Zinc in PDB 3q9e: Crystal Structure of H159A Apah Complexed with Acetylspermine
Protein crystallography data
The structure of Crystal Structure of H159A Apah Complexed with Acetylspermine, PDB code: 3q9e
was solved by
P.M.Lombardi,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
2.50
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
117.636,
119.496,
118.440,
98.23,
94.89,
115.73
|
|
R / Rfree (%)
|
19 /
23
|
Other elements in 3q9e:
The structure of Crystal Structure of H159A Apah Complexed with Acetylspermine also contains other interesting chemical elements:
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Zinc atom in the Crystal Structure of H159A Apah Complexed with Acetylspermine
(pdb code 3q9e). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the
Crystal Structure of H159A Apah Complexed with Acetylspermine, PDB code: 3q9e:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 1 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn344
b:76.8
occ:1.00
|
OD2
|
A:ASP284
|
2.0
|
35.9
|
1.0
|
|
OAA
|
A:SP5401
|
2.2
|
75.8
|
1.0
|
|
OD1
|
A:ASP195
|
2.3
|
28.6
|
1.0
|
|
ND1
|
A:HIS197
|
2.5
|
26.8
|
1.0
|
|
OD2
|
A:ASP195
|
2.8
|
28.8
|
1.0
|
|
CG
|
A:ASP195
|
2.9
|
27.3
|
1.0
|
|
CG
|
A:ASP284
|
3.1
|
34.1
|
1.0
|
|
CAC
|
A:SP5401
|
3.3
|
75.9
|
1.0
|
|
CE1
|
A:HIS197
|
3.4
|
28.9
|
1.0
|
|
CG
|
A:HIS197
|
3.5
|
26.5
|
1.0
|
|
OD1
|
A:ASP284
|
3.5
|
34.4
|
1.0
|
|
OH
|
A:TYR323
|
3.8
|
71.3
|
1.0
|
|
CB
|
A:HIS197
|
3.8
|
25.5
|
1.0
|
|
CA
|
A:GLY321
|
3.9
|
39.6
|
1.0
|
|
N
|
A:HIS197
|
3.9
|
26.3
|
1.0
|
|
NAD
|
A:SP5401
|
4.1
|
76.6
|
1.0
|
|
CAE
|
A:SP5401
|
4.1
|
76.1
|
1.0
|
|
CAB
|
A:SP5401
|
4.2
|
75.0
|
1.0
|
|
NE2
|
A:HIS158
|
4.3
|
33.1
|
1.0
|
|
CB
|
A:ASP284
|
4.3
|
31.3
|
1.0
|
|
N
|
A:PHE196
|
4.4
|
24.6
|
1.0
|
|
CB
|
A:ASP195
|
4.4
|
25.7
|
1.0
|
|
CE2
|
A:TYR323
|
4.5
|
71.4
|
1.0
|
|
CA
|
A:HIS197
|
4.5
|
27.2
|
1.0
|
|
N
|
A:GLY321
|
4.5
|
37.5
|
1.0
|
|
CE1
|
A:HIS158
|
4.5
|
33.0
|
1.0
|
|
NE2
|
A:HIS197
|
4.6
|
31.1
|
1.0
|
|
CZ
|
A:TYR323
|
4.6
|
71.8
|
1.0
|
|
CD2
|
A:HIS197
|
4.6
|
28.6
|
1.0
|
|
N
|
A:GLY322
|
4.6
|
45.7
|
1.0
|
|
CB
|
A:PHE196
|
4.7
|
24.7
|
1.0
|
|
C
|
A:GLY321
|
4.7
