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Magnesium in PDB 4dgt: Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate

Protein crystallography data

The structure of Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate, PDB code: 4dgt was solved by I.G.Shabalin, O.Onopriyenko, M.Kudritska, M.Chruszcz, S.Grimshaw, P.J.Porebski, D.R.Cooper, A.Savchenko, W.F.Anderson, W.Minor, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.744, 55.624, 79.133, 90.00, 91.25, 90.00
R / Rfree (%) 14.7 / 18.1

Other elements in 4dgt:

The structure of Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate (pdb code 4dgt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate, PDB code: 4dgt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4dgt

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Magnesium binding site 1 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:30.3
occ:1.00
 O A:HOH752 2.0 39.9 1.0
O A:HOH841 2.1 39.8 1.0
O A:HOH873 2.1 28.9 1.0
O A:HOH651 2.2 25.7 1.0
O A:HOH645 2.3 26.2 1.0
O A:PRO312 2.4 17.8 1.0
C A:PRO312 3.3 17.4 1.0
CA A:PRO312 3.6 17.0 1.0
O A:LEU314 3.8 15.1 1.0
CB A:PRO312 4.0 17.9 1.0
O A:HOH758 4.3 30.5 1.0
OD1 A:ASN308 4.5 17.6 1.0
N A:LYS313 4.6 16.9 1.0
O A:ASN308 4.7 17.4 1.0
O A:HOH597 4.8 15.9 1.0
C A:LEU314 4.9 14.1 1.0
O A:HOH876 5.0 36.7 1.0

Magnesium binding site 2 out of 9 in 4dgt

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Magnesium binding site 2 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:33.6
occ:1.00
 O A:HOH699 1.9 29.1 1.0
O A:HOH824 2.0 33.7 1.0
O A:HOH691 2.1 32.8 1.0
O A:SER218 2.2 13.5 1.0
O A:HOH775 2.7 35.7 1.0
O A:HOH823 2.9 44.8 1.0
C A:SER218 3.4 12.5 1.0
CA A:SER218 4.1 11.9 1.0
O A:HOH548 4.2 16.5 1.0
O A:HOH605 4.2 17.8 1.0
CB A:SER218 4.2 12.4 1.0
O A:HOH579 4.3 25.4 1.0
N A:ILE219 4.4 11.8 1.0
O A:ILE219 4.4 13.9 1.0
C A:ILE219 4.5 12.8 1.0
O A:ASN82 4.5 15.2 1.0
CA A:ILE219 4.6 12.5 1.0
OG A:SER218 4.7 12.9 1.0
O A:HOH822 4.8 39.0 1.0
N A:SER220 4.9 12.4 1.0

Magnesium binding site 3 out of 9 in 4dgt

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Magnesium binding site 3 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:28.2
occ:1.00
 O A:HOH900 2.0 31.6 1.0
O A:HOH784 2.0 34.9 1.0
O A:HOH869 2.0 27.8 1.0
O A:HOH781 2.0 31.8 1.0
O A:HOH680 2.1 21.2 1.0
OD1 A:ASN53 4.3 25.5 1.0
O A:ASN53 4.4 12.9 1.0
OE1 A:GLU56 4.5 32.0 1.0
CB A:ASN53 4.6 17.1 1.0
CB A:GLU56 4.7 17.8 1.0
CA A:ASN53 4.7 14.4 1.0
CG A:ASN53 4.7 20.4 1.0

Magnesium binding site 4 out of 9 in 4dgt

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Magnesium binding site 4 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:16.3
occ:1.00
 O A:HOH856 2.0 16.9 1.0
OE2 A:GLU222 2.0 17.0 1.0
O A:HOH855 2.1 20.1 1.0
O A:HOH664 2.1 18.3 1.0
O A:HOH769 2.2 20.0 1.0
O A:HOH767 2.2 17.1 1.0
CD A:GLU222 3.0 17.7 1.0
OE1 A:GLU222 3.3 20.0 1.0
OD1 A:ASP188 3.8 18.5 1.0
O A:HOH627 4.0 17.6 1.0
CG A:GLU222 4.4 17.0 1.0
O A:HOH614 4.5 19.5 1.0
CG A:ASP188 4.7 17.3 1.0

Magnesium binding site 5 out of 9 in 4dgt

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Magnesium binding site 5 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:30.9
occ:1.00
 O B:HOH869 1.9 35.2 1.0
O B:HOH876 2.1 23.6 1.0
O B:HOH801 2.2 40.8 1.0
O B:PRO312 2.2 20.6 1.0
O B:HOH629 2.3 27.6 1.0
O B:HOH880 2.3 24.7 1.0
C B:PRO312 3.2 20.3 1.0
CA B:PRO312 3.6 19.3 1.0
O B:LEU314 3.7 19.8 1.0
CB B:PRO312 4.0 20.3 1.0
O B:HOH774 4.4 37.2 1.0
N B:LYS313 4.4 19.9 1.0
OD1 B:ASN308 4.5 19.0 1.0
O B:ASN308 4.7 20.2 1.0
O B:HOH902 4.7 41.1 1.0
O B:HOH802 4.7 32.5 1.0
O B:HOH775 4.7 27.8 1.0
CA B:LYS313 4.8 21.4 1.0
C B:LEU314 4.9 17.8 1.0
C B:LYS313 4.9 19.9 1.0
O B:HOH600 4.9 31.7 1.0
O B:HOH656 5.0 22.3 1.0
N B:PRO312 5.0 19.3 1.0

