Zinc in PDB 5t8r: Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
Protein crystallography data
The structure of Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer, PDB code: 5t8r
was solved by
A.Amato,
M.S.Gadd,
A.Bortoluzzi,
A.Ciulli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.62 /
2.40
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.607,
72.607,
99.431,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
23.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
(pdb code 5t8r). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer, PDB code: 5t8r:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 1 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
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 Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1801
b:35.3
occ:1.00
|
ND1
|
A:HIS1702
|
2.1
|
41.0
|
1.0
|
SG
|
A:CYS1705
|
2.3
|
37.1
|
1.0
|
SG
|
A:CYS1682
|
2.3
|
42.6
|
1.0
|
SG
|
A:CYS1679
|
2.3
|
40.0
|
1.0
|
CE1
|
A:HIS1702
|
3.1
|
43.4
|
1.0
|
CG
|
A:HIS1702
|
3.1
|
39.5
|
1.0
|
CB
|
A:CYS1679
|
3.1
|
43.8
|
1.0
|
CB
|
A:CYS1705
|
3.3
|
34.5
|
1.0
|
CB
|
A:CYS1682
|
3.4
|
44.7
|
1.0
|
CB
|
A:HIS1702
|
3.4
|
37.1
|
1.0
|
N
|
A:CYS1682
|
3.9
|
43.3
|
1.0
|
N
|
A:HIS1702
|
4.1
|
36.9
|
1.0
|
NE2
|
A:HIS1702
|
4.2
|
42.5
|
1.0
|
CA
|
A:CYS1682
|
4.2
|
46.3
|
1.0
|
CD2
|
A:HIS1702
|
4.2
|
40.6
|
1.0
|
O
|
A:HOH1918
|
4.2
|
42.3
|
1.0
|
CA
|
A:HIS1702
|
4.4
|
35.8
|
1.0
|
CE1
|
A:TYR1704
|
4.4
|
35.9
|
1.0
|
CB
|
A:VAL1681
|
4.6
|
40.1
|
1.0
|
CA
|
A:CYS1679
|
4.6
|
45.6
|
1.0
|
CA
|
A:CYS1705
|
4.7
|
32.9
|
1.0
|
C
|
A:CYS1682
|
4.9
|
50.5
|
1.0
|
C
|
A:VAL1681
|
4.9
|
43.1
|
1.0
|
CZ
|
A:TYR1704
|
5.0
|
37.6
|
1.0
|
N
|
A:CYS1705
|
5.0
|
31.7
|
1.0
|
N
|
A:ARG1683
|
5.0
|
52.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 2 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
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 Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1802
b:43.5
occ:1.00
|
SG
|
A:CYS1697
|
2.3
|
48.7
|
1.0
|
SG
|
A:CYS1694
|
2.3
|
46.5
|
1.0
|
SG
|
A:CYS1723
|
2.3
|
48.5
|
1.0
|
SG
|
A:CYS1720
|
2.3
|
45.8
|
1.0
|
CB
|
A:CYS1694
|
3.2
|
46.8
|
1.0
|
CB
|
A:CYS1720
|
3.4
|
41.9
|
1.0
|
CB
|
A:CYS1697
|
3.4
|
52.5
|
1.0
|
CB
|
A:CYS1723
|
3.4
|
47.3
|
1.0
|
N
|
A:CYS1697
|
3.7
|
52.7
|
1.0
|
N
|
A:CYS1720
|
3.7
|
42.1
|
1.0
|
N
|
A:CYS1723
|
4.0
|
44.8
|
1.0
|
CA
|
A:CYS1720
|
4.0
|
41.4
|
1.0
|
CA
|
A:CYS1697
|
4.1
|
53.9
|
1.0
|
C
|
A:GLY1696
|
4.2
|
54.9
|
1.0
|
CA
|
A:CYS1723
|
4.3
|
46.6