|
42.3
|
1.0
|
|
CA
|
A:PHE196
|
4.9
|
25.5
|
1.0
|
|
C
|
A:PHE196
|
4.9
|
26.5
|
1.0
|
|
C
|
A:ASP195
|
5.0
|
24.4
|
1.0
|
|
Zinc binding site 2 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 2 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn344
b:0.1
occ:1.00
|
ND1
|
B:HIS197
|
2.2
|
37.7
|
1.0
|
|
OD2
|
B:ASP284
|
2.4
|
48.8
|
1.0
|
|
OAA
|
B:SP5402
|
2.5
|
52.0
|
1.0
|
|
OD1
|
B:ASP195
|
2.7
|
36.3
|
1.0
|
|
OD2
|
B:ASP195
|
3.0
|
37.2
|
1.0
|
|
CAC
|
B:SP5402
|
3.2
|
51.3
|
1.0
|
|
CE1
|
B:HIS197
|
3.2
|
39.1
|
1.0
|
|
CG
|
B:ASP195
|
3.2
|
38.0
|
1.0
|
|
CG
|
B:HIS197
|
3.2
|
36.7
|
1.0
|
|
CG
|
B:ASP284
|
3.4
|
44.2
|
1.0
|
|
CB
|
B:HIS197
|
3.5
|
34.9
|
1.0
|
|
OD1
|
B:ASP284
|
3.7
|
45.5
|
1.0
|
|
N
|
B:HIS197
|
3.8
|
34.4
|
1.0
|
|
NAD
|
B:SP5402
|
3.8
|
50.9
|
1.0
|
|
CAE
|
B:SP5402
|
3.8
|
50.7
|
1.0
|
|
CAB
|
B:SP5402
|
4.1
|
50.6
|
1.0
|
|
CA
|
B:GLY321
|
4.1
|
39.3
|
1.0
|
|
NE2
|
B:HIS158
|
4.1
|
28.8
|
1.0
|
|
CA
|
B:HIS197
|
4.3
|
34.1
|
1.0
|
|
NE2
|
B:HIS197
|
4.3
|
40.8
|
1.0
|
|
CD2
|
B:HIS197
|
4.3
|
37.4
|
1.0
|
|
CE1
|
B:HIS158
|
4.4
|
27.8
|
1.0
|
|
CE2
|
B:TYR323
|
4.4
|
50.9
|
1.0
|
|
OH
|
B:TYR323
|
4.5
|
51.0
|
1.0
|
|
N
|
B:PHE196
|
4.5
|
33.1
|
1.0
|
|
N
|
B:GLY321
|
4.6
|
38.4
|
1.0
|
|
CB
|
B:ASP284
|
4.7
|
41.7
|
1.0
|
|
CB
|
B:ASP195
|
4.7
|
35.4
|
1.0
|
|
CB
|
B:PHE196
|
4.7
|
31.4
|
1.0
|
|
C
|
B:PHE196
|
4.8
|
34.8
|
1.0
|
|
CA
|
B:PHE196
|
4.9
|
32.9
|
1.0
|
|
CZ
|
B:TYR323
|
5.0
|
51.6
|
1.0
|
|
Zinc binding site 3 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 3 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn344
b:80.2
occ:1.00
|
OD2
|
C:ASP284
|
2.0
|
45.7
|
1.0
|
|
OAA
|
C:SP5403
|
2.1
|
63.2
|
1.0
|
|
OD1
|
C:ASP195
|
2.3
|
30.8
|
1.0
|
|
ND1
|
C:HIS197
|
2.5
|
33.5
|
1.0
|
|
OD2
|
C:ASP195
|
2.8
|
28.8
|
1.0
|
|
CG
|
C:ASP195
|
2.9
|
29.9
|
1.0
|
|
CG
|
C:ASP284
|
3.1
|
41.1
|
1.0
|
|
CAC
|
C:SP5403
|
3.2
|
63.3
|
1.0
|
|
CE1
|
C:HIS197
|
3.3
|
35.4
|
1.0
|
|
CG
|
C:HIS197
|
3.4
|
31.3
|
1.0
|
|
OD1
|
C:ASP284
|
3.6
|
40.6
|
1.0
|
|
OH
|
C:TYR323
|
3.6
|
48.0
|
1.0
|
|
CB
|
C:HIS197
|
3.7
|
27.9
|
1.0
|
|
CA
|
C:GLY321
|
3.8
|
39.0
|
1.0
|
|
N
|
C:HIS197
|
