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Magnesium in PDB 3i3o: 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone

Protein crystallography data

The structure of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone, PDB code: 3i3o was solved by A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, S.Peterson, 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) 29.95 / 2.06
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 131.757, 168.156, 107.194, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.5

Other elements in 3i3o:

The structure of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone also contains other interesting chemical elements:

Arsenic (As) 9 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone (pdb code 3i3o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone, PDB code: 3i3o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3i3o

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Magnesium binding site 1 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:35.4
occ:1.00
O A:HOH550 1.9 9.7 1.0
OD2 A:ASP53 2.1 21.4 1.0
OG A:SER54 2.2 16.8 1.0
O A:HOH551 2.2 17.4 1.0
OE2 A:GLU78 2.3 31.8 1.0
O3' A:NAE311 2.4 26.6 0.9
CG A:ASP53 2.9 20.7 1.0
CB A:SER54 3.0 18.5 1.0
CD A:GLU78 3.3 26.9 1.0
OD1 A:ASP53 3.3 17.8 1.0
C3' A:NAE311 3.5 31.7 0.9
CG A:GLU78 3.8 20.3 1.0
O A:GLY20 3.9 26.6 1.0
N A:SER54 4.0 18.6 1.0
OD2 A:ASP81 4.0 25.5 1.0
O2A A:NAE311 4.1 31.5 0.9
CA A:SER54 4.1 17.9 1.0
O1A A:NAE311 4.2 32.6 0.9
OE1 A:GLU78 4.2 23.1 1.0
O2' A:NAE311 4.2 29.9 0.9
CB A:ASP53 4.2 19.3 1.0
CB A:GLU78 4.2 18.0 1.0
C2' A:NAE311 4.3 33.2 0.9
C A:ASP53 4.4 19.4 1.0
PA A:NAE311 4.5 30.8 0.9
O5' A:NAE311 4.6 30.5 0.9
CB A:PRO19 4.6 27.5 1.0
CB A:ASP81 4.7 19.8 1.0
C4' A:NAE311 4.7 31.7 0.9
O A:ASP53 4.9 20.0 1.0
CA A:ASP53 4.9 19.1 1.0
CG A:ASP81 4.9 22.8 1.0
C A:SER54 4.9 17.5 1.0

Magnesium binding site 2 out of 7 in 3i3o

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Magnesium binding site 2 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:34.3
occ:1.00
O B:HOH484 2.0 5.6 1.0
OE2 B:GLU78 2.1 23.4 1.0
OD2 B:ASP53 2.1 17.2 1.0
OG B:SER54 2.2 15.0 1.0
O B:HOH465 2.3 4.3 1.0
O3' B:NAE311 2.3 25.8 0.9
CG B:ASP53 3.0 16.1 1.0
CD B:GLU78 3.2 18.8 1.0
CB B:SER54 3.2 14.1 1.0
OD1 B:ASP53 3.2 16.0 1.0
C3' B:NAE311 3.3 25.3 0.9
O B:GLY20 3.7 11.9 1.0
CG B:GLU78 3.7 17.3 1.0
O2' B:NAE311 4.0 25.1 0.9
C2' B:NAE311 4.1 25.4 0.9
O2A B:NAE311 4.1 30.1 0.9
N B:SER54 4.1 15.7 1.0
O1A B:NAE311 4.2 25.2 0.9
OE1 B:GLU78 4.2 17.1 1.0
OD2 B:ASP81 4.2 16.7 1.0
CB B:GLU78 4.3 16.2 1.0
CA B:SER54 4.3 14.2 1.0
CB B:ASP53 4.3 15.3 1.0
PA B:NAE311 4.4 27.5 0.9
C B:ASP53 4.6 16.1 1.0
C4' B:NAE311 4.6 25.6 0.9
O5' B:NAE311 4.6 27.2 0.9
CB B:PRO19 4.7 13.8 1.0
C B:GLY20 4.9 12.8 1.0
CB B:ASP81 5.0 12.5 1.0
CA B:ASP53 5.0 15.7 1.0

Magnesium binding site 3 out of 7 in 3i3o

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Magnesium binding site 3 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:38.5
occ:1.00
O C:HOH433 1.9 2.9 1.0
OE2 C:GLU78 2.1 20.8 0.6
OD2 C:ASP53 2.2 21.8 1.0
O C:HOH458 2.3 8.8 1.0
OG C:SER54 2.3 19.8 1.0
O3' C:NAE311 2.5 26.9 0.8
CD C:GLU78 3.1 17.1 0.6
CG C:ASP53 3.1 19.5 1.0
CB C:SER54 3.2 15.7 1.0
OD1 C:ASP53 3.5 14.6 1.0
CG C:GLU78 3.5 19.9 0.6
C3' C:NAE311 3.5 31.7 0.8
O C:GLY20 3.7 20.7 1.0
CB C:GLU78 4.0 21.1 0.6
OD2 C:ASP81 4.1 22.8 1.0
OE1 C:GLU78 4.1 10.7 0.6
CG C:GLU78 4.1 20.3 0.4
O2' C:NAE311 4.2 27.9 0.8
CB C:GLU78 4.2 21.0 0.4
C2' C:NAE311 4.2 31.4 0.8
O1A C:NAE311 4.3 31.8 0.8
N C:SER54 4.3 15.5 1.0
O2A C:NAE311 4.3 34.5 0.8
CA C:SER54 4.4 15.1 1.0
CB C:ASP53 4.4 16.6 1.0
CB C:PRO19 4.5 22.2 1.0
C C:ASP53 4.6 15.4 1.0
CB C:ASP81 4.7 16.9 1.0
PA C:NAE311 4.7 33.1 0.8
CG C:PRO229 4.8 18.6 1.0
C4' C:NAE311 4.9 31.5 0.8
CG C:ASP81 4.9 19.7 1.0
C C:GLY20 4.9 20.9 1.0
O5' C:NAE311 4.9 31.6 0.8

Magnesium binding site 4 out of 7 in 3i3o

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Magnesium binding site 4 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:39.3
occ:1.00
OE2 D:GLU78 2.0 25.8 1.0
O D:HOH534 2.1 10.9 1.0
O D:HOH468 2.1 14.8 1.0
OD2 D:ASP53 2.2 17.3 1.0
O3' D:NAE311 2.2 27.9 0.8
OG D:SER54 2.5 18.4 1.0
CD D:GLU78 3.0 26.8 1.0
CG D:ASP53 3.1 19.4 1.0
C3' D:NAE311 3.3 29.4 0.8
CB D:SER54 3.3 18.2 1.0
OD1 D:ASP53 3.5 18.6 1.0
CG D:GLU78 3.5 24.9 1.0
O D:GLY20 3.7 20.3 1.0
O2' D:NAE311 4.0 32.4 0.8
C2' D:NAE311 4.0 30.4 0.8
OE1 D:GLU78 4.1 24.9 1.0
CB D:GLU78 4.1 25.4 1.0
O1A D:NAE311 4.2 29.7 0.8
OD2 D:ASP81 4.2 27.3 1.0
N D:SER54 4.3 18.6 1.0
CB D:ASP53 4.4 18.2 1.0
CA D:SER54 4.4 18.3 1.0
O2A D:NAE311 4.5 25.6 0.8
CB D:PRO19 4.6 21.8 1.0
C4' D:NAE311 4.6 26.2 0.8
PA D:NAE311 4.6 30.1 0.8
O5' D:NAE311 4.7 26.4 0.8
C D:ASP53 4.8 18.5 1.0
CB D:ASP81 4.9 20.4 1.0
C D:GLY20 5.0 20.8 1.0

Magnesium binding site 5 out of 7 in 3i3o

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Magnesium binding site 5 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg305

b:45.8
occ:1.00
O E:HOH453 1.9 7.3 1.0
OD2 E:ASP53 2.1 20.2 1.0
O E:HOH497 2.1 7.7 1.0
OG E:SER54 2.2 19.1 1.0
O3' E:NAE311 2.3 28.1 0.8
OE2 E:GLU78 2.4 28.8 1.0
CG E:ASP53 2.8 17.7 1.0
OD1 E:ASP53 3.1 17.9 1.0
CB E:SER54 3.1 17.2 1.0
CD E:GLU78 3.3 26.6 1.0
C3' E:NAE311 3.4 33.2 0.8
CG E:GLU78 3.8 24.0 1.0
N E:SER54 3.9 18.3 1.0
O E:GLY20 4.0 23.3 1.0
OD2 E:ASP81 4.1 21.6 1.0
CA E:SER54 4.1 18.1 1.0
CB E:ASP53 4.1 18.9 1.0
O2A E:NAE311 4.2 35.5 0.8
O2' E:NAE311 4.2 32.0 0.8
C2' E:NAE311 4.2 31.8 0.8
CB E:GLU78 4.2 23.3 1.0
OE1 E:GLU78 4.3 23.9 1.0
C E:ASP53 4.3 18.9 1.0
O1A E:NAE311 4.4 33.2 0.8
C4' E:NAE311 4.7 32.2 0.8
PA E:NAE311 4.7 36.4 0.8
CB E:ASP81 4.7 19.3 1.0
CA E:ASP53 4.8 18.9 1.0
CG E:PRO229 4.8 13.2 1.0
O E:ASP53 4.8 20.9 1.0
CB E:PRO19 4.8 23.8 1.0
O5' E:NAE311 4.9 37.2 0.8
CG E:ASP81 4.9 18.6 1.0
C E:SER54 4.9 16.8 1.0

