Nickel in PDB 5fpv: Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Enzymatic activity of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
All present enzymatic activity of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A:
1.14.11.27;
Protein crystallography data
The structure of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A, PDB code: 5fpv
was solved by
V.Srikannathasan,
C.Gileadi,
F.Von Delft,
C.H.Arrowsmith,
C.Bountra,
A.Edwards,
U.Oppermann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
85.327 /
2.44
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
111.346,
103.509,
157.103,
90.00,
106.37,
90.00
|
R / Rfree (%)
|
19.55 /
22.89
|
Other elements in 5fpv:
The structure of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A also contains other interesting chemical elements:
Nickel Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Nickel atom in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
(pdb code 5fpv). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 15 binding sites of Nickel where determined in the
Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A, PDB code: 5fpv:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Nickel binding site 1 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 1 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni1360
b:65.2
occ:1.00
|
NZ
|
H:LYS106
|
2.5
|
47.8
|
1.0
|
N
|
A:GLY230
|
3.5
|
42.9
|
1.0
|
CA
|
A:GLY230
|
3.7
|
43.4
|
1.0
|
CE
|
H:LYS106
|
3.8
|
44.8
|
1.0
|
N
|
A:SER231
|
3.9
|
44.1
|
1.0
|
CA
|
A:PHE228
|
4.0
|
40.7
|
1.0
|
C
|
A:PHE228
|
4.0
|
43.3
|
1.0
|
OG
|
A:SER231
|
4.2
|
45.2
|
1.0
|
CD
|
A:PRO229
|
4.2
|
44.2
|
1.0
|
N
|
A:PRO229
|
4.2
|
43.7
|
1.0
|
C
|
A:GLY230
|
4.3
|
44.7
|
1.0
|
CB
|
A:PHE228
|
4.4
|
37.7
|
1.0
|
O
|
A:PHE228
|
4.5
|
45.2
|
1.0
|
CD1
|
A:PHE228
|
4.5
|
37.9
|
1.0
|
CD
|
H:LYS106
|
4.6
|
42.5
|
1.0
|
C
|
A:PRO229
|
4.6
|
43.0
|
1.0
|
CG
|
A:PRO229
|
4.8
|
44.9
|
1.0
|
CG
|
A:PHE228
|
4.9
|
37.0
|
1.0
|
CB
|
A:SER231
|
5.0
|
45.1
|
1.0
|
CA
|
A:SER231
|
5.0
|
44.1
|
1.0
|
|
Nickel binding site 2 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 2 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni1361
b:87.5
occ:1.00
|
N
|
A:LYS91
|
3.6
|
38.4
|
1.0
|
NZ
|
A:LYS90
|
3.8
|
45.0
|
1.0
|
CE
|
A:LYS90
|
4.0
|
43.2
|
1.0
|
CB
|
A:LYS91
|
4.0
|
43.7
|
1.0
|
CG
|
A:LYS91
|
4.0
|
48.6
|
1.0
|
CD
|
A:LYS90
|
4.1
|
41.5
|
1.0
|
CA
|
A:LYS90
|
4.3
|
38.9
|
1.0
|
CB
|
A:LYS90
|
4.3
|
39.8
|
1.0
|
CA
|
A:LYS91
|
4.4
|
38.7
|
1.0
|
C
|
A:LYS90
|
4.5
|
38.7
|
1.0
|
CD
|
A:LYS91
|
4.7
|
54.7
|
1.0
|
CG
|
A:LYS90
|
4.9
|
40.2
|
1.0
|
|
Nickel binding site 3 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 3 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni1362