3.9
|
24.1
|
1.0
|
|
NAD
|
C:SP5403
|
4.1
|
63.4
|
1.0
|
|
CAE
|
C:SP5403
|
4.1
|
63.9
|
1.0
|
|
CAB
|
C:SP5403
|
4.1
|
62.7
|
1.0
|
|
CE2
|
C:TYR323
|
4.1
|
49.5
|
1.0
|
|
NE2
|
C:HIS158
|
4.2
|
31.5
|
1.0
|
|
CZ
|
C:TYR323
|
4.4
|
50.1
|
1.0
|
|
CB
|
C:ASP284
|
4.4
|
38.0
|
1.0
|
|
CB
|
C:ASP195
|
4.4
|
27.1
|
1.0
|
|
N
|
C:GLY321
|
4.4
|
36.6
|
1.0
|
|
N
|
C:PHE196
|
4.4
|
24.8
|
1.0
|
|
CA
|
C:HIS197
|
4.4
|
26.1
|
1.0
|
|
NE2
|
C:HIS197
|
4.4
|
36.9
|
1.0
|
|
CD2
|
C:HIS197
|
4.5
|
32.9
|
1.0
|
|
CE1
|
C:HIS158
|
4.6
|
30.2
|
1.0
|
|
CB
|
C:PHE196
|
4.8
|
23.4
|
1.0
|
|
C
|
C:GLY321
|
4.8
|
40.0
|
1.0
|
|
C
|
C:PHE196
|
4.9
|
25.2
|
1.0
|
|
N
|
C:GLY322
|
5.0
|
41.6
|
1.0
|
|
CA
|
C:PHE196
|
5.0
|
23.6
|
1.0
|
|
C
|
C:ASP195
|
5.0
|
25.4
|
1.0
|
|
Zinc binding site 4 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 4 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn344
b:74.7
occ:1.00
|
OD2
|
D:ASP284
|
2.2
|
38.9
|
1.0
|
|
OAA
|
D:SP5404
|
2.2
|
76.6
|
1.0
|
|
OD1
|
D:ASP195
|
2.3
|
34.5
|
1.0
|
|
ND1
|
D:HIS197
|
2.4
|
26.7
|
1.0
|
|
OD2
|
D:ASP195
|
3.0
|
35.3
|
1.0
|
|
CG
|
D:ASP195
|
3.0
|
34.0
|
1.0
|
|
CE1
|
D:HIS197
|
3.2
|
28.3
|
1.0
|
|
CAC
|
D:SP5404
|
3.2
|
76.3
|
1.0
|
|
CG
|
D:ASP284
|
3.3
|
34.9
|
1.0
|
|
CG
|
D:HIS197
|
3.4
|
28.0
|
1.0
|
|
OH
|
D:TYR323
|
3.6
|
73.5
|
1.0
|
|
CA
|
D:GLY321
|
3.8
|
36.0
|
1.0
|
|
OD1
|
D:ASP284
|
3.8
|
33.9
|
1.0
|
|
CB
|
D:HIS197
|
3.8
|
27.4
|
1.0
|
|
CAB
|
D:SP5404
|
4.0
|
76.8
|
1.0
|
|
N
|
D:HIS197
|
4.1
|
27.7
|
1.0
|
|
NAD
|
D:SP5404
|
4.1
|
75.8
|
1.0
|
|
NE2
|
D:HIS158
|
4.1
|
30.7
|
1.0
|
|
CAE
|
D:SP5404
|
4.2
|
74.8
|
1.0
|
|
NE2
|
D:HIS197
|
4.3
|
28.2
|
1.0
|
|
CE1
|
D:HIS158
|
4.3
|
30.6
|
1.0
|
|
N
|
D:GLY321
|
4.4
|
33.4
|
1.0
|
|
CB
|
D:ASP195
|
4.4
|
31.7
|
1.0
|
|
CZ
|
D:TYR323
|
4.5
|
73.6
|
1.0
|
|
CD2
|
D:HIS197
|
4.5
|
27.3
|
1.0
|
|
CE2
|
D:TYR323
|
4.6
|
73.0
|
1.0
|
|
CB
|
D:ASP284
|
4.6
|
31.4
|
1.0
|
|
CA
|
D:HIS197
|
4.6
|
28.6
|
1.0
|
|
N
|
D:PHE196
|
4.6
|
29.1
|
1.0
|
|
C
|
D:GLY321
|
4.7
|
38.0
|
1.0
|
|
N
|
D:GLY322
|
4.7
|
40.6
|
1.0
|
|
CB
|
D:PHE196
|
5.0
|
27.1
|
1.0
|
|
