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Magnesium in PDB 3a28: Crystal Structure of L-2,3-Butanediol Dehydrogenase

Protein crystallography data

The structure of Crystal Structure of L-2,3-Butanediol Dehydrogenase, PDB code: 3a28 was solved by M.Otagiri, G.Kurisu, S.Ui, M.Kusunoki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.800, 69.200, 127.400, 96.10, 100.20, 109.60
R / Rfree (%) 19.3 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-2,3-Butanediol Dehydrogenase (pdb code 3a28). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of L-2,3-Butanediol Dehydrogenase, PDB code: 3a28:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3a28

Go back to Magnesium Binding Sites List in 3a28
Magnesium binding site 1 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


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 L-2,3-Butanediol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg804

b:37.0
occ:1.00
O B:HOH1094 2.9 29.7 1.0
O C:HOH655 3.0 26.5 1.0
CA B:PHE235 3.9 16.3 1.0
CA C:PHE235 3.9 16.6 1.0
OD1 C:ASN240 4.0 22.4 1.0
CB B:PHE235 4.0 15.2 1.0
CB C:PHE235 4.0 15.2 1.0
OD1 B:ASN240 4.0 22.2 1.0
O B:HOH1418 4.0 33.9 1.0
CD1 B:PHE235 4.1 14.9 1.0
CD1 C:PHE235 4.1 16.4 1.0
N C:PHE235 4.4 15.0 1.0
OG B:SER238 4.4 19.1 1.0
N B:PHE235 4.4 16.3 1.0
OG C:SER238 4.5 17.6 1.0
CG B:PHE235 4.5 16.1 1.0
CG C:PHE235 4.6 17.4 1.0
CB B:ASN240 4.7 17.4 1.0
CB C:ASN240 4.8 15.8 1.0
CG C:ASN240 4.8 17.5 1.0
CG B:ASN240 4.8 20.0 1.0
C C:SER234 5.0 14.7 1.0

Magnesium binding site 2 out of 4 in 3a28

Go back to Magnesium Binding Sites List in 3a28
Magnesium binding site 2 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


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 L-2,3-Butanediol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg805

b:41.1
occ:1.00
O A:HOH668 2.8 30.7 1.0
O D:HOH790 2.9 26.6 1.0
CB A:PHE235 3.8 17.9 1.0
CB D:PHE235 3.8 19.4 1.0
CA D:PHE235 3.8 19.1 1.0
CA A:PHE235 3.9 18.3 1.0
CD1 D:PHE235 4.0 21.4 1.0
OD1 D:ASN240 4.0 23.8 1.0
OD1 A:ASN240 4.1 23.2 1.0
CD1 A:PHE235 4.1 17.9 1.0
OG D:SER238 4.3 24.9 1.0
N A:PHE235 4.4 19.3 1.0
N D:PHE235 4.4 19.6 1.0
CG D:PHE235 4.4 19.9 1.0
O A:HOH1398 4.4 38.1 1.0
OG A:SER238 4.4 26.8 1.0
CG A:PHE235 4.4 19.3 1.0
CB D:ASN240 4.7 21.2 1.0
CG D:ASN240 4.8 22.5 1.0
CB A:ASN240 4.8 22.1 1.0
CG A:ASN240 4.9 23.2 1.0
C A:SER234 5.0 20.2 1.0
C D:SER234 5.0 20.3 1.0

Magnesium binding site 3 out of 4 in 3a28

Go back to Magnesium Binding Sites List in 3a28
Magnesium binding site 3 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


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 L-2,3-Butanediol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1288

b:44.3
occ:1.00
O E:HOH1155 3.1 46.4 1.0
CA E:PHE235 3.9 29.9 1.0
OD1 H:ASN240 3.9 33.2 1.0
CB H:PHE235 3.9 30.3 1.0
CB E:PHE235 3.9 31.5 1.0
CA H:PHE235 4.0 30.1 1.0
CD1 H:PHE235 4.1 30.0 1.0
OD1 E:ASN240 4.2 29.2 1.0
CD1 E:PHE235 4.3 31.7 1.0
OG H:SER238 4.3 39.1 1.0
OG E:SER238 4.3 34.8 1.0
N E:PHE235 4.3 30.7 1.0
CG H:PHE235 4.5 30.2 1.0
N H:PHE235 4.6 30.9 1.0
CG E:PHE235 4.6 31.9 1.0
CB H:ASN240 4.6 35.1 1.0
CG H:ASN240 4.7 34.4 1.0
CB E:ASN240 4.9 27.4 1.0
C E:SER234 4.9 30.6 1.0
OG E:SER234 5.0 35.5 1.0
CG E:ASN240 5.0 28.4 1.0

Magnesium binding site 4 out of 4 in 3a28

Go back to Magnesium Binding Sites List in 3a28
Magnesium binding site 4 out of 4 in the Crystal Structure of L-2,3-Butanediol Dehydrogenase


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 L-2,3-Butanediol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg948

b:34.0
occ:1.00
O F:HOH906 3.0 26.7 1.0
O G:HOH1023 3.2 29.6 1.0
OD1 F:ASN240 3.7 19.6 1.0
CB F:PHE235 3.7 15.5 1.0
CA F:PHE235 3.8 15.6 1.0
CB G:PHE235 3.8 15.4 1.0
CA G:PHE235 3.9 16.6 1.0
CD1 F:PHE235 3.9 15.9 1.0
CD1 G:PHE235 4.0 15.6 1.0
OD1 G:ASN240 4.2 17.1 1.0
CG F:PHE235 4.3 16.8 1.0
N F:PHE235 4.3 16.1 1.0
OG F:SER238 4.4 18.5 1.0
CG G:PHE235 4.4 16.6 1.0
N G:PHE235 4.4 14.8 1.0
O F:HOH1113 4.5 41.6 1.0
OG G:SER238 4.5 17.1 1.0
CB F:ASN240 4.6 16.0 1.0
CG F:ASN240 4.6 18.3 1.0
CB G:ASN240 4.9 14.5 1.0
C G:SER234 5.0 15.9 1.0
CE1 F:PHE235 5.0 16.6 1.0
C F:SER234 5.0 16.7 1.0
CG G:ASN240 5.0 17.0 1.0

Reference:

M.Otagiri, S.Ui, Y.Takusagawa, T.Ohtsuki, G.Kurisu, M.Kusunoki. Structural Basis For Chiral Substrate Recognition By Two 2,3-Butanediol Dehydrogenases Febs Lett. V. 584 219 2010.
ISSN: ISSN 0014-5793
PubMed: 19941855
DOI: 10.1016/J.FEBSLET.2009.11.068
Page generated: Mon Dec 14 07:52:23 2020

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