Magnesium binding site 6 out of 9 in 4dgt

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Magnesium binding site 6 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:27.8
occ:1.00
 O B:HOH904 2.0 19.9 1.0
O B:HOH532 2.0 25.4 1.0
O B:HOH785 2.1 37.4 1.0
O B:HOH784 2.1 33.3 1.0
O B:HOH878 2.1 28.1 1.0
O B:HOH783 2.2 28.6 1.0
O B:HOH782 4.2 39.5 1.0
OE1 B:GLU56 4.3 28.2 1.0
OD1 B:ASN53 4.3 21.2 1.0
O B:ASN53 4.3 12.6 1.0
CB B:ASN53 4.6 15.0 1.0
CB B:GLU56 4.7 16.1 1.0
CA B:ASN53 4.7 12.7 1.0
CG B:ASN53 4.7 17.6 1.0
C B:ASN53 4.9 11.7 1.0

Magnesium binding site 7 out of 9 in 4dgt

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Magnesium binding site 7 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg406

b:45.9
occ:1.00
 O B:HOH763 2.0 41.9 1.0
O B:HOH646 2.0 36.6 1.0
O B:HOH711 2.2 31.7 1.0
O B:HOH764 2.3 40.1 1.0
OG1 B:THR64 4.0 22.5 1.0
O B:ARG65 4.1 16.3 1.0
O A:HOH708 4.2 34.1 1.0
O A:SER20 4.5 22.6 1.0
O B:HOH547 4.5 18.8 1.0
O A:HOH706 4.5 31.2 1.0
OD1 B:ASP67 4.8 23.9 1.0
CG A:GLU21 4.9 28.1 1.0
C B:ARG65 5.0 13.9 1.0
CA B:PRO66 5.0 14.0 1.0

Magnesium binding site 8 out of 9 in 4dgt

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Magnesium binding site 8 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


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 Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:31.0
occ:1.00
 O B:HIS193 2.1 15.6 1.0
O B:HOH707 2.1 31.5 1.0
O B:HOH938 2.1 48.4 1.0
O B:HOH675 2.3 32.1 1.0
O B:HOH835 2.4 37.3 1.0
O B:HOH758 2.4 31.7 1.0
C B:HIS193 3.1 16.1 1.0
O B:LYS160 3.5 28.4 1.0
CA B:HIS193 3.8 17.1 1.0
CB B:HIS193 3.9 18.1 1.0
O B:HOH936 4.0 35.0 1.0
N B:ASN194 4.1 15.2 1.0
O B:HOH900 4.2 32.0 1.0
O B:VAL162 4.2 14.2 1.0
O B:ASN194 4.3 15.1 1.0
C B:ASN194 4.4 14.9 1.0
CB B:ASN194 4.4 16.2 1.0
CA B:ASN194 4.5 15.2 1.0
C B:LYS160 4.6 25.5 1.0
CG2 B:VAL195 4.7 13.8 1.0
CG B:HIS193 4.9 20.0 1.0
ND1 B:HIS193 5.0 22.9 1.0

Magnesium binding site 9 out of 9 in 4dgt

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Magnesium binding site 9 out of 9 in the Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Plp-Bound Putative Aminotransferase From Clostridium Difficile 630 Crystallized with Magnesium Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:29.8
occ:1.00
 O B:HOH848 2.1 30.9 1.0
O B:HOH893 2.1 27.0 1.0
O B:HOH854 2.1 25.8 1.0
O B:HOH660 2.1 20.6 1.0
O B:HOH695 2.1 32.7 1.0
O B:HOH897 2.2 44.0 1.0
OE1 B:GLU377 3.9 29.3 1.0
OE2 B:GLU377 4.0 27.3 1.0
CD B:GLU377 4.4 24.2 1.0
O B:HOH737 4.6 37.4 1.0
O B:HOH838 4.7 31.4 1.0
O B:HOH818 4.7 35.2 1.0
O B:HOH655 4.8 24.6 1.0

Reference:

I.G.Shabalin, O.Onopriyenko, M.Kudritska, S.Grimshaw, M.Chruszcz, P.J.Porebski, D.R.Cooper, A.Savchenko, W.F.Anderson, W.Minor. Crystal Structures of Putative Aminotransferase From Clostridium Difficile 630 To Be Published.
Page generated: Mon Aug 11 07:29:47 2025

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