Zinc binding site 5 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 5 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn344
b:88.8
occ:1.00
|
OD1
|
E:ASP195
|
2.2
|
38.7
|
1.0
|
|
ND1
|
E:HIS197
|
2.3
|
37.6
|
1.0
|
|
OD2
|
E:ASP284
|
2.3
|
47.3
|
1.0
|
|
OAA
|
E:SP5405
|
2.6
|
61.4
|
1.0
|
|
CG
|
E:ASP195
|
3.0
|
36.4
|
1.0
|
|
CE1
|
E:HIS197
|
3.2
|
38.7
|
1.0
|
|
OD2
|
E:ASP195
|
3.2
|
38.7
|
1.0
|
|
CG
|
E:HIS197
|
3.3
|
36.2
|
1.0
|
|
CAC
|
E:SP5405
|
3.4
|
60.6
|
1.0
|
|
CG
|
E:ASP284
|
3.4
|
44.0
|
1.0
|
|
CB
|
E:HIS197
|
3.6
|
35.2
|
1.0
|
|
N
|
E:HIS197
|
3.8
|
33.8
|
1.0
|
|
OD1
|
E:ASP284
|
3.8
|
44.9
|
1.0
|
|
NAD
|
E:SP5405
|
4.0
|
60.2
|
1.0
|
|
CAE
|
E:SP5405
|
4.0
|
58.8
|
1.0
|
|
CA
|
E:GLY321
|
4.2
|
34.3
|
1.0
|
|
NE2
|
E:HIS158
|
4.2
|
35.6
|
1.0
|
|
CAB
|
E:SP5405
|
4.2
|
59.7
|
1.0
|
|
NE2
|
E:HIS197
|
4.3
|
38.6
|
1.0
|
|
CD2
|
E:HIS197
|
4.3
|
36.4
|
1.0
|
|
CA
|
E:HIS197
|
4.3
|
35.1
|
1.0
|
|
N
|
E:PHE196
|
4.4
|
31.8
|
1.0
|
|
CE1
|
E:HIS158
|
4.4
|
34.3
|
1.0
|
|
OH
|
E:TYR323
|
4.5
|
43.6
|
1.0
|
|
CB
|
E:ASP195
|
4.5
|
34.5
|
1.0
|
|
CE2
|
E:TYR323
|
4.5
|
44.1
|
1.0
|
|
CB
|
E:PHE196
|
4.6
|
31.6
|
1.0
|
|
N
|
E:GLY321
|
4.7
|
33.4
|
1.0
|
|
CB
|
E:ASP284
|
4.7
|
41.8
|
1.0
|
|
C
|
E:PHE196
|
4.8
|
33.6
|
1.0
|
|
CA
|
E:PHE196
|
4.8
|
32.4
|
1.0
|
|
C
|
E:ASP195
|
4.9
|
31.6
|
1.0
|
|
CZ
|
E:TYR323
|
5.0
|
43.8
|
1.0
|
|
Zinc binding site 6 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 6 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn344
b:79.8
occ:1.00
|
OAA
|
F:SP5406
|
2.1
|
77.6
|
1.0
|
|
OD2
|
F:ASP284
|
2.1
|
41.9
|
1.0
|
|
OD1
|
F:ASP195
|
2.4
|
34.4
|
1.0
|
|
ND1
|
F:HIS197
|
2.5
|
36.2
|
1.0
|
|
OD2
|
F:ASP195
|
2.7
|
34.6
|
1.0
|
|
CG
|
F:ASP195
|
2.9
|
33.8
|
1.0
|
|
CAC
|
F:SP5406
|
3.1
|
77.7
|
1.0
|
|
CG
|
F:ASP284
|
3.2
|
39.2
|
1.0
|
|
CE1
|
F:HIS197
|
3.3
|
37.9
|
1.0
|
|
OH
|
F:TYR323
|
3.4
|
72.4
|
1.0
|
|
CG
|
F:HIS197
|
3.5
|
35.2
|
1.0
|
|
OD1
|
F:ASP284
|
3.5
|
37.9
|
1.0
|
|
CB
|
F:HIS197
|
3.9
|
32.4
|
1.0
|
|
CA
|
F:GLY321
|
3.9
|
41.6
|
1.0
|
|
CAE
|
F:SP5406
|
3.9
|
78.2
|
1.0
|
|
NAD
|
F:SP5406
|
3.9
|
78.3
|
1.0
|
|
N
|
F:HIS197
|
4.1
|
33.0
|
1.0
|
|
CAB
|
F:SP5406
|
4.1
|
77.6
|
1.0
|
|
NE2
|
F:HIS158
