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Magnesium in PDB 6pic: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide, PDB code: 6pic 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) 51.97 / 2.03
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.340, 67.040, 167.531, 90.00, 90.00, 92.60
R / Rfree (%) 22 / 24.7

Other elements in 6pic:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide also contains other interesting chemical elements:

Potassium (K) 16 atoms
Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide (pdb code 6pic). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide, PDB code: 6pic:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6pic

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Magnesium binding site 1 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:8.1
occ:1.00
 OD1 A:ASP106 2.1 7.9 1.0
O A:HOH582 2.1 8.4 1.0
OD1 A:ASP104 2.2 8.7 1.0
O A:HOH502 2.2 9.1 1.0
O A:HOH591 2.3 9.8 1.0
O A:HOH576 2.3 8.0 1.0
CG A:ASP104 3.1 7.7 1.0
CG A:ASP106 3.1 7.6 1.0
OD2 A:ASP104 3.3 9.2 1.0
CB A:ASP106 3.4 6.8 1.0
NZ A:LYS83 3.7 9.7 1.0
OD2 A:ASP106 4.2 7.7 1.0
N A:ASP106 4.4 6.6 1.0
CB A:ASP104 4.4 6.1 1.0
CA A:ASP106 4.5 6.9 1.0
CE A:LYS83 4.6 10.1 1.0

Magnesium binding site 2 out of 8 in 6pic

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Magnesium binding site 2 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:9.5
occ:1.00
 O B:HOH506 2.0 8.9 1.0
OD2 B:ASP106 2.0 11.8 1.0
OD1 B:ASP104 2.1 9.9 1.0
O B:HOH561 2.1 9.4 1.0
O B:HOH573 2.3 11.0 1.0
O B:HOH504 2.3 8.4 1.0
CG B:ASP104 3.0 9.8 1.0
CG B:ASP106 3.0 11.8 1.0
OD2 B:ASP104 3.3 9.7 1.0
CB B:ASP106 3.3 10.7 1.0
NZ B:LYS83 3.7 16.2 1.0
OD1 B:ASP106 4.2 12.1 1.0
CB B:ASP104 4.3 9.4 1.0
N B:ASP106 4.3 9.2 1.0
CA B:ASP106 4.4 10.8 1.0
CE B:LYS83 4.6 15.8 1.0
O B:HOH501 4.9 17.9 1.0

Magnesium binding site 3 out of 8 in 6pic

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Magnesium binding site 3 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:7.8
occ:1.00
 O C:HOH510 2.0 6.7 1.0
O C:HOH567 2.0 6.5 1.0
OD2 C:ASP106 2.1 7.0 1.0
O C:HOH561 2.1 5.9 1.0
O C:HOH578 2.2 6.7 1.0
OD1 C:ASP104 2.3 8.2 1.0
CG C:ASP104 3.1 9.3 1.0
CG C:ASP106 3.1 7.6 1.0
OD2 C:ASP104 3.2 9.4 1.0
CB C:ASP106 3.5 7.2 1.0
NZ C:LYS83 3.7 9.0 1.0
OD1 C:ASP106 4.3 6.9 1.0
CB C:ASP104 4.4 8.5 1.0
N C:ASP106 4.4 7.4 1.0
CE C:LYS83 4.6 10.3 1.0
CA C:ASP106 4.6 7.2 1.0

Magnesium binding site 4 out of 8 in 6pic

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Magnesium binding site 4 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:9.2
occ:1.00
 OD1 D:ASP106 2.0 8.4 1.0
O D:HOH549 2.0 9.3 1.0
OD2 D:ASP104 2.1 8.4 1.0
O D:HOH502 2.2 5.6 1.0
O D:HOH571 2.3 7.7 1.0
O D:HOH561 2.4 9.0 1.0
CG D:ASP104 2.9 9.0 1.0
CG D:ASP106 3.0 8.0 1.0
OD1 D:ASP104 3.2 8.8 1.0
CB D:ASP106 3.3 7.3 1.0
NZ D:LYS83 3.9 10.6 1.0
O D:HOH577 4.0 14.2 1.0
OD2 D:ASP106 4.1 7.6 1.0
N D:ASP106 4.3 5.8 1.0
CB D:ASP104 4.3 9.7 1.0
CA D:ASP106 4.4 7.2 1.0
CE D:LYS83 4.7 10.3 1.0

