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Zinc in PDB 6pia: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide, PDB code: 6pia 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) 46.27 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.744, 163.170, 65.744, 90.00, 94.44, 90.00
R / Rfree (%) 17.5 / 21.2

Other elements in 6pia:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide 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 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide (pdb code 6pia). 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 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide, PDB code: 6pia:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6pia

Go back to Zinc Binding Sites List in 6pia
Zinc binding site 1 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide


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 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:10.7
occ:0.54
 OD2 A:ASP284 2.0 13.9 1.0
O14 A:XS6407 2.0 13.3 1.0
OD1 A:ASP195 2.0 14.1 1.0
ND1 A:HIS197 2.1 9.6 1.0
O12 A:XS6407 2.3 18.0 1.0
OD2 A:ASP195 2.6 11.1 1.0
CG A:ASP195 2.6 11.6 1.0
N13 A:XS6407 2.6 16.2 1.0
C11 A:XS6407 2.7 19.1 1.0
CE1 A:HIS197 2.9 10.2 1.0
CG A:ASP284 3.0 13.4 1.0
CG A:HIS197 3.2 11.7 1.0
OD1 A:ASP284 3.4 12.6 1.0
CB A:HIS197 3.7 13.1 1.0
N A:HIS197 3.8 8.3 1.0
C10 A:XS6407 4.1 20.3 1.0
NE2 A:HIS197 4.1 9.7 1.0
NE2 A:HIS158 4.1 11.4 1.0
CB A:ASP195 4.2 10.5 1.0
CA A:GLY321 4.2 10.5 1.0
N A:PHE196 4.2 9.9 1.0
CD2 A:HIS197 4.3 10.1 1.0
CB A:ASP284 4.3 11.6 1.0
CA A:HIS197 4.4 8.2 1.0
CE1 A:HIS158 4.5 11.4 1.0
N A:GLY321 4.5 11.6 1.0
OH A:TYR323 4.6 8.6 1.0
CE1 A:TYR323 4.6 11.3 1.0
CB A:PHE196 4.7 13.1 1.0
C A:PHE196 4.7 13.1 1.0
CA A:PHE196 4.8 11.1 1.0
C A:ASP195 4.8 10.7 1.0
NE2 A:HIS159 4.9 9.4 1.0
CA A:ASP195 4.9 11.4 1.0
C A:GLY321 4.9 14.9 1.0

Zinc binding site 2 out of 4 in 6pia

Go back to Zinc Binding Sites List in 6pia
Zinc binding site 2 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide


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 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:12.2
occ:0.56
 OD1 B:ASP195 2.0 14.2 1.0
OD2 B:ASP284 2.0 13.7 1.0
O14 B:XS6406 2.0 17.0 1.0
ND1 B:HIS197 2.1 10.2 1.0
O12 B:XS6406 2.3 20.2 1.0
OD2 B:ASP195 2.6 12.6 1.0
CG B:ASP195 2.6 16.4 1.0
N13 B:XS6406 2.6 18.5 1.0
C11 B:XS6406 2.7 22.4 1.0
CE1 B:HIS197 3.0 10.2 1.0
CG B:ASP284 3.0 13.9 1.0
CG B:HIS197 3.2 10.2 1.0
OD1 B:ASP284 3.4 13.6 1.0
CB B:HIS197 3.6 9.8 1.0
N B:HIS197 3.7 10.4 1.0
CB B:ASP195 4.1 17.3 1.0
C10 B:XS6406 4.1 22.8 1.0
N B:PHE196 4.1 9.6 1.0
NE2 B:HIS158 4.1 12.8 1.0
NE2 B:HIS197 4.2 14.3 1.0
CA B:GLY321 4.2 15.6 1.0
CD2 B:HIS197 4.3 11.6 1.0
CA B:HIS197 4.3 12.2 1.0
CB B:ASP284 4.3 12.5 1.0
CE1 B:HIS158 4.4 13.0 1.0
N B:GLY321 4.5 13.9 1.0
CB B:PHE196 4.6 9.7 1.0
C B:PHE196 4.6 12.8 1.0
OH B:TYR323 4.7 12.2 1.0
CA B:PHE196 4.7 10.1 1.0
C B:ASP195 4.7 12.5 1.0
CE1 B:TYR323 4.7 14.6 1.0
CA B:ASP195 4.8 10.0 1.0
NE2 B:HIS159 4.9 12.1 1.0
C B:GLY321 4.9 18.6 1.0
C9 B:XS6406 4.9 17.1 1.0