|
1.0
|
C
|
A:CYS1720
|
4.5
|
42.0
|
1.0
|
O
|
A:CYS1720
|
4.5
|
41.9
|
1.0
|
CB
|
A:ARG1699
|
4.6
|
48.4
|
1.0
|
CA
|
A:GLY1696
|
4.7
|
54.5
|
1.0
|
CD
|
A:ARG1699
|
4.7
|
49.4
|
1.0
|
CA
|
A:CYS1694
|
4.7
|
46.9
|
1.0
|
NH1
|
A:ARG1699
|
4.7
|
54.4
|
1.0
|
N
|
A:GLY1696
|
4.7
|
53.5
|
1.0
|
C
|
A:CYS1697
|
4.7
|
54.6
|
1.0
|
C
|
A:PHE1719
|
4.9
|
43.0
|
1.0
|
O
|
A:GLY1696
|
4.9
|
57.0
|
1.0
|
CB
|
A:VAL1722
|
5.0
|
45.6
|
1.0
|
C
|
A:VAL1722
|
5.0
|
46.0
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 3 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
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 Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1801
b:46.4
occ:1.00
|
ND1
|
B:HIS1702
|
2.1
|
48.9
|
1.0
|
SG
|
B:CYS1679
|
2.3
|
48.1
|
1.0
|
SG
|
B:CYS1705
|
2.3
|
45.9
|
1.0
|
SG
|
B:CYS1682
|
2.4
|
59.4
|
1.0
|
CG
|
B:HIS1702
|
3.1
|
46.9
|
1.0
|
CE1
|
B:HIS1702
|
3.1
|
51.0
|
1.0
|
CB
|
B:CYS1679
|
3.1
|
52.9
|
1.0
|
CB
|
B:HIS1702
|
3.3
|
44.1
|
1.0
|
CB
|
B:CYS1705
|
3.4
|
45.1
|
1.0
|
CB
|
B:CYS1682
|
3.4
|
60.1
|
1.0
|
N
|
B:CYS1682
|
3.8
|
57.8
|
1.0
|
CA
|
B:CYS1682
|
4.2
|
61.4
|
1.0
|
NE2
|
B:HIS1702
|
4.2
|
49.5
|
1.0
|
CD2
|
B:HIS1702
|
4.2
|
46.6
|
1.0
|
N
|
B:HIS1702
|
4.2
|
43.3
|
1.0
|
CA
|
B:HIS1702
|
4.4
|
42.3
|
1.0
|
CE1
|
B:TYR1704
|
4.5
|
45.2
|
1.0
|
CA
|
B:CYS1679
|
4.6
|
54.7
|
1.0
|
CB
|
B:VAL1681
|
4.7
|
51.7
|
1.0
|
CA
|
B:CYS1705
|
4.8
|
42.0
|
1.0
|
O
|
B:LYS1684
|
4.9
|
62.4
|
1.0
|
C
|
B:VAL1681
|
4.9
|
57.5
|
1.0
|
C
|
B:CYS1682
|
4.9
|
64.1
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 4 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
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 Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1802
b:46.9
occ:1.00
|
SG
|
B:CYS1697
|
2.3
|
57.2
|
1.0
|
SG
|
B:CYS1694
|
2.3
|
54.0
|
1.0
|
SG
|
B:CYS1723
|
2.3
|
60.3
|
1.0
|
SG
|
B:CYS1720
|
2.4
|
53.3
|
1.0
|
CB
|
B:CYS1697
|
3.3
|
62.6
|
1.0
|
CB
|
B:CYS1694
|
3.3
|
52.9
|
1.0
|
CB
|
B:CYS1723
|
3.4
|
60.6
|
1.0
|
CB
|
B:CYS1720
|
3.4
|
50.3
|
1.0
|
N
|
B:CYS1697
|
3.9
|
60.7
|
1.0
|
N
|
B:CYS1720
|
3.9
|
50.6
|
1.0
|
N
|
B:CYS1723
|
4.0
|
60.0
|
1.0
|
CA
|
B:CYS1697
|
4.2
|
63.6
|
1.0
|
CA
|
B:CYS1720
|
4.2
|
49.8
|
1.0
|
CA
|
B:CYS1723
|
4.2
|
62.6
|
1.0
|
C
|
B:GLY1696
|
4.4
|
61.6
|
1.0
|
O
|
B:CYS1720
|
4.7
|
51.7
|
1.0
|
CA
|
B:GLY1696
|
4.7
|
59.6
|
1.0
|
C
|
B:CYS1720
|
4.7
|
51.0
|
1.0
|
CA
|
B:CYS1694
|
4.8
|
52.5
|
1.0
|
CD
|
B:ARG1699
|
4.8
|
67.5
|
1.0
|
C
|
B:CYS1697
|
4.8
|
65.0
|
1.0
|
N
