Magnesium in PDB 8gst: Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form)

Protein crystallography data

The structure of Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form), PDB code: 8gst was solved by S.Fukuhara, Y.Watanabe, S.Watanabe, H.Nishiwaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.99 / 1.71
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.254, 66.228, 75.256, 90.27, 91.43, 105.2
R / Rfree (%) 18 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form) (pdb code 8gst). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form), PDB code: 8gst:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8gst

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Magnesium binding site 1 out of 5 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form)


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-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:15.0
occ:1.00
 OE1 A:GLU121 2.0 14.4 1.0
OD2 A:ASP150 2.1 13.0 1.0
O A:HOH460 2.1 15.6 1.0
OE2 A:GLU119 2.1 16.2 1.0
O A:HOH633 2.1 29.0 1.0
O A:HOH649 2.2 23.6 1.0
CD A:GLU121 3.0 12.0 1.0
CG A:ASP150 3.1 16.9 1.0
CD A:GLU119 3.4 15.0 1.0
OE2 A:GLU121 3.5 13.5 1.0
CB A:ASP150 3.5 12.8 1.0
NZ A:LYS168 3.8 17.2 1.0
O A:ILE71 3.9 18.4 1.0
O A:HOH470 4.1 24.9 1.0
OE1 A:GLU119 4.1 15.7 1.0
OD1 A:ASP150 4.2 15.5 1.0
O A:HOH416 4.3 30.7 1.0
CG A:GLU121 4.3 12.6 1.0
CB A:GLU119 4.3 15.7 1.0
CG A:GLU119 4.4 15.2 1.0
CZ A:PHE93 4.5 19.6 1.0
CA A:GLY237 4.6 14.6 1.0
O A:HOH700 4.6 32.4 1.0
CE1 A:PHE93 4.8 20.9 1.0
CE A:LYS168 4.9 18.3 1.0
C A:GLY237 4.9 13.9 1.0
CD1 A:ILE235 4.9 21.2 1.0
CB A:THR238 4.9 16.7 1.0
O A:ASP150 5.0 12.6 1.0
N A:GLY237 5.0 13.2 1.0

Magnesium binding site 2 out of 5 in 8gst

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Magnesium binding site 2 out of 5 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form)


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-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:19.1
occ:1.00
 OE1 B:GLU121 2.0 19.4 1.0
OD2 B:ASP150 2.0 16.6 1.0
O B:HOH460 2.0 18.9 1.0
OE2 B:GLU119 2.1 19.8 1.0
O B:HOH591 2.2 29.4 1.0
O B:HOH581 2.3 30.1 1.0
CD B:GLU121 3.0 18.6 1.0
CG B:ASP150 3.0 17.1 1.0
CD B:GLU119 3.3 22.6 1.0
OE2 B:GLU121 3.4 16.3 1.0
CB B:ASP150 3.5 14.4 1.0
NZ B:LYS168 3.6 18.6 1.0
O B:ILE71 3.9 20.7 1.0
O B:HOH464 4.0 25.9 1.0
OE1 B:GLU119 4.1 23.2 1.0
OD1 B:ASP150 4.1 19.1 1.0
CG B:GLU121 4.3 17.5 1.0
CB B:GLU119 4.3 18.9 1.0
O B:HOH620 4.4 36.2 1.0
CG B:GLU119 4.4 20.9 1.0
CA B:GLY237 4.5 16.9 1.0
CZ B:PHE93 4.6 19.7 1.0
CE B:LYS168 4.8 18.7 1.0
C B:GLY237 4.8 19.7 1.0
N B:GLY237 4.9 18.8 1.0
CB B:THR238 4.9 21.9 1.0
N B:THR238 4.9 20.6 1.0
O B:ASP150 4.9 17.6 1.0
CE1 B:PHE93 5.0 24.6 1.0
CA B:ASP150 5.0 13.9 1.0

Magnesium binding site 3 out of 5 in 8gst

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Magnesium binding site 3 out of 5 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form)


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-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:15.1
occ:1.00
 OE1 C:GLU121 2.0 14.8 1.0
OD2 C:ASP150 2.0 16.0 1.0
O C:HOH468 2.1 14.3 1.0
OE2 C:GLU119 2.2 18.5 1.0
O3 C:PYR302 2.2 21.4 1.0
O1 C:PYR302 2.2 18.7 1.0
C2 C:PYR302 2.9 24.8 1.0
C1 C:PYR302 2.9 24.8 1.0
CD C:GLU121 3.0 16.0 1.0
CG C:ASP150 3.0 16.8 1.0
CD C:GLU119 3.4 17.5 1.0
OE2 C:GLU121 3.4 13.4 1.0
CB C:ASP150 3.5 15.9 1.0
NZ C:LYS168 3.6 17.6 1.0
O C:ILE71 4.0 22.2 1.0
O2 C:PYR302 4.1 26.1 1.0
OE1 C:GLU119 4.1 22.8 1.0
OD1 C:ASP150 4.2 15.5 1.0
CG C:GLU121 4.3 13.1 1.0
C3 C:PYR302 4.3 27.8 1.0
CB C:GLU119 4.4 15.7 1.0
CG C:GLU119 4.5 16.2 1.0
CA C:GLY237 4.5 16.2 1.0
N C:THR238 4.7 18.5 1.0
CZ C:PHE93 4.7 30.1 1.0
CE C:LYS168 4.8 19.1 1.0
CB C:THR238 4.8 14.8 1.0
C C:GLY237 4.8 16.4 1.0
CG2 C:THR238 4.9 17.7 1.0
CD1 C:ILE235 4.9 18.8 1.0
O C:ASP150 5.0 13.4 1.0
CA C:ASP150 5.0 13.5 1.0
N C:GLY237 5.0 17.1 1.0

Magnesium binding site 4 out of 5 in 8gst

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Magnesium binding site 4 out of 5 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form)


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-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:28.9
occ:1.00
 O C:HOH459 2.0 29.3 1.0
O C:HOH460 2.1 26.2 1.0
O C:HOH494 2.1 26.8 1.0
O C:HOH430 2.1 25.1 1.0
OD1 C:ASP191 3.7 26.1 1.0
OD2 C:ASP191 4.1 29.1 1.0
OE1 C:GLU264 4.2 27.2 1.0
CG C:ASP191 4.2 25.6 1.0
OE2 C:GLU264 4.2 21.4 1.0
O C:HOH679 4.5 32.3 1.0
OD2 C:ASP193 4.5 31.9 1.0
CD C:GLU264 4.7 26.1 1.0
O C:ASP191 4.7 22.5 1.0
ND2 C:ASN207 4.8 22.3 1.0

Magnesium binding site 5 out of 5 in 8gst

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Magnesium binding site 5 out of 5 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Pyruvate Bound-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:17.7
occ:1.00
 OE2 D:GLU121 1.9 21.1 1.0
O D:HOH553 2.0 27.2 1.0
OD2 D:ASP150 2.0 18.7 1.0
O D:HOH533 2.1 31.4 1.0
O D:HOH431 2.1 19.2 1.0
OE1 D:GLU119 2.2 22.8 1.0
CD D:GLU121 3.0 18.6 1.0
CG D:ASP150 3.1 18.1 1.0
OE1 D:GLU121 3.4 20.4 1.0
CD D:GLU119 3.4 23.4 1.0
CB D:ASP150 3.5 18.7 1.0
NZ D:LYS168 3.8 17.6 1.0
O D:ILE71 3.8 20.0 1.0
O D:HOH439 3.9 20.0 1.0
O D:HOH412 4.0 31.6 1.0
OE2 D:GLU119 4.2 24.0 1.0
OD1 D:ASP150 4.2 16.3 1.0
CG D:GLU121 4.2 20.3 1.0
CB D:GLU119 4.4 21.7 1.0
CG D:GLU119 4.5 22.6 1.0
CA D:GLY237 4.5 20.4 1.0
O D:HOH586 4.5 35.3 1.0
CZ D:PHE93 4.6 19.0 1.0
C D:GLY237 4.9 20.1 1.0
N D:GLY237 4.9 17.8 1.0
CE D:LYS168 4.9 17.4 1.0
CE1 D:PHE93 4.9 19.8 1.0
CB D:THR238 4.9 20.3 1.0
CD1 D:ILE235 4.9 20.3 1.0
O D:ASP150 4.9 17.7 1.0
N D:THR238 5.0 18.9 1.0

Reference:

S.Fukuhara, S.Watanabe, Y.Watanabe, H.Nishiwaki. Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase Involved in the Nonphosphorylated L-Rhamnose Pathway From Bacteria. Biochemistry V. 62 524 2023.
ISSN: ISSN 0006-2960
PubMed: 36563174
DOI: 10.1021/ACS.BIOCHEM.2C00596
Page generated: Fri Apr 7 11:21:39 2023

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