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Magnesium in PDB 6pi1: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide, PDB code: 6pi1 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) 60.71 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.624, 163.013, 65.624, 90.00, 94.51, 90.00
R / Rfree (%) 16.3 / 19.9

Other elements in 6pi1:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide also contains other interesting chemical elements:

Potassium (K) 8 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide (pdb code 6pi1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide, PDB code: 6pi1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6pi1

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Magnesium binding site 1 out of 5 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:12.7
occ:1.00
 O B:HOH610 2.1 9.8 1.0
O A:HOH652 2.1 12.0 1.0
OD2 A:ASP106 2.1 14.1 1.0
OD2 A:ASP104 2.1 15.4 1.0
O B:HOH549 2.1 16.4 1.0
O A:HOH586 2.2 12.8 1.0
CG A:ASP104 3.0 11.4 1.0
CG A:ASP106 3.2 9.0 1.0
OD1 A:ASP104 3.4 17.3 1.0
CB A:ASP106 3.5 7.5 1.0
O A:HOH699 4.0 31.4 1.0
NZ A:LYS83 4.0 10.2 1.0
O B:HOH505 4.0 13.9 1.0
O B:LEU223 4.2 10.1 1.0
O B:HOH713 4.2 28.0 1.0
OD1 A:ASP106 4.3 11.7 1.0
O A:HOH698 4.3 27.4 1.0
CB A:ASP104 4.3 11.4 1.0
NE2 B:HIS227 4.4 11.4 1.0
N A:ASP106 4.4 10.4 1.0
O B:HOH736 4.5 30.0 1.0
CA A:ASP106 4.6 9.3 1.0
CE1 B:HIS227 4.7 10.4 1.0
CE A:LYS83 4.7 12.3 1.0

Magnesium binding site 2 out of 5 in 6pi1

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Magnesium binding site 2 out of 5 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:13.5
occ:1.00
 OD2 B:ASP106 2.0 12.5 1.0
OD2 B:ASP104 2.0 14.5 1.0
O A:HOH646 2.0 13.9 1.0
O B:HOH629 2.1 16.2 1.0
O B:HOH625 2.2 14.4 1.0
O A:HOH579 2.3 13.5 1.0
CG B:ASP104 3.0 14.2 1.0
CG B:ASP106 3.1 11.8 1.0
OD1 B:ASP104 3.4 14.2 1.0
CB B:ASP106 3.5 9.5 1.0
NZ B:LYS83 4.0 12.6 1.0
O B:HOH711 4.1 30.1 1.0
O A:HOH503 4.2 14.9 1.0
OD1 B:ASP106 4.2 10.4 1.0
O A:LEU223 4.3 12.5 1.0
O B:HOH705 4.3 28.4 1.0
O A:HOH743 4.3 30.1 1.0
CB B:ASP104 4.3 11.9 1.0
O A:HOH726 4.3 31.4 1.0
N B:ASP106 4.4 9.2 1.0
NE2 A:HIS227 4.4 8.7 1.0
CA B:ASP106 4.5 6.1 1.0
CE B:LYS83 4.6 12.4 1.0
CE1 A:HIS227 4.6 10.4 1.0

Magnesium binding site 3 out of 5 in 6pi1

Go back to Magnesium Binding Sites List in 6pi1
Magnesium binding site 3 out of 5 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:29.7
occ:1.00
 OE2 B:GLU288 2.0 36.2 1.0
O B:HOH664 2.0 26.1 1.0
O B:HOH517 2.0 24.3 1.0
O B:HOH534 2.2 17.5 1.0
O B:HOH582 2.2 33.4 1.0
O B:HOH611 2.3 28.0 1.0
CD B:GLU288 3.1 36.8 1.0
OE1 B:GLU288 3.6 36.8 1.0
OD1 B:ASP324 4.1 20.0 1.0
O B:HOH734 4.1 33.0 1.0
OD2 B:ASP324 4.2 20.2 1.0
O B:HOH696 4.2 31.7 1.0
OD1 B:ASP326 4.2 23.3 1.0
CG B:GLU288 4.3 27.1 1.0
CG B:ASP324 4.5 18.2 1.0
CB B:ASP326 4.6 14.2 1.0
CB B:GLU288 4.7 14.8 1.0
CG B:ASP326 4.9 26.8 1.0

Magnesium binding site 4 out of 5 in 6pi1

Go back to Magnesium Binding Sites List in 6pi1
Magnesium binding site 4 out of 5 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:13.9
occ:1.00
 OD2 C:ASP106 2.1 14.2 1.0
O C:HOH634 2.1 18.2 1.0
OD2 C:ASP104 2.1 15.6 1.0
O C:HOH615 2.2 12.5 1.0
CG C:ASP104 3.1 15.2 1.0
CG C:ASP106 3.1 13.6 1.0
OD1 C:ASP104 3.4 16.4 1.0
CB C:ASP106 3.5 13.6 1.0
NZ C:LYS83 3.9 10.0 1.0
OD1 C:ASP106 4.2 11.8 1.0
O C:HOH710 4.2 32.1 1.0
CB C:ASP104 4.4 13.0 1.0
N C:ASP106 4.4 12.7 1.0
CA C:ASP106 4.6 10.7 1.0
CE C:LYS83 4.6 11.3 1.0

Magnesium binding site 5 out of 5 in 6pi1

Go back to Magnesium Binding Sites List in 6pi1
Magnesium binding site 5 out of 5 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:13.0
occ:1.00
 OD2 D:ASP106 2.0 11.6 1.0
O D:HOH624 2.1 14.9 1.0
OD1 D:ASP104 2.1 14.1 1.0
O D:HOH606 2.3 14.9 1.0
CG D:ASP104 3.0 17.9 1.0
CG D:ASP106 3.1 16.1 1.0
OD2 D:ASP104 3.3 14.6 1.0
CB D:ASP106 3.5 11.9 1.0
NZ D:LYS83 4.0 12.1 1.0
O D:HOH686 4.1 30.3 1.0
OD1 D:ASP106 4.2 11.1 1.0
CB D:ASP104 4.3 11.3 1.0
N D:ASP106 4.4 10.6 1.0
CA D:ASP106 4.5 7.4 1.0
CE D:LYS83 4.7 14.1 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 1 14:09:09 2024

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