|
B:GLY1696
|
4.8
|
56.6
|
1.0
|
CB
|
B:ARG1699
|
4.8
|
61.9
|
1.0
|
CB
|
B:VAL1722
|
5.0
|
59.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 5 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
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 Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1801
b:32.7
occ:1.00
|
ND1
|
C:HIS1702
|
2.1
|
34.7
|
1.0
|
SG
|
C:CYS1705
|
2.3
|
33.8
|
1.0
|
SG
|
C:CYS1682
|
2.3
|
39.0
|
1.0
|
SG
|
C:CYS1679
|
2.3
|
32.4
|
1.0
|
CG
|
C:HIS1702
|
3.0
|
34.8
|
1.0
|
CE1
|
C:HIS1702
|
3.0
|
36.3
|
1.0
|
CB
|
C:CYS1679
|
3.1
|
34.5
|
1.0
|
CB
|
C:CYS1705
|
3.3
|
33.5
|
1.0
|
CB
|
C:HIS1702
|
3.3
|
33.5
|
1.0
|
CB
|
C:CYS1682
|
3.4
|
41.6
|
1.0
|
N
|
C:CYS1682
|
3.9
|
38.6
|
1.0
|
N
|
C:HIS1702
|
4.1
|
32.5
|
1.0
|
NE2
|
C:HIS1702
|
4.2
|
35.8
|
1.0
|
CD2
|
C:HIS1702
|
4.2
|
34.8
|
1.0
|
CA
|
C:CYS1682
|
4.2
|
40.9
|
1.0
|
CA
|
C:HIS1702
|
4.3
|
32.5
|
1.0
|
CA
|
C:CYS1679
|
4.6
|
35.1
|
1.0
|
CE1
|
C:TYR1704
|
4.6
|
36.7
|
1.0
|
CA
|
C:CYS1705
|
4.7
|
33.5
|
1.0
|
CB
|
C:VAL1681
|
4.7
|
35.9
|
1.0
|
C
|
C:CYS1682
|
4.9
|
41.6
|
1.0
|
C
|
C:VAL1681
|
4.9
|
37.1
|
1.0
|
N
|
C:CYS1705
|
5.0
|
33.1
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 6 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
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 Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1802
b:33.4
occ:1.00
|
SG
|
C:CYS1697
|
2.3
|
36.5
|
1.0
|
SG
|
C:CYS1694
|
2.3
|
38.8
|
1.0
|
SG
|
C:CYS1720
|
2.3
|
35.8
|
1.0
|
SG
|
C:CYS1723
|
2.3
|
40.4
|
1.0
|
CB
|
C:CYS1723
|
3.3
|
40.7
|
1.0
|
CB
|
C:CYS1694
|
3.3
|
37.7
|
1.0
|
CB
|
C:CYS1697
|
3.4
|
40.2
|
1.0
|
CB
|
C:CYS1720
|
3.5
|
34.2
|
1.0
|
N
|
C:CYS1720
|
3.9
|
37.9
|
1.0
|
N
|
C:CYS1697
|
3.9
|
42.3
|
1.0
|
N
|
C:CYS1723
|
4.0
|
37.5
|
1.0
|
CA
|
C:CYS1697
|
4.2
|
42.0
|
1.0
|
CA
|
C:CYS1723
|
4.2
|
40.4
|
1.0
|
CA
|
C:CYS1720
|
4.2
|
35.0
|
1.0
|
C
|
C:GLY1696
|
4.4
|
44.4
|
1.0
|
O
|
C:HOH1910
|
4.6
|
36.7
|
1.0
|
NH1
|
C:ARG1699
|
4.6
|
34.4
|
1.0
|
CD
|
C:ARG1699
|
4.6
|
31.1
|
1.0
|
O
|
C:CYS1720
|
4.7
|
34.3
|
1.0
|
N
|
C:GLY1696
|
4.7
|
45.0
|
1.0
|
C
|
C:CYS1720
|
4.7
|
34.5
|
1.0
|
CB
|
C:ARG1699
|
4.7
|
31.3
|
1.0
|
CA
|
C:GLY1696
|
4.7
|
45.3
|
1.0
|
C
|
C:CYS1697
|
4.7
|
40.9
|
1.0
|
CA
|
C:CYS1694
|
4.8
|
38.5
|
1.0
|
O
|
C:CYS1697
|
5.0
|
39.9
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 7 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1801
b:38.6
occ:1.00
|
ND1
|
D:HIS1702
|
2.1
|
44.6
|
1.0
|
SG
|
D:CYS1682
|
2.3
|
49.2
|
1.0
|
SG
|
D:CYS1705
|
2.3
|
41.5
|
1.0
|
SG
|
D:CYS1679
|
2.3
|
44.3
|
1.0
|
CG
|
D:HIS1702
|
3.1
|
43.3
|
1.0
|
CB
|
D:CYS1679
|
3.1
|
44.3
|
1.0
|
CE1
|
D:HIS1702
|
3.1
|
46.0
|
1.0
|
CB
|
D:CYS1682
|
3.3
|
50.0
|
1.0
|
CB
|
D:HIS1702
|
3.4
|
42.2
|
1.0
|
CB
|
D:CYS1705
|
3.4
|
40.7
|
1.0
|
N
|
D:CYS1682
|
3.9
|
47.8
|
1.0
|
N
|
D:HIS1702
|
4.0
|
38.9
|
1.0
|
CA
|
D:CYS1682
|
4.2
|
50.6
|
1.0
|
NE2
|
D:HIS1702
|
4.2
|
44.7
|
1.0
|
CD2
|
D:HIS1702
|
4.3
|
43.8
|
1.0
|
CA
|
D:HIS1702
|
4.3
|
40.7
|
1.0
|
CE1
|
D:TYR1704
|
4.4
|
40.6
|
1.0
|
CA
|
D:CYS1679
|
4.6
|
43.7
|
1.0
|
CB
|
D:VAL1681
|
4.7
|
45.9
|
1.0
|
O
|
D:HOH1902
|
4.7
|
41.6
|
1.0
|
CA
|
D:CYS1705
|
4.8
|
40.7
|
1.0
|
C
|
D:CYS1682
|
4.8
|
52.5
|
1.0
|
O
|
D:LYS1684
|
4.9
|
48.9
|
1.0
|
CZ
|
D:TYR1704
|
4.9
|
40.4
|
1.0
|
C
|
D:VAL1681
|
5.0
|
48.0
|
1.0
|
N
|
D:ARG1683
|
5.0
|
52.3
|
1.0
|
OH
|
D:TYR1704
|
5.0
|
40.5
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5t8r
Go back to
Zinc Binding Sites List in 5t8r
Zinc binding site 8 out
of 8 in the Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Human BAZ2A Phd Zinc Finger in Complex with Unmodified H3 10-Mer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1802
b:37.7
occ:1.00
|
SG
|
D:CYS1697
|
2.3
|
41.7
|
1.0
|
SG
|
D:CYS1694
|
2.3
|
42.6
|
1.0
|
SG
|
D:CYS1720
|
2.3
|
37.5
|
1.0
|
SG
|
D:CYS1723
|
2.3
|
37.6
|
1.0
|
CB
|
D:CYS1694
|
3.2
|
42.9
|
1.0
|
CB
|
D:CYS1697
|
3.3
|
46.4
|
1.0
|
CB
|
D:CYS1723
|
3.3
|
36.4
|
1.0
|
CB
|
D:CYS1720
|
3.5
|
36.2
|
1.0
|
N
|
D:CYS1697
|
3.7
|
47.2
|
1.0
|
N
|
D:CYS1720
|
4.0
|
36.1
|
1.0
|
N
|
D:CYS1723
|
4.0
|
35.2
|
1.0
|
CA
|
D:CYS1697
|
4.1
|
48.6
|
1.0
|
CA
|
D:CYS1720
|
4.2
|
35.2
|
1.0
|
C
|
D:GLY1696
|
4.2
|
49.1
|
1.0
|
CA
|
D:CYS1723
|
4.2
|
35.4
|
1.0
|
O
|
D:CYS1720
|
4.5
|
35.7
|
1.0
|
C
|
D:CYS1720
|
4.6
|
34.4
|
1.0
|
CA
|
D:GLY1696
|
4.6
|
49.3
|
1.0
|
CA
|
D:CYS1694
|
4.7
|
45.6
|
1.0
|
C
|
D:CYS1697
|
4.7
|
51.4
|
1.0
|
NH1
|
D:ARG1699
|
4.7
|
42.4
|
1.0
|
N
|
D:GLY1696
|
4.7
|
48.6
|
1.0
|
CB
|
D:ARG1699
|
4.7
|
39.5
|
1.0
|
CD
|
D:ARG1699
|
4.8
|
38.8
|
1.0
|
O
|
D:GLY1696
|
4.9
|
50.6
|
1.0
|
CB
|
D:VAL1722
|
4.9
|
35.7
|
1.0
|
O
|
D:CYS1697
|
4.9
|
52.0
|
1.0
|
C
|
D:VAL1722
|
5.0
|
35.6
|
1.0
|
|
Reference:
A.Bortoluzzi,
A.Amato,
X.Lucas,
M.Blank,
A.Ciulli.
Structural Basis of Molecular Recognition of Helical Histone H3 Tail By Phd Finger Domains. Biochem. J. V. 474 1633 2017.
ISSN: ESSN 1470-8728
PubMed: 28341809
DOI: 10.1042/BCJ20161053
Page generated: Mon Oct 28 08:22:04 2024
|