Magnesium binding site 6 out of 7 in 3i3o

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Magnesium binding site 6 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg303

b:40.0
occ:1.00
O F:HOH406 1.9 12.3 1.0
O F:HOH480 2.1 25.1 1.0
OD2 F:ASP53 2.1 22.3 1.0
OG F:SER54 2.2 16.1 1.0
O3' F:NAE311 2.3 35.0 0.8
OE2 F:GLU78 2.4 29.4 1.0
CG F:ASP53 3.0 21.1 1.0
CB F:SER54 3.2 18.6 1.0
OD1 F:ASP53 3.4 18.4 1.0
CD F:GLU78 3.4 27.1 1.0
C3' F:NAE311 3.4 37.4 0.8
O F:GLY20 3.6 29.2 1.0
CG F:GLU78 3.7 24.1 1.0
O2' F:NAE311 4.1 34.6 0.8
C2' F:NAE311 4.1 37.8 0.8
O1A F:NAE311 4.1 37.5 0.8
N F:SER54 4.1 18.9 1.0
O2A F:NAE311 4.2 36.4 0.8
OD2 F:ASP81 4.2 23.1 1.0
CB F:GLU78 4.2 22.3 1.0
CA F:SER54 4.3 18.7 1.0
CB F:ASP53 4.3 19.6 1.0
OE1 F:GLU78 4.4 25.0 1.0
PA F:NAE311 4.5 34.0 0.8
C F:ASP53 4.5 20.2 1.0
CB F:PRO19 4.6 30.7 1.0
C4' F:NAE311 4.7 38.3 0.8
CG F:PRO229 4.7 18.5 1.0
O5' F:NAE311 4.7 35.0 0.8
CB F:ASP81 4.8 21.1 1.0
C F:GLY20 4.9 29.3 1.0
O F:ASP53 4.9 20.1 1.0

Magnesium binding site 7 out of 7 in 3i3o

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Magnesium binding site 7 out of 7 in the 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg307

b:40.9
occ:1.00
O H:HOH500 1.9 2.1 1.0
OG H:SER54 2.2 19.1 1.0
OD2 H:ASP53 2.2 23.6 1.0
OE2 H:GLU78 2.3 16.2 0.6
O3' H:NAE311 2.3 45.2 0.8
O H:HOH511 2.4 17.1 1.0
CG H:ASP53 3.0 21.3 1.0
CB H:SER54 3.0 18.6 1.0
CD H:GLU78 3.3 17.2 0.6
OD1 H:ASP53 3.4 18.8 1.0
C3' H:NAE311 3.5 42.5 0.8
CG H:GLU78 3.8 18.6 0.6
N H:SER54 3.9 19.2 1.0
O H:GLY20 3.9 33.3 1.0
OD2 H:ASP81 4.0 26.4 1.0
O H:HOH514 4.1 2.0 0.4
CA H:SER54 4.1 18.6 1.0
CB H:ASP53 4.1 20.4 1.0
O2' H:NAE311 4.1 36.5 0.8
CG H:GLU78 4.1 20.9 0.4
C2' H:NAE311 4.1 40.6 0.8
O2A H:NAE311 4.2 44.1 0.8
C H:ASP53 4.2 19.6 1.0
OE1 H:GLU78 4.2 16.3 0.6
CB H:GLU78 4.3 20.7 0.4
CB H:GLU78 4.3 19.9 0.6
O1A H:NAE311 4.4 48.0 0.8
O H:ASP53 4.5 19.4 1.0
CB H:ASP81 4.6 20.6 1.0
PA H:NAE311 4.6 45.4 0.8
CA H:ASP53 4.7 20.7 1.0
C4' H:NAE311 4.7 42.5 0.8
O5' H:NAE311 4.7 41.9 0.8
CG H:ASP81 4.7 23.4 1.0
CB H:PRO19 4.8 34.9 1.0
C H:SER54 4.9 18.2 1.0
CG H:PRO229 4.9 20.4 1.0

Reference:

A.S.Halavaty, G.Minasov, T.Skarina, O.Onopriyenko, S.Peterson, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.06 Angstrom Resolution Crystal Structure of A Short Chain Dehydrogenase From Bacillus Anthracis Str. 'Ames Ancestor' in Complex with Nad-Acetone To Be Published.
Page generated: Mon Dec 14 08:15:29 2020

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