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Magnesium in PDB 3ijr: 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+

Protein crystallography data

The structure of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+, PDB code: 3ijr was solved by A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, E.Gordon, K.Kwon, A.Savchenko, W.F.Anderson, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.749, 123.203, 169.767, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 19.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ (pdb code 3ijr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+, PDB code: 3ijr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ijr

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Magnesium binding site 1 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg300

b:37.2
occ:0.70
OD2 A:ASP53 1.9 13.9 1.0
OE2 A:GLU78 2.1 5.8 1.0
O A:HOH918 2.2 5.8 1.0
O3B A:NAD301 2.2 35.6 0.8
O A:HOH428 2.3 2.6 1.0
OG A:SER54 2.3 7.6 1.0
CG A:ASP53 2.9 10.9 1.0
CD A:GLU78 3.0 9.3 1.0
CB A:SER54 3.2 8.9 1.0
C3B A:NAD301 3.3 34.1 0.8
OD1 A:ASP53 3.4 6.8 1.0
CG A:GLU78 3.5 10.1 1.0
O2B A:NAD301 3.8 38.4 0.8
O A:GLY20 3.8 9.4 1.0
C2B A:NAD301 4.0 36.9 0.8
OE1 A:GLU78 4.1 10.8 1.0
N A:SER54 4.1 7.0 1.0
CB A:GLU78 4.1 11.1 1.0
OD2 A:ASP81 4.2 9.6 1.0
CB A:ASP53 4.2 8.1 1.0
O1A A:NAD301 4.2 36.0 0.8
CA A:SER54 4.2 7.9 1.0
O2A A:NAD301 4.3 31.6 0.8
C A:ASP53 4.5 9.6 1.0
C4B A:NAD301 4.6 34.4 0.8
PA A:NAD301 4.6 35.6 0.8
O5B A:NAD301 4.8 26.3 0.8
CB A:ASP81 4.9 6.6 1.0
CB A:PRO19 4.9 13.9 1.0
CA A:ASP53 5.0 9.4 1.0
O A:ASP53 5.0 9.2 1.0

Magnesium binding site 2 out of 8 in 3ijr

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Magnesium binding site 2 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:41.8
occ:0.70
O B:HOH796 1.9 11.9 1.0
O3B B:NAD301 2.1 49.1 0.8
OE2 B:GLU78 2.1 21.8 1.0
OD2 B:ASP53 2.2 17.6 1.0
OG B:SER54 2.2 11.7 1.0
O B:HOH795 2.2 18.7 1.0
CB B:SER54 3.1 14.4 1.0
C3B B:NAD301 3.1 48.8 0.8
CG B:ASP53 3.2 16.6 1.0
CD B:GLU78 3.2 18.3 1.0
OD1 B:ASP53 3.5 17.9 1.0
CG B:GLU78 3.7 18.4 1.0
O B:GLY20 3.8 19.9 1.0
O2B B:NAD301 3.8 43.5 0.8
C2B B:NAD301 3.9 47.3 0.8
O2A B:NAD301 4.1 43.9 0.8
O1A B:NAD301 4.1 43.0 0.8
OE1 B:GLU78 4.2 17.3 1.0
N B:SER54 4.2 15.0 1.0
CA B:SER54 4.2 14.0 1.0
CB B:GLU78 4.3 16.5 1.0
OD2 B:ASP81 4.3 22.3 1.0
C4B B:NAD301 4.4 45.8 0.8
CB B:ASP53 4.4 17.5 1.0
PA B:NAD301 4.5 42.6 0.8
C B:ASP53 4.6 16.7 1.0
O5B B:NAD301 4.6 35.5 0.8
CB B:PRO19 4.8 20.4 1.0
O B:ASP53 4.9 18.2 1.0
CB B:ASP81 5.0 14.5 1.0
C B:GLY20 5.0 21.3 1.0
C5B B:NAD301 5.0 44.9 0.8

Magnesium binding site 3 out of 8 in 3ijr

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Magnesium binding site 3 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg300

b:43.8
occ:0.90
OD2 C:ASP53 2.0 14.3 1.0
O C:HOH697 2.1 2.6 1.0
O C:HOH380 2.1 2.6 1.0
OE2 C:GLU78 2.2 3.8 1.0
O3B C:NAD301 2.3 33.0 0.8
OG C:SER54 2.3 2.7 1.0
CG C:ASP53 3.0 10.7 1.0
CD C:GLU78 3.1 8.2 1.0
CB C:SER54 3.2 5.7 1.0
C3B C:NAD301 3.3 33.1 0.8
OD1 C:ASP53 3.4 9.2 1.0
CG C:GLU78 3.6 10.3 1.0
O2B C:NAD301 3.8 33.1 0.8
O C:GLY20 3.9 2.6 1.0
C2B C:NAD301 4.0 35.6 0.8
CB C:GLU78 4.1 8.7 1.0
N C:SER54 4.1 5.4 1.0
OE1 C:GLU78 4.2 12.6 1.0
O1A C:NAD301 4.2 29.9 0.8
O2A C:NAD301 4.2 32.4 0.8
OD2 C:ASP81 4.3 12.6 1.0
CB C:ASP53 4.3 7.4 1.0
CA C:SER54 4.3 5.5 1.0
PA C:NAD301 4.5 35.3 0.8
C4B C:NAD301 4.6 33.8 0.8
C C:ASP53 4.6 7.4 1.0
O5B C:NAD301 4.7 28.3 0.8
CB C:PRO19 4.8 2.6 1.0
CB C:ASP81 4.9 5.6 1.0
CG C:PRO229 5.0 10.4 1.0

Magnesium binding site 4 out of 8 in 3ijr

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Magnesium binding site 4 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg300

b:44.5
occ:1.00
OD2 D:ASP53 1.9 15.8 1.0
O D:HOH849 2.1 8.6 1.0
O D:HOH738 2.1 5.3 1.0
O3B D:NAD301 2.2 38.2 0.9
OE2 D:GLU78 2.3 8.0 1.0
OG D:SER54 2.3 6.2 1.0
CG D:ASP53 3.0 14.4 1.0
CD D:GLU78 3.1 11.5 1.0
CB D:SER54 3.2 7.6 1.0
C3B D:NAD301 3.3 43.4 0.9
OD1 D:ASP53 3.4 15.8 1.0
CG D:GLU78 3.5 16.1 1.0
O D:GLY20 3.8 8.6 1.0
O2B D:NAD301 3.9 37.4 0.9
C2B D:NAD301 4.0 39.5 0.9
CB D:GLU78 4.1 14.6 1.0
O2A D:NAD301 4.1 40.8 0.9
O1A D:NAD301 4.2 38.1 0.9
OE1 D:GLU78 4.2 16.1 1.0
N D:SER54 4.3 10.9 1.0
CA D:SER54 4.3 9.0 1.0
CB D:ASP53 4.3 12.6 1.0
OD2 D:ASP81 4.3 16.8 1.0
PA D:NAD301 4.5 38.9 0.9
C4B D:NAD301 4.6 42.0 0.9
C D:ASP53 4.7 12.1 1.0
CB D:PRO19 4.7 10.8 1.0
O5B D:NAD301 4.7 35.5 0.9

Magnesium binding site 5 out of 8 in 3ijr

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Magnesium binding site 5 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg300

b:57.6
occ:0.90
O E:HOH815 2.0 8.5 1.0
OD2 E:ASP53 2.1 22.4 1.0
O3B E:NAD301 2.1 54.7 0.8
OE2 E:GLU78 2.2 11.2 1.0
OG E:SER54 2.2 17.0 1.0
O E:HOH645 2.2 2.6 1.0
CG E:ASP53 3.0 19.7 1.0
CD E:GLU78 3.2 17.3 1.0
CB E:SER54 3.2 15.8 1.0
C3B E:NAD301 3.3 52.7 0.8
OD1 E:ASP53 3.4 16.5 1.0
CG E:GLU78 3.6 20.8 1.0
O2B E:NAD301 3.8 54.2 0.8
O E:GLY20 4.0 2.6 1.0
C2B E:NAD301 4.0 53.7 0.8
N E:SER54 4.2 16.0 1.0
CB E:GLU78 4.2 19.7 1.0
OE1 E:GLU78 4.2 13.8 1.0
OD2 E:ASP81 4.3 21.3 1.0
O2A E:NAD301 4.3 51.3 0.8
CB E:ASP53 4.3 19.2 1.0
CA E:SER54 4.3 15.6 1.0
O1A E:NAD301 4.3 47.6 0.8
C4B E:NAD301 4.5 52.1 0.8
C E:ASP53 4.6 18.1 1.0
PA E:NAD301 4.7 48.1 0.8
CB E:ASP81 4.8 17.8 1.0
O5B E:NAD301 4.8 48.2 0.8
CG E:PRO229 4.8 2.6 1.0
CB E:PRO19 4.9 2.6 1.0

Magnesium binding site 6 out of 8 in 3ijr

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Magnesium binding site 6 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg300

b:53.7
occ:0.90
OD2 F:ASP53 2.1 25.5 1.0
O F:HOH752 2.1 13.3 1.0
O F:HOH751 2.1 14.9 1.0
OG F:SER54 2.2 17.3 1.0
OE2 F:GLU78 2.3 20.8 1.0
O3B F:NAD301 2.4 49.7 0.8
CB F:SER54 3.1 15.4 1.0
CD F:GLU78 3.2 20.0 1.0
CG F:ASP53 3.2 20.1 1.0
CG F:GLU78 3.5 20.8 1.0
C3B F:NAD301 3.5 50.8 0.8
OD1 F:ASP53 3.7 22.3 1.0
O F:GLY20 3.9 16.1 1.0
O2B F:NAD301 4.0 51.8 0.8
OD2 F:ASP81 4.0 24.1 1.0
CB F:GLU78 4.0 19.1 1.0
O1A F:NAD301 4.2 45.9 0.8
C2B F:NAD301 4.2 51.9 0.8
N F:SER54 4.2 16.8 1.0
OE1 F:GLU78 4.2 18.9 1.0
CA F:SER54 4.3 16.0 1.0
O2A F:NAD301 4.3 47.0 0.8
CB F:ASP53 4.4 18.9 1.0
PA F:NAD301 4.7 44.1 0.8
C F:ASP53 4.7 16.9 1.0
CB F:PRO19 4.7 19.3 1.0
CB F:ASP81 4.8 18.0 1.0
C4B F:NAD301 4.8 50.0 0.8
CG F:ASP81 4.9 20.6 1.0
O5B F:NAD301 4.9 41.3 0.8
CG F:PRO229 4.9 14.1 1.0

Magnesium binding site 7 out of 8 in 3ijr

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Magnesium binding site 7 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg300

b:54.2
occ:1.00
OD2 G:ASP53 2.1 19.9 1.0
O G:HOH480 2.1 9.1 1.0
O G:HOH522 2.2 6.0 1.0
O3B G:NAD301 2.3 39.9 0.8
OE2 G:GLU78 2.3 18.1 1.0
OG G:SER54 2.3 17.8 1.0
CG G:ASP53 3.0 15.9 1.0
CD G:GLU78 3.2 18.7 1.0
OD1 G:ASP53 3.3 16.9 1.0
CB G:SER54 3.3 15.3 1.0
C3B G:NAD301 3.3 44.4 0.8
CG G:GLU78 3.6 19.5 1.0
O2B G:NAD301 3.8 45.0 0.8
O G:GLY20 3.9 12.1 1.0
C2B G:NAD301 4.0 43.5 0.8
O1A G:NAD301 4.1 46.4 0.8
CB G:GLU78 4.2 19.5 1.0
O2A G:NAD301 4.2 41.0 0.8
OD2 G:ASP81 4.2 16.2 1.0
OE1 G:GLU78 4.3 17.4 1.0
N G:SER54 4.3 15.0 1.0
CB G:ASP53 4.4 15.2 1.0
CA G:SER54 4.4 15.1 1.0
PA G:NAD301 4.6 43.4 0.8
C4B G:NAD301 4.6 42.5 0.8
C G:ASP53 4.7 14.5 1.0
O5B G:NAD301 4.8 37.8 0.8
CB G:ASP81 4.9 15.8 1.0
CB G:PRO19 4.9 12.1 1.0

Magnesium binding site 8 out of 8 in 3ijr

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Magnesium binding site 8 out of 8 in the 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg300

b:53.2
occ:1.00
OD2 H:ASP53 2.0 19.8 1.0
O3B H:NAD301 2.1 40.8 0.8
O H:HOH474 2.2 9.3 1.0
O H:HOH527 2.2 16.0 1.0
OE2 H:GLU78 2.3 19.8 1.0
OG H:SER54 2.4 18.2 1.0
CG H:ASP53 3.0 17.7 1.0
C3B H:NAD301 3.1 45.3 0.8
CD H:GLU78 3.2 18.1 1.0
OD1 H:ASP53 3.3 14.8 1.0
CB H:SER54 3.3 13.3 1.0
CG H:GLU78 3.6 22.0 1.0
O2B H:NAD301 3.8 41.9 0.8
O H:GLY20 3.8 10.7 1.0
C2B H:NAD301 3.9 43.1 0.8
O1A H:NAD301 4.0 45.1 0.8
O2A H:NAD301 4.1 38.5 0.8
CB H:GLU78 4.2 19.5 1.0
N H:SER54 4.2 14.1 1.0
OE1 H:GLU78 4.2 19.8 1.0
CB H:ASP53 4.3 17.4 1.0
CA H:SER54 4.3 13.8 1.0
C4B H:NAD301 4.4 43.9 0.8
OD2 H:ASP81 4.4 19.2 1.0
PA H:NAD301 4.5 39.7 0.8
O5B H:NAD301 4.7 38.0 0.8
C H:ASP53 4.7 14.9 1.0
CB H:PRO19 4.9 16.7 1.0
C5B H:NAD301 5.0 43.8 0.8

Reference:

A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, E.Gordon, K.Kwon, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.05 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad+ To Be Published.
Page generated: Mon Dec 14 08:17:09 2020

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