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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:

Magnesium (Mg) 5 atoms
Potassium (K) 8 atoms

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

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