Magnesium binding site 5 out of 8 in 6pic

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Magnesium binding site 5 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg404

b:9.6
occ:1.00
 OD2 E:ASP106 2.0 8.9 1.0
O E:HOH514 2.0 9.9 1.0
OD2 E:ASP104 2.2 10.0 1.0
O E:HOH573 2.3 9.5 1.0
O E:HOH546 2.3 7.0 1.0
O E:HOH576 2.3 6.1 1.0
CG E:ASP106 3.0 8.6 1.0
CG E:ASP104 3.1 9.0 1.0
OD1 E:ASP104 3.4 9.6 1.0
CB E:ASP106 3.4 8.1 1.0
NZ E:LYS83 3.6 10.0 1.0
OD1 E:ASP106 4.1 8.4 1.0
N E:ASP106 4.4 8.4 1.0
CB E:ASP104 4.4 8.4 1.0
CA E:ASP106 4.5 7.9 1.0
CE E:LYS83 4.5 10.1 1.0

Magnesium binding site 6 out of 8 in 6pic

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Magnesium binding site 6 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg404

b:8.9
occ:1.00
 O F:HOH565 2.1 5.9 1.0
O F:HOH505 2.1 6.7 1.0
OD1 F:ASP106 2.1 6.5 1.0
O F:HOH579 2.2 7.1 1.0
O F:HOH584 2.3 9.8 1.0
OD1 F:ASP104 2.3 7.2 1.0
CG F:ASP104 3.1 8.0 1.0
CG F:ASP106 3.2 7.0 1.0
OD2 F:ASP104 3.3 7.7 1.0
CB F:ASP106 3.6 6.3 1.0
NZ F:LYS83 3.8 5.2 1.0
OD2 F:ASP106 4.3 5.2 1.0
CB F:ASP104 4.4 7.0 1.0
N F:ASP106 4.5 6.6 1.0
CE F:LYS83 4.5 8.4 1.0
CA F:ASP106 4.7 6.1 1.0

Magnesium binding site 7 out of 8 in 6pic

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Magnesium binding site 7 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg404

b:13.1
occ:1.00
 OD2 G:ASP106 2.0 11.6 1.0
O G:HOH563 2.1 6.9 1.0
O G:HOH538 2.2 14.4 1.0
OD2 G:ASP104 2.2 11.1 1.0
O G:HOH561 2.2 11.3 1.0
O G:HOH522 2.5 12.2 1.0
CG G:ASP106 3.0 11.9 1.0
CG G:ASP104 3.1 11.1 1.0
OD1 G:ASP104 3.3 11.2 1.0
CB G:ASP106 3.4 10.7 1.0
NZ G:LYS83 3.8 11.8 1.0
OD1 G:ASP106 4.2 11.9 1.0
N G:ASP106 4.3 10.5 1.0
CB G:ASP104 4.4 10.3 1.0
CA G:ASP106 4.5 10.9 1.0
CE G:LYS83 4.6 12.0 1.0

Magnesium binding site 8 out of 8 in 6pic

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Magnesium binding site 8 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg404

b:10.7
occ:1.00
 O H:HOH525 2.0 15.3 1.0
OD2 H:ASP106 2.1 9.0 1.0
O H:HOH567 2.1 9.1 1.0
OD2 H:ASP104 2.3 12.5 1.0
O H:HOH561 2.3 14.5 1.0
O H:HOH566 2.4 10.6 1.0
CG H:ASP104 3.1 11.7 1.0
CG H:ASP106 3.1 8.9 1.0
OD1 H:ASP104 3.3 12.1 1.0
CB H:ASP106 3.5 8.8 1.0
NZ H:LYS83 3.7 11.7 1.0
OD1 H:ASP106 4.2 8.7 1.0
CE H:LYS83 4.4 11.7 1.0
CB H:ASP104 4.4 10.0 1.0
N H:ASP106 4.4 10.2 1.0
CA H:ASP106 4.6 9.3 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 14:10:23 2024

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