Atomistry » Magnesium » PDB 4d4i-4dh8 » 4dgt
Atomistry »
  Magnesium »
    PDB 4d4i-4dh8 »
      4dgt »

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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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

Go back to Magnesium Binding Sites List in 4dgt
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: Thu Aug 15 17:07:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy