
|
|
HB2
|
B:HIS1264
|
3.0
|
18.9
|
1.0
|
|
HE1
|
B:HIS1264
|
3.1
|
20.5
|
1.0
|
|
H
|
B:CYS1245
|
3.1
|
19.8
|
1.0
|
|
CG
|
B:HIS1264
|
3.1
|
18.8
|
1.0
|
|
CB
|
B:CYS1245
|
3.2
|
18.1
|
1.0
|
|
HB2
|
B:CYS1267
|
3.2
|
24.1
|
1.0
|
|
CB
|
B:CYS1267
|
3.3
|
19.8
|
1.0
|
|
H
|
B:HIS1264
|
3.3
|
24.5
|
1.0
|
|
H51
|
B:EPE1406
|
3.4
|
36.0
|
1.0
|
|
HB3
|
B:CYS1267
|
3.5
|
24.1
|
1.0
|
|
CB
|
B:HIS1264
|
3.6
|
15.4
|
1.0
|
|
N
|
B:CYS1245
|
3.8
|
16.1
|
1.0
|
|
HB3
|
B:ARG1244
|
3.9
|
21.5
|
1.0
|
|
HB2
|
B:CYS1245
|
3.9
|
22.2
|
1.0
|
|
H61
|
B:EPE1406
|
4.0
|
36.2
|
1.0
|
|
H62
|
B:EPE1406
|
4.0
|
36.2
|
1.0
|
|
N
|
B:HIS1264
|
4.1
|
20.1
|
1.0
|
|
NE2
|
B:HIS1264
|
4.1
|
16.6
|
1.0
|
|
CA
|
B:CYS1245
|
4.1
|
17.9
|
1.0
|
|
CD2
|
B:HIS1264
|
4.2
|
17.0
|
1.0
|
|
HB3
|
B:HIS1264
|
4.3
|
18.9
|
1.0
|
|
C5
|
B:EPE1406
|
4.3
|
29.7
|
1.0
|
|
C6
|
B:EPE1406
|
4.3
|
29.9
|
1.0
|
|
H
|
B:ASP1247
|
4.4
|
21.0
|
1.0
|
|
CA
|
B:HIS1264
|
4.4
|
17.6
|
1.0
|
|
CA
|
B:CYS1242
|
4.5
|
14.4
|
1.0
|
|
HB2
|
B:ASP1247
|
4.5
|
21.2
|
1.0
|
|
H
|
B:ARG1244
|
4.5
|
21.5
|
1.0
|
|
H
|
B:CYS1267
|
4.6
|
32.3
|
1.0
|
|
CA
|
B:CYS1267
|
4.7
|
25.4
|
1.0
|
|
H
|
B:GLY1246
|
4.7
|
21.4
|
1.0
|
|
HA
|
B:TYR1263
|
4.8
|
21.6
|
1.0
|
|
CB
|
B:ARG1244
|
4.8
|
17.6
|
1.0
|
|
HE2
|
B:HIS1264
|
4.8
|
20.3
|
1.0
|
|
HA
|
B:CYS1242
|
4.8
|
17.7
|
1.0
|
|
C
|
B:ARG1244
|
4.9
|
19.3
|
1.0
|
|
C
|
B:CYS1245
|
4.9
|
13.1
|
1.0
|
|
H81
|
B:EPE1406
|
4.9
|
27.2
|
1.0
|
|
HA
|
B:CYS1245
|
4.9
|
21.9
|
1.0
|
|
H
|
B:CYS1242
|
5.0
|
19.2
|
1.0
|
|
HA
|
B:CYS1267
|
5.0
|
30.9
|
1.0
|
|
H52
|
B:EPE1406
|
5.0
|
36.0
|
1.0
|
|
Zinc binding site 6 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 6 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1402
b:14.9
occ:1.00
|
NE2
|
B:HIS1283
|
2.0
|
19.2
|
1.0
|
|
SG
|
B:CYS1259
|
2.3
|
15.8
|
1.0
|
|
SG
|
B:CYS1254
|
2.3
|
14.4
|
1.0
|
|
SG
|
B:CYS1280
|
2.3
|
17.5
|
1.0
|
|
CD2
|
B:HIS1283
|
3.0
|
13.6
|
1.0
|
|
CE1
|
B:HIS1283
|
3.0
|
18.9
|
1.0
|
|
HB3
|
B:CYS1254
|
3.1
|
20.9
|
1.0
|
|
HB2
|
B:CYS1254
|
3.1
|
20.9
|
1.0
|
|
CB
|
B:CYS1254
|
3.1
|
17.1
|
1.0
|
|
H
|
B:CYS1280
|
3.1
|
21.6
|
1.0
|
|
HD2
|
B:HIS1283
|
3.1
|
16.7
|
1.0
|
|
CB
|
B:CYS1259
|
3.2
|
14.1
|
1.0
|
|
HB3
|
B:CYS1259
|
3.2
|
17.4
|
1.0
|
|
HB2
|
B:CYS1259
|
3.2
|
17.4
|
1.0
|
|
HE1
|
B:HIS1283
|
3.2
|
23.1
|
1.0
|
|
HB3
|
B:CYS1280
|
3.4
|
19.4
|
1.0
|
|
CB
|
B:CYS1280
|
3.5
|
17.8
|
1.0
|
|
HB3
|
B:ARG1256
|
3.5
|
21.3
|
1.0
|
|
HB2
|
B:LYS1261
|
3.8
|
15.4
|
1.0
|
|
N
|
B:CYS1280
|
3.9
|
17.9
|
1.0
|
|
ND1
|
B:HIS1283
|
4.1
|
15.5
|
1.0
|
|
CG
|
B:HIS1283
|
4.1
|
19.7
|
1.0
|
|
CA
|
B:CYS1280
|
4.2
|
17.8
|
1.0
|
|
HB2
|
B:CYS1280
|
4.3
|
19.4
|
1.0
|
|
H
|
B:LYS1261
|
4.4
|
17.9
|
1.0
|
|
CB
|
B:ARG1256
|
4.4
|
17.4
|
1.0
|
|
H
|
B:ARG1256
|
4.4
|
19.7
|
1.0
|
|
HE3
|
B:TRP1282
|
4.5
|
15.9
|
1.0
|
|
HB3
|
B:TRP1282
|
4.5
|
18.4
|
1.0
|
|
HB2
|
B:ARG1256
|
4.5
|
21.3
|
1.0
|
|
HH
|
B:TYR1263
|
4.5
|
18.6
|
1.0
|
|
HE1
|
B:TYR1263
|
4.6
|
24.2
|
1.0
|
|
CA
|
B:CYS1254
|
4.6
|
16.8
|
1.0
|
|
CA
|
B:CYS1259
|
4.6
|
14.4
|
1.0
|
|
HG2
|
B:LYS1261
|
4.7
|
23.9
|
1.0
|
|
HA
|
B:GLU1279
|
4.7
|
29.3
|
1.0
|
|
CB
|
B:LYS1261
|
4.7
|
12.5
|
1.0
|
|
HG2
|
B:ARG1256
|
4.7
|
18.5
|
1.0
|
|
C
|
B:CYS1280
|
4.8
|
16.5
|
1.0
|
|
HD1
|
B:HIS1283
|
4.9
|
19.0
|
1.0
|
|
O
|
B:CYS1280
|
4.9
|
18.2
|
1.0
|
|
HA
|
B:CYS1259
|
4.9
|
17.6
|
1.0
|
|
HA
|
B:CYS1254
|
4.9
|
20.5
|
1.0
|
|
H
|
B:HIS1283
|
5.0
|
17.2
|
1.0
|
|
HB2
|
B:TRP1282
|
5.0
|
18.4
|
1.0
|
|
Zinc binding site 7 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 7 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1403
b:18.8
occ:1.00
|
NE2
|
B:HIS1326
|
2.0
|
24.2
|
1.0
|
|
SG
|
B:CYS1296
|
2.3
|
18.5
|
1.0
|
|
SG
|
B:CYS1323
|
2.3
|
25.2
|
1.0
|
|
SG
|
B:CYS1299
|
2.3
|
16.3
|
1.0
|
|
HB3
|
B:CYS1299
|
3.0
|
25.3
|
1.0
|
|
CD2
|
B:HIS1326
|
3.0
|
26.0
|
1.0
|
|
CE1
|
B:HIS1326
|
3.1
|
25.7
|
1.0
|
|
HD2
|
B:HIS1326
|
3.2
|
29.3
|
1.0
|
|
H
|
B:CYS1323
|
3.2
|
30.0
|
1.0
|
|
CB
|
B:CYS1299
|
3.2
|
20.8
|
1.0
|
|
HE1
|
B:HIS1326
|
3.3
|
31.2
|
1.0
|
|
CB
|
B:CYS1296
|
3.3
|
16.2
|
1.0
|
|
HB3
|
B:CYS1296
|
3.4
|
19.8
|
1.0
|
|
HB2
|
B:CYS1296
|
3.4
|
19.8
|
1.0
|
|
HB3
|
B:CYS1323
|
3.4
|
33.2
|
1.0
|
|
HB2
|
B:ASN1301
|
3.5
|
25.2
|
1.0
|
|
CB
|
B:CYS1323
|
3.5
|
27.3
|
1.0
|
|
HD21
|
B:ASN1301
|
3.6
|
31.5
|
1.0
|
|
H
|
B:CYS1299
|
3.7
|
18.4
|
1.0
|
|
HB2
|
B:LEU1298
|
3.7
|
29.0
|
1.0
|
|
N
|
B:CYS1299
|
3.8
|
15.0
|
1.0
|
|
HB3
|
B:GLU1325
|
3.8
|
35.4
|
1.0
|
|
N
|
B:CYS1323
|
4.0
|
26.7
|
1.0
|
|
CA
|
B:CYS1299
|
4.0
|
16.1
|
1.0
|
|
HB2
|
B:CYS1299
|
4.0
|
25.3
|
1.0
|
|
ND1
|
B:HIS1326
|
4.1
|
25.8
|
1.0
|
|
CG
|
B:HIS1326
|
4.1
|
27.1
|
1.0
|
|
ND2
|
B:ASN1301
|
4.1
|
25.9
|
1.0
|
|
H
|
B:LEU1298
|
4.2
|
26.4
|
1.0
|
|
HB2
|
B:CYS1323
|
4.2
|
33.2
|
1.0
|
|
C
|
B:LEU1298
|
4.3
|
23.4
|
1.0
|
|
CA
|
B:CYS1323
|
4.3
|
26.6
|
1.0
|
|
H
|
B:ASN1301
|
4.3
|
21.0
|
1.0
|
|
CB
|
B:ASN1301
|
4.4
|
20.6
|
1.0
|
|
C
|
B:CYS1299
|
4.5
|
16.2
|
1.0
|
|
CB
|
B:LEU1298
|
4.5
|
23.9
|
1.0
|
|
HD22
|
B:ASN1301
|
4.6
|
31.5
|
1.0
|
|
O
|
B:CYS1299
|
4.6
|
15.0
|
1.0
|
|
CG
|
B:ASN1301
|
4.6
|
24.3
|
1.0
|
|
HB3
|
B:LEU1298
|
4.7
|
29.0
|
1.0
|
|
H
|
B:GLU1325
|
4.7
|
38.1
|
1.0
|
|
CB
|
B:GLU1325
|
4.7
|
29.2
|
1.0
|
|
HA
|
B:TYR1322
|
4.7
|
32.1
|
1.0
|
|
CA
|
B:LEU1298
|
4.8
|
20.8
|
1.0
|
|
CA
|
B:CYS1296
|
4.8
|
18.5
|
1.0
|
|
HB2
|
B:TYR1322
|
4.8
|
32.7
|
1.0
|
|
C
|
B:CYS1323
|
4.8
|
30.6
|
1.0
|
|
N
|
B:LEU1298
|
4.8
|
21.7
|
1.0
|
|
HB2
|
B:GLU1325
|
4.9
|
35.4
|
1.0
|
|
HA
|
B:CYS1299
|
4.9
|
19.7
|
1.0
|
|
O
|
B:LEU1298
|
4.9
|
19.9
|
1.0
|
|
HB3
|
B:ASN1301
|
4.9
|
25.2
|
1.0
|
|
HD1
|
B:HIS1326
|
4.9
|
31.1
|
1.0
|
|
O
|
B:CYS1323
|
4.9
|
28.9
|
1.0
|
|
HA
|
B:CYS1296
|
5.0
|
22.6
|
1.0
|
|
H
|
B:HIS1326
|
5.0
|
35.4
|
1.0
|
|
Zinc binding site 8 out
of 8 in 9gbf
Go back to
Zinc Binding Sites List in 9gbf
Zinc binding site 8 out
of 8 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1404
b:18.2
occ:1.00
|
ND1
|
B:HIS1307
|
2.1
|
27.3
|
1.0
|
|
SG
|
B:CYS1304
|
2.3
|
20.7
|
1.0
|
|
SG
|
B:CYS1288
|
2.3
|
19.1
|
1.0
|
|
SG
|
B:CYS1285
|
2.3
|
17.9
|
1.0
|
|
CE1
|
B:HIS1307
|
3.0
|
19.5
|
1.0
|
|
HB2
|
B:HIS1307
|
3.0
|
26.9
|
1.0
|
|
HE1
|
B:HIS1307
|
3.1
|
23.8
|
1.0
|
|
HB3
|
B:CYS1285
|
3.1
|
15.8
|
1.0
|
|
CG
|
B:HIS1307
|
3.2
|
18.5
|
1.0
|
|
CB
|
B:CYS1285
|
3.2
|
12.9
|
1.0
|
|
H
|
B:CYS1288
|
3.2
|
24.7
|
1.0
|
|
HB2
|
B:CYS1285
|
3.3
|
15.8
|
1.0
|
|
H
|
B:CYS1304
|
3.4
|
18.7
|
1.0
|
|
HB
|
B:VAL1287
|
3.4
|
27.7
|
1.0
|
|
HB3
|
B:CYS1304
|
3.4
|
23.8
|
1.0
|
|
CB
|
B:CYS1304
|
3.5
|
19.5
|
1.0
|
|
HB3
|
B:CYS1288
|
3.6
|
32.9
|
1.0
|
|
CB
|
B:CYS1288
|
3.6
|
27.1
|
1.0
|
|
CB
|
B:HIS1307
|
3.6
|
22.1
|
1.0
|
|
HB2
|
B:LYS1290
|
3.8
|
21.0
|
1.0
|
|
N
|
B:CYS1288
|
3.9
|
20.3
|
1.0
|
|
HB2
|
B:GLU1306
|
4.1
|
42.0
|
1.0
|
|
NE2
|
B:HIS1307
|
4.1
|
26.4
|
1.0
|
|
N
|
B:CYS1304
|
4.2
|
15.2
|
1.0
|
|
H
|
B:HIS1307
|
4.2
|
36.2
|
1.0
|
|
H
|
B:LYS1290
|
4.2
|
20.5
|
1.0
|
|
HB3
|
B:HIS1307
|
4.2
|
26.9
|
1.0
|
|
CD2
|
B:HIS1307
|
4.2
|
24.2
|
1.0
|
|
HB2
|
B:CYS1304
|
4.3
|
23.8
|
1.0
|
|
CA
|
B:CYS1288
|
4.3
|
20.7
|
1.0
|
|
HE2
|
B:LYS1290
|
4.3
|
39.3
|
1.0
|
|
HB2
|
B:CYS1288
|
4.3
|
32.9
|
1.0
|
|
CB
|
B:VAL1287
|
4.4
|
22.7
|
1.0
|
|
CA
|
B:CYS1304
|
4.4
|
19.6
|
1.0
|
|
H
|
B:VAL1287
|
4.4
|
19.0
|
1.0
|
|
HG12
|
B:VAL1287
|
4.4
|
30.9
|
1.0
|
|
HG3
|
B:LYS1290
|
4.5
|
31.1
|
1.0
|
|
N
|
B:HIS1307
|
4.5
|
29.9
|
1.0
|
|
H
|
B:GLY1289
|
4.6
|
19.6
|
1.0
|
|
CA
|
B:CYS1285
|
4.7
|
20.1
|
1.0
|
|
CA
|
B:HIS1307
|
4.7
|
21.8
|
1.0
|
|
CB
|
B:LYS1290
|
4.7
|
17.1
|
1.0
|
|
H
|
B:GLU1306
|
4.7
|
32.7
|
1.0
|
|
HD1
|
B:PHE1303
|
4.8
|
28.4
|
1.0
|
|
HA
|
B:PHE1303
|
4.8
|
15.2
|
1.0
|
|
HB3
|
B:PHE1303
|
4.9
|
19.8
|
1.0
|
|
CG1
|
B:VAL1287
|
4.9
|
25.4
|
1.0
|
|
HE2
|
B:HIS1307
|
4.9
|
32.0
|
1.0
|
|
C
|
B:VAL1287
|
4.9
|
20.7
|
1.0
|
|
C
|
B:CYS1288
|
4.9
|
20.3
|
1.0
|
|
N
|
B:LYS1290
|
4.9
|
16.8
|
1.0
|
|
N
|
B:GLY1289
|
5.0
|
16.0
|
1.0
|
|
C
|
B:CYS1304
|
5.0
|
22.3
|
1.0
|
|
Reference:
A.Berardi,
C.L.Kaestner,
M.Ghitti,
G.Quilici,
P.Cocomazzi,
J.Li,
F.Ballabio,
C.Zucchelli,
S.Knapp,
J.D.Licht,
G.Musco.
The C-Terminal PHDVC5HCH Tandem Domain of NSD2 Is A Combinatorial Reader of Unmodified H3K4 and Tri-Methylated H3K27 That Regulates Transcription of Cell Adhesion Genes in Multiple Myeloma Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAE1121
Page generated: Sun Feb 9 01:21:35 2025
|
