Atomistry » Magnesium » PDB 6pen-6pry » 6pi1
Atomistry »
  Magnesium »
    PDB 6pen-6pry »
      6pi1 »

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

Go back to Magnesium Binding Sites List in 6pi1
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

Go back to Magnesium Binding Sites List in 6pi1
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy