Zinc in PDB 6pht: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid
Protein crystallography data
The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid, PDB code: 6pht
was solved by
J.D.Osko,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
65.44 /
1.80
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.630,
163.480,
65.720,
90.00,
94.33,
90.00
|
R / Rfree (%)
|
19.4 /
22.6
|
Other elements in 6pht:
The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid
(pdb code 6pht). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid, PDB code: 6pht:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6pht
Go back to
Zinc Binding Sites List in 6pht
Zinc binding site 1 out
of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid
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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn406
b:20.0
occ:0.30
|
OD2
|
A:ASP284
|
1.9
|
9.5
|
1.0
|
OD1
|
A:ASP195
|
2.0
|
6.7
|
1.0
|
ND1
|
A:HIS197
|
2.1
|
11.7
|
1.0
|
O13
|
A:OKP401
|
2.1
|
13.2
|
1.0
|
B11
|
A:OKP401
|
2.2
|
13.2
|
1.0
|
OD2
|
A:ASP195
|
2.4
|
10.5
|
1.0
|
O12
|
A:OKP401
|
2.5
|
11.6
|
1.0
|
CG
|
A:ASP195
|
2.5
|
8.8
|
1.0
|
CE1
|
A:HIS197
|
2.8
|
9.4
|
1.0
|
CG
|
A:ASP284
|
3.0
|
12.2
|
1.0
|
CG
|
A:HIS197
|
3.2
|
8.3
|
1.0
|
C10
|
A:OKP401
|
3.3
|
13.2
|
1.0
|
OD1
|
A:ASP284
|
3.5
|
10.6
|
1.0
|
N
|
A:HIS197
|
3.8
|
7.7
|
1.0
|
CB
|
A:HIS197
|
3.8
|
8.6
|
1.0
|
NE2
|
A:HIS197
|
4.0
|
6.6
|
1.0
|
C09
|
A:OKP401
|
4.0
|
16.1
|
1.0
|
CB
|
A:ASP195
|
4.1
|
9.3
|
1.0
|
NE2
|
A:HIS158
|
4.1
|
10.4
|
1.0
|
N
|
A:PHE196
|
4.1
|
8.3
|
1.0
|
CA
|
A:GLY321
|
4.2
|
12.2
|
1.0
|
CD2
|
A:HIS197
|
4.2
|
4.9
|
1.0
|
CB
|
A:ASP284
|
4.3
|
11.7
|
1.0
|
CA
|
A:HIS197
|
4.4
|
7.0
|
1.0
|
CE2
|
A:TYR323
|
4.4
|
10.0
|
1.0
|
CE1
|
A:HIS158
|
4.4
|
8.5
|
1.0
|
OH
|
A:TYR323
|
4.5
|
12.1
|
1.0
|
N
|
A:GLY321
|
4.5
|
10.9
|
1.0
|
CB
|
A:PHE196
|
4.6
|
8.8
|
1.0
|
C
|
A:PHE196
|
4.6
|
8.5
|
1.0
|
CA
|
A:PHE196
|
4.7
|
8.0
|
1.0
|
C
|
A:ASP195
|
4.7
|
7.7
|
1.0
|
NE2
|
A:HIS159
|
4.8
|
9.8
|
1.0
|
CA
|
A:ASP195
|
4.8
|
8.9
|
1.0
|
CZ
|
A:TYR323
|
4.9
|
8.9
|
1.0
|
C
|
A:GLY321
|
5.0
|
13.1
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6pht
Go back to
Zinc Binding Sites List in 6pht
Zinc binding site 2 out
of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid
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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn405
b:19.3
occ:0.30
|
OD2
|
B:ASP284
|
1.9
|
14.8
|
1.0
|
OD1
|
B:ASP195
|
2.0
|
10.2
|
1.0
|
ND1
|
B:HIS197
|
2.1
|
10.0
|
1.0
|
O12
|
B:OKP401
|
2.2
|
13.9
|
1.0
|
B11
|
B:OKP401
|
2.3
|
13.3
|
1.0
|
O13
|
B:OKP401
|
2.4
|
13.3
|
1.0
|
OD2
|
B:ASP195
|
2.6
|
7.3
|
1.0
|
CG
|
B:ASP195
|
2.6
|
10.6
|
1.0
|
CE1
|
B:HIS197
|
2.9
|
12.4
|
1.0
|
CG
|
B:ASP284
|
3.0
|
8.2
|
1.0
|
CG
|
B:HIS197
|
3.2
|
8.4
|
1.0
|
C10
|
B:OKP401
|
3.4
|
17.4
|
1.0
|
OD1
|
B:ASP284
|
3.4
|
8.6
|
1.0
|
CB
|
B:HIS197
|
3.7
|
9.2
|
1.0
|
N
|
B:HIS197
|
3.7
|
7.2
|
1.0
|
CB
|
B:ASP195
|
4.1
|
10.0
|
1.0
|
NE2
|
B:HIS197
|
4.1
|
9.1
|
1.0
|
N
|
B:PHE196
|
4.1
|
5.6
|
1.0
|
NE2
|
B:HIS158
|
4.2
|
12.2
|
1.0
|
CD2
|
B:HIS197
|
4.3
|
9.0
|
1.0
|
C09
|
B:OKP401
|
4.3
|
11.8
|
1.0
|
CB
|
B:ASP284
|
4.3
|
12.1
|
1.0
|
CA
|
B:GLY321
|
4.3
|
8.8
|
1.0
|
CA
|
B:HIS197
|
4.3
|
7.4
|
1.0
|
CE2
|
B:TYR323
|
4.4
|
8.9
|
1.0
|
CE1
|
B:HIS158
|
4.4
|
9.1
|
1.0
|
OH
|
B:TYR323
|
4.5
|
13.3
|
1.0
|
CB
|
B:PHE196
|
4.5
|
9.0
|
1.0
|
C
|
B:PHE196
|
4.6
|
9.3
|
1.0
|
C
|
B:ASP195
|
4.6
|
9.6
|
1.0
|
CA
|
B:PHE196
|
4.6
|
7.6
|
1.0
|
N
|
B:GLY321
|
4.7
|
9.0
|
1.0
|
CA
|
B:ASP195
|
4.8
|
9.4
|
1.0
|
NE2
|
B:HIS159
|
4.8
|
10.7
|
1.0
|
CZ
|
B:TYR323
|
5.0
|
11.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6pht
Go back to
Zinc Binding Sites List in 6pht
Zinc binding site 3 out
of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid
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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn405
b:13.6
occ:0.31
|
OD2
|
C:ASP284
|
1.9
|
10.7
|
1.0
|
O13
|
C:OKP401
|
2.0
|
13.4
|
1.0
|
OD1
|
C:ASP195
|
2.0
|
6.7
|
1.0
|
ND1
|
C:HIS197
|
2.2
|
7.4
|
1.0
|
B11
|
C:OKP401
|
2.2
|
12.9
|
1.0
|
O12
|
C:OKP401
|
2.6
|
11.8
|
1.0
|
OD2
|
C:ASP195
|
2.6
|
7.6
|
1.0
|
CG
|
C:ASP195
|
2.6
|
7.9
|
1.0
|
C10
|
C:OKP401
|
2.9
|
16.9
|
1.0
|
CE1
|
C:HIS197
|
2.9
|
9.8
|
1.0
|
CG
|
C:ASP284
|
2.9
|
11.8
|
1.0
|
CG
|
C:HIS197
|
3.3
|
7.9
|
1.0
|
OD1
|
C:ASP284
|
3.4
|
8.6
|
1.0
|
CB
|
C:HIS197
|
3.8
|
6.3
|
1.0
|
N
|
C:HIS197
|
3.9
|
7.0
|
1.0
|
NE2
|
C:HIS197
|
4.1
|
8.3
|
1.0
|
CB
|
C:ASP195
|
4.1
|
7.5
|
1.0
|
N
|
C:PHE196
|
4.2
|
5.9
|
1.0
|
CB
|
C:ASP284
|
4.2
|
10.7
|
1.0
|
CA
|
C:GLY321
|
4.2
|
12.0
|
1.0
|
NE2
|
C:HIS158
|
4.2
|
9.4
|
1.0
|
C09
|
C:OKP401