Zinc binding site 3 out of 4 in 6pia

Go back to Zinc Binding Sites List in 6pia
Zinc binding site 3 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide


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 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:10.5
occ:0.53
 OD1 C:ASP195 2.0 14.6 1.0
OD2 C:ASP284 2.0 14.6 1.0
O14 C:XS6406 2.0 11.8 1.0
ND1 C:HIS197 2.1 11.7 1.0
O12 C:XS6406 2.2 16.4 1.0
CG C:ASP195 2.6 12.8 1.0
OD2 C:ASP195 2.6 12.2 1.0
N13 C:XS6406 2.7 13.7 1.0
C11 C:XS6406 2.7 15.8 1.0
CE1 C:HIS197 2.9 11.4 1.0
CG C:ASP284 3.1 13.7 1.0
CG C:HIS197 3.2 12.8 1.0
OD1 C:ASP284 3.5 15.2 1.0
CB C:HIS197 3.7 11.8 1.0
N C:HIS197 3.8 11.2 1.0
NE2 C:HIS197 4.1 11.7 1.0
CB C:ASP195 4.1 9.4 1.0
NE2 C:HIS158 4.1 14.8 1.0
C10 C:XS6406 4.2 21.8 1.0
CA C:GLY321 4.2 7.9 1.0
CD2 C:HIS197 4.2 10.8 1.0
N C:PHE196 4.2 12.1 1.0
CB C:ASP284 4.4 15.0 1.0
CA C:HIS197 4.4 9.6 1.0
CE1 C:HIS158 4.5 9.0 1.0
N C:GLY321 4.5 13.5 1.0
OH C:TYR323 4.6 11.9 1.0
CE1 C:TYR323 4.6 15.4 1.0
CB C:PHE196 4.7 10.3 1.0
C C:PHE196 4.7 13.8 1.0
C C:ASP195 4.8 12.8 1.0
CA C:PHE196 4.8 10.9 1.0
NE2 C:HIS159 4.9 10.0 1.0
CA C:ASP195 4.9 14.1 1.0
C C:GLY321 4.9 16.0 1.0

Zinc binding site 4 out of 4 in 6pia

Go back to Zinc Binding Sites List in 6pia
Zinc binding site 4 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide


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 6-[(3-Aminopropyl)Amino]-N- Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:12.5
occ:0.59
 OD1 D:ASP195 2.0 15.8 1.0
OD2 D:ASP284 2.0 17.4 1.0
ND1 D:HIS197 2.1 14.9 1.0
O14 D:XS6405 2.1 15.3 0.9
O12 D:XS6405 2.2 18.2 0.9
OD2 D:ASP195 2.5 12.9 1.0
CG D:ASP195 2.6 11.4 1.0
N13 D:XS6405 2.7 16.2 0.9
C11 D:XS6405 2.7 17.2 0.9
CE1 D:HIS197 2.9 15.2 1.0
CG D:ASP284 3.1 16.1 1.0
CG D:HIS197 3.2 14.8 1.0
OD1 D:ASP284 3.4 17.1 1.0
CB D:HIS197 3.7 10.7 1.0
N D:HIS197 3.8 12.8 1.0
NE2 D:HIS197 4.1 15.6 1.0
C10 D:XS6405 4.1 23.9 0.9
CB D:ASP195 4.1 10.6 1.0
NE2 D:HIS158 4.2 14.0 1.0
CA D:GLY321 4.2 13.5 1.0
N D:PHE196 4.2 13.4 1.0
CD2 D:HIS197 4.2 13.5 1.0
CA D:HIS197 4.4 10.8 1.0
CB D:ASP284 4.4 17.0 1.0
N D:GLY321 4.4 14.2 1.0
CE1 D:HIS158 4.5 15.1 1.0
CE2 D:TYR323 4.6 15.2 1.0
OH D:TYR323 4.6 13.5 1.0
CB D:PHE196 4.7 14.0 1.0
C D:PHE196 4.7 13.3 1.0
C D:ASP195 4.8 14.6 1.0
CA D:PHE196 4.8 12.5 1.0
NE2 D:HIS159 4.8 9.4 1.0
CA D:ASP195 4.9 12.3 1.0
C D:GLY321 4.9 18.1 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 05:08:10 2024

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