|
4.3
|
33.7
|
1.0
|
|
CZ
|
F:TYR323
|
4.3
|
72.2
|
1.0
|
|
CB
|
F:ASP195
|
4.4
|
32.7
|
1.0
|
|
N
|
F:GLY321
|
4.4
|
38.2
|
1.0
|
|
NE2
|
F:HIS197
|
4.5
|
36.9
|
1.0
|
|
CB
|
F:ASP284
|
4.5
|
37.8
|
1.0
|
|
CD2
|
F:HIS197
|
4.6
|
36.3
|
1.0
|
|
CA
|
F:HIS197
|
4.6
|
32.6
|
1.0
|
|
C
|
F:GLY321
|
4.6
|
43.4
|
1.0
|
|
CE2
|
F:TYR323
|
4.6
|
72.6
|
1.0
|
|
N
|
F:GLY322
|
4.6
|
46.2
|
1.0
|
|
N
|
F:PHE196
|
4.6
|
32.8
|
1.0
|
|
CE1
|
F:HIS158
|
4.6
|
32.1
|
1.0
|
|
Zinc binding site 7 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 7 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn344
b:94.8
occ:1.00
|
OD1
|
G:ASP195
|
2.2
|
36.1
|
1.0
|
|
OD2
|
G:ASP284
|
2.4
|
47.8
|
1.0
|
|
OAA
|
G:SP5407
|
2.4
|
68.6
|
1.0
|
|
ND1
|
G:HIS197
|
2.6
|
32.6
|
1.0
|
|
OD2
|
G:ASP195
|
2.8
|
33.7
|
1.0
|
|
CG
|
G:ASP195
|
2.8
|
33.0
|
1.0
|
|
CAC
|
G:SP5407
|
3.0
|
67.6
|
1.0
|
|
CG
|
G:HIS197
|
3.5
|
31.4
|
1.0
|
|
CG
|
G:ASP284
|
3.5
|
43.9
|
1.0
|
|
CE1
|
G:HIS197
|
3.6
|
33.9
|
1.0
|
|
CB
|
G:HIS197
|
3.6
|
30.4
|
1.0
|
|
CAB
|
G:SP5407
|
3.7
|
66.7
|
1.0
|
|
NAD
|
G:SP5407
|
3.7
|
67.2
|
1.0
|
|
OD1
|
G:ASP284
|
3.8
|
43.8
|
1.0
|
|
N
|
G:HIS197
|
3.9
|
31.7
|
1.0
|
|
CAE
|
G:SP5407
|
3.9
|
65.8
|
1.0
|
|
NE2
|
G:HIS158
|
4.0
|
34.1
|
1.0
|
|
CA
|
G:GLY321
|
4.0
|
37.0
|
1.0
|
|
OH
|
G:TYR323
|
4.2
|
47.4
|
1.0
|
|
CB
|
G:ASP195
|
4.3
|
31.0
|
1.0
|
|
CA
|
G:HIS197
|
4.3
|
30.5
|
1.0
|
|
CE1
|
G:HIS158
|
4.4
|
33.2
|
1.0
|
|
N
|
G:GLY321
|
4.4
|
36.3
|
1.0
|
|
CE2
|
G:TYR323
|
4.5
|
45.9
|
1.0
|
|
N
|
G:PHE196
|
4.5
|
29.3
|
1.0
|
|
CD2
|
G:HIS197
|
4.6
|
33.3
|
1.0
|
|
NE2
|
G:HIS197
|
4.7
|
34.1
|
1.0
|
|
CB
|
G:ASP284
|
4.8
|
40.7
|
1.0
|
|
CZ
|
G:TYR323
|
4.9
|
46.1
|
1.0
|
|
O
|
G:HIS197
|
4.9
|
30.1
|
1.0
|
|
C
|
G:PHE196
|
4.9
|
32.5
|
1.0
|
|
C
|
G:ASP195
|
5.0
|
29.3
|
1.0
|
|
Zinc binding site 8 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 8 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 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 H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn344
b:75.9
occ:1.00
|
OD2
|
H:ASP284
|
2.3
|
41.1
|
1.0
|
|
OAA
|
H:SP5408
|
2.3
|
64.6
|
1.0
|
|
OD1
|
H:ASP195
|
2.4
|
39.8
|
1.0
|
|
OD2
|
H:ASP195
|
2.5
|
40.9
|
1.0
|
|
ND1
|
H:HIS197
|
2.7
|
33.1
|
1.0
|
|
CG
|
H:ASP195
|
2.8
|
39.2
|
1.0
|
|
CAC
|
H:SP5408
|
3.2
|
62.4
|
1.0
|
|
CG
|
H:ASP284
|
3.4
|
37.3
|
1.0
|
|
CG
|
H:HIS197
|
3.6
|
33.8
|
1.0
|
|
CE1
|
H:HIS197
|
3.7
|
34.8
|
1.0
|
|
CA
|
H:GLY321
|
3.7
|
40.9
|
1.0
|
|
CB
|
H:HIS197
|
3.8
|
32.3
|
1.0
|
|
OD1
|
H:ASP284
|
3.8
|
35.2
|
1.0
|
|
CAB
|
H:SP5408
|
4.0
|
61.4
|
1.0
|
|
NE2
|
H:HIS158
|
4.0
|
38.2
|
1.0
|
|
NAD
|
H:SP5408
|
4.0
|
62.0
|
1.0
|
|
OH
|
H:TYR323
|
4.0
|
51.6
|
1.0
|
|
N
|
H:HIS197
|
4.1
|
31.5
|
1.0
|
|
N
|
H:GLY321
|
4.1
|
40.4
|
1.0
|
|
CAE
|
H:SP5408
|
4.2
|
60.4
|
1.0
|
|
CE1
|
H:HIS158
|
4.3
|
38.1
|
1.0
|
|
CB
|
H:ASP195
|
4.3
|
35.7
|
1.0
|
|
CE2
|
H:TYR323
|
4.4
|
52.4
|
1.0
|
|
CA
|
H:HIS197
|
4.6
|
32.1
|
1.0
|
|
CB
|
H:ASP284
|
4.6
|
36.8
|
1.0
|
|
N
|
H:PHE196
|
4.6
|
31.7
|
1.0
|
|
CZ
|
H:TYR323
|
4.7
|
52.2
|
1.0
|
|
C
|
H:GLY321
|
4.7
|
41.8
|
1.0
|
|
CD2
|
H:HIS197
|
4.8
|
35.2
|
1.0
|
|
NE2
|
H:HIS197
|
4.8
|
36.2
|
1.0
|
|
N
|
H:GLY322
|
5.0
|
42.7
|
1.0
|
|
Zinc binding site 9 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 9 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Crystal Structure of H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn344
b:0.1
occ:1.00
|
OD2
|
I:ASP284
|
2.2
|
41.3
|
1.0
|
|
OAA
|
I:SP5409
|
2.2
|
45.7
|
1.0
|
|
ND1
|
I:HIS197
|
2.5
|
35.6
|
1.0
|
|
OD1
|
I:ASP195
|
2.5
|
28.2
|
1.0
|
|
OD2
|
I:ASP195
|
2.8
|
30.8
|
1.0
|
|
CAC
|
I:SP5409
|
3.0
|
43.9
|
1.0
|
|
CG
|
I:ASP195
|
3.0
|
31.1
|
1.0
|
|
CE1
|
I:HIS197
|
3.1
|
37.0
|
1.0
|
|
CG
|
I:ASP284
|
3.2
|
35.6
|
1.0
|
|
CG
|
I:HIS197
|
3.6
|
31.5
|
1.0
|
|
OD1
|
I:ASP284
|
3.6
|
34.4
|
1.0
|
|
CA
|
I:GLY321
|
3.7
|
34.2
|
1.0
|
|
CAB
|
I:SP5409
|
3.8
|
42.6
|
1.0
|
|
NAD
|
I:SP5409
|
3.8
|
44.5
|
1.0
|
|
OH
|
I:TYR323
|
3.8
|
29.0
|
1.0
|
|
CAE
|
I:SP5409
|
3.9
|
43.5
|
1.0
|
|
CE2
|
I:TYR323
|
4.0
|
30.0
|
1.0
|
|
NE2
|
I:HIS158
|
4.1
|
30.3
|
1.0
|
|
CB
|
I:HIS197
|
4.2
|
27.9
|
1.0
|
|
N
|
I:GLY321
|
4.2
|
33.4
|
1.0
|
|
NE2
|
I:HIS197
|
4.2
|
37.1
|
1.0
|
|
N
|
I:HIS197
|
4.3
|
27.1
|
1.0
|
|
CZ
|
I:TYR323
|
4.4
|
30.3
|
1.0
|
|
CB
|
I:ASP284
|
4.5
|
34.1
|
1.0
|
|
CB
|
I:ASP195
|
4.5
|
29.7
|
1.0
|
|
CD2
|
I:HIS197
|
4.5
|
34.0
|
1.0
|
|
CE1
|
I:HIS158
|
4.6
|
26.9
|
1.0
|
|
C
|
I:GLY321
|
4.7
|
36.4
|
1.0
|
|
N
|
I:PHE196
|
4.7
|
26.6
|
1.0
|
|
N
|
I:GLY322
|
4.8
|
37.4
|
1.0
|
|
CA
|
I:HIS197
|
4.9
|
28.6
|
1.0
|
|
Zinc binding site 10 out
of 12 in 3q9e
Go back to
Zinc Binding Sites List in 3q9e
Zinc binding site 10 out
of 12 in the Crystal Structure of H159A Apah Complexed with Acetylspermine
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Crystal Structure of H159A Apah Complexed with Acetylspermine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn344
b:0.6
occ:1.00
|
OAA
|
J:SP5410
|
2.1
|
57.1
|
1.0
|
|
OD1
|
J:ASP195
|
2.3
|
33.1
|
1.0
|
|
OD2
|
J:ASP284
|
2.4
|
45.2
|
1.0
|
|
ND1
|
J:HIS197
|
2.6
|
42.3
|
1.0
|
|
OD2
|
J:ASP195
|
2.6
|
33.6
|
1.0
|
|
CG
|
J:ASP195
|
2.8
|
34.3
|
1.0
|
|
CAC
|
J:SP5410
|
3.0
|
55.7
|
1.0
|
|
CE1
|
J:HIS197
|
3.4
|
41.9
|
1.0
|
|
CG
|
J:ASP284
|
3.5
|
43.3
|
1.0
|
|
CG
|
J:HIS197
|
3.6
|
40.3
|
1.0
|
|
CAB
|
J:SP5410
|
3.8
|
56.6
|
1.0
|
|
CA
|
J:GLY321
|
3.8
|
45.0
|
1.0
|
|
OD1
|
J:ASP284
|
3.8
|
42.3
|
1.0
|
|
OH
|
J:TYR323
|
3.8
|
51.1
|
1.0
|
|
CB
|
J:HIS197
|
3.9
|
36.3
|
1.0
|
|
NE2
|
J:HIS158
|
3.9
|
33.7
|
1.0
|
|
NAD
|
J:SP5410
|
3.9
|
55.7
|
1.0
|
|
CAE
|
J:SP5410
|
4.1
|
53.9
|
1.0
|
|
N
|
J:HIS197
|
4.2
|
35.6
|
1.0
|
|
CE1
|
J:HIS158
|
4.2
|
31.7
|
1.0
|
|
CB
|
J:ASP195
|
4.3
|
33.8
|
1.0
|
|
CE2
|
J:TYR323
|
4.3
|
51.8
|
1.0
|
|
N
|
J:GLY321
|
4.3
|
43.6
|
1.0
|
|
NE2
|
J:HIS197
|
4.5
|
42.0
|
1.0
|
|
CZ
|
J:TYR323
|
4.6
|
51.5
|
1.0
|
|
CD2
|
J:HIS197
|
4.6
|
41.2
|
1.0
|
|
CA
|
J:HIS197
|
4.7
|
36.2
|
1.0
|
|
CB
|
J:ASP284
|
4.8
|
41.9
|
1.0
|
|
N
|
J:PHE196
|
4.8
|
33.8
|
1.0
|
|
C
|
J:GLY321
|
4.8
|
46.4
|
1.0
|
|
N
|
J:GLY322
|
5.0
|
47.9
|
1.0
|
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Reference:
P.M.Lombardi,
H.D.Angell,
D.A.Whittington,
E.F.Flynn,
K.R.Rajashankar,
D.W.Christianson.
Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases . Biochemistry V. 50 1808 2011.
ISSN: ISSN 0006-2960
PubMed: 21268586
DOI: 10.1021/BI101859K
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