b:85.3
occ:1.00
|
O
|
A:TYR60
|
3.7
|
44.0
|
1.0
|
CE1
|
A:PHE203
|
4.2
|
24.4
|
1.0
|
CZ
|
A:PHE203
|
4.3
|
23.8
|
1.0
|
CE2
|
A:PHE284
|
4.6
|
27.4
|
1.0
|
CB
|
A:TYR60
|
4.6
|
35.9
|
1.0
|
C
|
A:TYR60
|
4.6
|
42.8
|
1.0
|
CD1
|
A:PHE203
|
4.6
|
24.4
|
1.0
|
NE
|
A:ARG99
|
4.7
|
39.4
|
1.0
|
CE2
|
A:PHE203
|
4.8
|
22.7
|
1.0
|
OD1
|
A:ASP64
|
4.8
|
42.8
|
1.0
|
NH2
|
A:ARG99
|
4.9
|
40.0
|
1.0
|
|
Nickel binding site 4 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 4 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni1360
b:73.4
occ:1.00
|
N
|
B:GLY230
|
3.6
|
49.6
|
1.0
|
CA
|
B:GLY230
|
3.7
|
49.5
|
1.0
|
N
|
B:SER231
|
3.7
|
50.5
|
1.0
|
OG
|
B:SER231
|
3.8
|
54.6
|
1.0
|
CA
|
B:PHE228
|
4.1
|
43.7
|
1.0
|
C
|
B:PHE228
|
4.1
|
45.5
|
1.0
|
C
|
B:GLY230
|
4.2
|
49.9
|
1.0
|
CB
|
B:PHE228
|
4.3
|
40.3
|
1.0
|
N
|
B:PRO229
|
4.3
|
46.0
|
1.0
|
O
|
B:PHE228
|
4.4
|
45.9
|
1.0
|
CD1
|
B:PHE228
|
4.4
|
37.5
|
1.0
|
CD
|
B:PRO229
|
4.5
|
45.7
|
1.0
|
NZ
|
G:LYS106
|
4.7
|
54.5
|
1.0
|
CB
|
B:SER231
|
4.7
|
52.8
|
1.0
|
C
|
B:PRO229
|
4.7
|
48.6
|
1.0
|
CA
|
B:SER231
|
4.8
|
50.6
|
1.0
|
CG
|
B:PHE228
|
4.9
|
37.9
|
1.0
|
|
Nickel binding site 5 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 5 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni1361
b:69.4
occ:1.00
|
O
|
B:HOH2128
|
3.5
|
30.1
|
1.0
|
O
|
B:TYR60
|
3.9
|
36.8
|
1.0
|
NE
|
B:ARG99
|
4.1
|
33.2
|
1.0
|
CE1
|
B:PHE203
|
4.2
|
26.4
|
1.0
|
NH2
|
B:ARG99
|
4.2
|
33.7
|
1.0
|
CZ
|
B:PHE203
|
4.3
|
26.4
|
1.0
|
O
|
B:HOH2029
|
4.3
|
44.4
|
1.0
|
CE2
|
B:PHE284
|
4.3
|
22.9
|
1.0
|
CZ
|
B:ARG99
|
4.6
|
35.5
|
1.0
|
CD1
|
B:PHE203
|
4.7
|
25.9
|
1.0
|
OD1
|
B:ASP64
|
4.8
|
39.7
|
1.0
|
CZ
|
B:PHE284
|
4.8
|
22.6
|
1.0
|
CE2
|
B:PHE203
|
4.9
|
25.3
|
1.0
|
C
|
B:TYR60
|
4.9
|
35.6
|
1.0
|
|
Nickel binding site 6 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 6 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni1360
b:90.4
occ:1.00
|
CB
|
C:ARG96
|
3.5
|
27.1
|
1.0
|
OD1
|
C:ASP65
|
3.7
|
37.8
|
1.0
|
O
|
C:HOH2049
|
4.0
|
36.0
|
1.0
|
CB
|
C:ASP64
|
4.1
|
36.9
|
1.0
|
O
|
C:ASP64
|
4.1
|
34.9
|
1.0
|
C
|
C:ASP64
|
4.5
|
35.9
|
1.0
|
CG
|
C:ASP65
|
4.8
|
37.8
|
1.0
|
OD2
|
C:ASP64
|
4.9
|
38.7
|
1.0
|
CA
|
C:ASP64
|
4.9
|
36.3
|
1.0
|
CA
|
C:ARG96
|
5.0
|
29.1
|
1.0
|
|
Nickel binding site 7 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 7 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni1361
b:63.0
occ:1.00
|
O
|
C:TYR60
|
3.8
|
37.4
|
1.0
|
O
|
C:HOH2022
|
4.1
|
30.1
|
1.0
|
CE1
|
C:PHE203
|
4.1
|
26.5
|
1.0
|
CZ
|
C:PHE203
|
4.2
|
27.5
|
1.0
|
NH2
|
C:ARG99
|
4.4
|
31.6
|
1.0
|
CE2
|
C:PHE284
|
4.4
|
25.2
|
1.0
|
NE
|
C:ARG99
|
4.4
|
31.4
|
1.0
|
OD1
|
C:ASP64
|
4.5
|
40.2
|
1.0
|
CD1
|
C:PHE203
|
4.7
|
25.7
|
1.0
|
C
|
C:TYR60
|
4.8
|
35.6
|
1.0
|
CE2
|
C:PHE203
|
4.8
|
26.5
|
1.0
|
CZ
|
C:PHE284
|
4.8
|
26.1
|
1.0
|
CB
|
C:TYR60
|
4.9
|
30.5
|
1.0
|
CZ
|
C:ARG99
|
4.9
|
32.6
|
1.0
|
|
Nickel binding site 8 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 8 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni1360
b:64.3
occ:1.00
|
N
|
D:GLY230
|
3.6
|
39.0
|
1.0
|
CE
|
E:LYS106
|
3.6
|
46.9
|
1.0
|
CA
|
D:GLY230
|
3.7
|
39.9
|
1.0
|
N
|
D:SER231
|
3.8
|
40.6
|
1.0
|
OG
|
D:SER231
|
3.9
|
40.7
|
1.0
|
CA
|
D:PHE228
|
4.0
|
37.2
|
1.0
|
C
|
D:PHE228
|
4.0
|
38.8
|
1.0
|
NZ
|
E:LYS106
|
4.2
|
48.5
|
1.0
|
C
|
D:GLY230
|
4.2
|
40.9
|
1.0
|
CB
|
D:PHE228
|
4.3
|
35.9
|
1.0
|
N
|
D:PRO229
|
4.3
|
39.7
|
1.0
|
CD1
|
D:PHE228
|
4.3
|
31.7
|
1.0
|
CD
|
D:PRO229
|
4.4
|
39.9
|
1.0
|
O
|
D:PHE228
|
4.4
|
38.2
|
1.0
|
C
|
D:PRO229
|
4.7
|
37.0
|
1.0
|
CD
|
E:LYS106
|
4.7
|
45.6
|
1.0
|
CB
|
D:SER231
|
4.8
|
40.2
|
1.0
|
CG
|
D:PHE228
|
4.8
|
32.7
|
1.0
|
CA
|
D:SER231
|
4.9
|
41.1
|
1.0
|
|
Nickel binding site 9 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 9 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 9 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni1361
b:80.2
occ:1.00
|
O
|
D:TYR60
|
4.0
|
40.4
|
1.0
|
CE1
|
D:PHE203
|
4.0
|
21.3
|
1.0
|
CZ
|
D:PHE203
|
4.2
|
22.0
|
1.0
|
CD1
|
D:PHE203
|
4.5
|
19.9
|
1.0
|
CE2
|
D:PHE284
|
4.5
|
25.4
|
1.0
|
CB
|
D:TYR60
|
4.7
|
30.5
|
1.0
|
CE2
|
D:PHE203
|
4.8
|
20.9
|
1.0
|
NE
|
D:ARG99
|
4.8
|
41.2
|
1.0
|
C
|
D:TYR60
|
4.8
|
38.3
|
1.0
|
OD1
|
D:ASP64
|
5.0
|
39.3
|
1.0
|
CZ
|
D:PHE284
|
5.0
|
25.8
|
1.0
|
|
Nickel binding site 10 out
of 15 in 5fpv
Go back to
Nickel Binding Sites List in 5fpv
Nickel binding site 10 out
of 15 in the Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 10 of Crystal Structure of Human JMJD2A in Complex with Compound KDOAM20A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni1362
b:0.4
occ:1.00
|
O
|
D:HOH2039
|
3.3
|
27.0
|
1.0
|
O
|
D:HOH2030
|
3.5
|
29.6
|
1.0
|
O
|
D:HOH2068
|
4.0
|
48.7
|
1.0
|
O
|
D:SER185
|
4.1
|
19.7
|
1.0
|
NE2
|
D:GLN74
|
4.3
|
20.4
|
1.0
|
CE2
|
D:TYR133
|
4.3
|
28.9
|
1.0
|
CD2
|
D:TYR133
|
4.4
|
27.4
|
1.0
|
CB
|
D:ALA135
|
4.5
|
29.7
|
1.0
|
CD1
|
D:ILE72
|
4.6
|
62.3
|
1.0
|
CA
|
D:PHE186
|
4.8
|
24.3
|
1.0
|
CB
|
D:PHE186
|
4.8
|
18.9
|
1.0
|
OD2
|
D:ASP136
|
4.9
|
37.1
|
1.0
|
NE2
|
D:GLN85
|
5.0
|
24.9
|
1.0
|
OAU
|
D:MMK1358
|
5.0
|
31.0
|
1.0
|
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ISSN: ISSN 1552-4450
PubMed: 27214403
DOI: 10.1038/NCHEMBIO.2087
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