|
4.3
|
17.2
|
1.0
|
CD2
|
C:HIS197
|
4.3
|
8.4
|
1.0
|
CE1
|
C:TYR323
|
4.3
|
10.1
|
1.0
|
CA
|
C:HIS197
|
4.5
|
5.6
|
1.0
|
OH
|
C:TYR323
|
4.5
|
10.9
|
1.0
|
CE1
|
C:HIS158
|
4.5
|
6.7
|
1.0
|
N
|
C:GLY321
|
4.6
|
6.9
|
1.0
|
CB
|
C:PHE196
|
4.7
|
7.3
|
1.0
|
C
|
C:PHE196
|
4.7
|
6.1
|
1.0
|
C
|
C:ASP195
|
4.7
|
6.9
|
1.0
|
CA
|
C:PHE196
|
4.7
|
7.6
|
1.0
|
NE2
|
C:HIS159
|
4.8
|
9.0
|
1.0
|
CA
|
C:ASP195
|
4.8
|
7.0
|
1.0
|
CZ
|
C:TYR323
|
4.9
|
8.5
|
1.0
|
C08
|
C:OKP401
|
5.0
|
17.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6pht
Go back to
Zinc Binding Sites List in 6pht
Zinc binding site 4 out
of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid
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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn405
b:20.4
occ:0.36
|
OD1
|
D:ASP195
|
1.8
|
10.5
|
1.0
|
OD2
|
D:ASP284
|
2.0
|
11.4
|
1.0
|
O12
|
D:OKP401
|
2.1
|
15.0
|
1.0
|
ND1
|
D:HIS197
|
2.2
|
6.8
|
1.0
|
B11
|
D:OKP401
|
2.3
|
10.1
|
1.0
|
O13
|
D:OKP401
|
2.4
|
12.3
|
1.0
|
CG
|
D:ASP195
|
2.5
|
12.0
|
1.0
|
OD2
|
D:ASP195
|
2.5
|
9.9
|
1.0
|
CG
|
D:ASP284
|
3.0
|
12.2
|
1.0
|
CE1
|
D:HIS197
|
3.1
|
7.9
|
1.0
|
CG
|
D:HIS197
|
3.3
|
5.5
|
1.0
|
C10
|
D:OKP401
|
3.4
|
12.0
|
1.0
|
OD1
|
D:ASP284
|
3.5
|
11.9
|
1.0
|
CB
|
D:HIS197
|
3.7
|
7.7
|
1.0
|
N
|
D:HIS197
|
3.7
|
5.3
|
1.0
|
CB
|
D:ASP195
|
4.0
|
9.2
|
1.0
|
N
|
D:PHE196
|
4.1
|
6.5
|
1.0
|
NE2
|
D:HIS158
|
4.1
|
11.0
|
1.0
|
C09
|
D:OKP401
|
4.1
|
14.7
|
1.0
|
NE2
|
D:HIS197
|
4.2
|
11.2
|
1.0
|
CA
|
D:GLY321
|
4.3
|
9.9
|
1.0
|
CE1
|
D:HIS158
|
4.3
|
10.4
|
1.0
|
CB
|
D:ASP284
|
4.3
|
10.6
|
1.0
|
CA
|
D:HIS197
|
4.4
|
8.4
|
1.0
|
CD2
|
D:HIS197
|
4.4
|
5.4
|
1.0
|
CE2
|
D:TYR323
|
4.4
|
11.4
|
1.0
|
OH
|
D:TYR323
|
4.4
|
12.2
|
1.0
|
CB
|
D:PHE196
|
4.6
|
6.7
|
1.0
|
N
|
D:GLY321
|
4.6
|
10.1
|
1.0
|
C
|
D:ASP195
|
4.6
|
9.9
|
1.0
|
C
|
D:PHE196
|
4.6
|
8.6
|
1.0
|
CA
|
D:PHE196
|
4.7
|
7.9
|
1.0
|
CA
|
D:ASP195
|
4.7
|
10.6
|
1.0
|
NE2
|
D:HIS159
|
4.8
|
9.2
|
1.0
|
CZ
|
D:TYR323
|
4.9
|
11.7
|
1.0
|
|
Reference:
J.D.Osko,
B.W.Roose,
S.A.Shinsky,
D.W.Christianson.
Structure and Function of the Acetylpolyamine Amidohydrolase From the Deep Earth Halophilemarinobacter Subterrani. Biochemistry V. 58 3755 2019.
ISSN: ISSN 0006-2960
PubMed: 31436969
DOI: 10.1021/ACS.BIOCHEM.9B00582
Page generated: Tue Oct 29 05:08:11 2024
|