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Magnesium in PDB 4hgn: Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron

Enzymatic activity of Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron

All present enzymatic activity of Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron:
3.1.3.45;

Protein crystallography data

The structure of Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron, PDB code: 4hgn was solved by K.D.Daughtry, K.N.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.64 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.522, 91.198, 170.067, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron (pdb code 4hgn). 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 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron, PDB code: 4hgn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4hgn

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Magnesium binding site 1 out of 4 in the Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron


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 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg200

b:17.4
occ:1.00
 OD2 A:ASP17 2.0 17.3 1.0
OD1 A:ASP110 2.0 15.6 1.0
O A:ASP19 2.0 16.4 1.0
O A:HOH339 2.1 18.5 1.0
O A:HOH328 2.1 16.6 1.0
O A:HOH326 2.1 13.9 1.0
CG A:ASP110 3.1 16.1 1.0
CG A:ASP17 3.1 17.1 1.0
C A:ASP19 3.3 14.7 1.0
OD2 A:ASP110 3.4 15.9 1.0
OD1 A:ASP17 3.6 19.1 1.0
O A:HOH352 4.0 28.1 1.0
OD2 A:ASP114 4.0 15.1 1.0
CA A:ASP19 4.1 15.9 1.0
N A:GLY20 4.2 15.5 1.0
CB A:ASP19 4.2 19.4 1.0
N A:ASP19 4.3 15.8 1.0
CA A:GLY20 4.3 12.4 1.0
CB A:ASP17 4.3 15.4 1.0
CB A:ASP110 4.4 12.3 1.0
O A:HOH355 4.5 19.3 1.0
O A:HOH327 4.6 21.3 1.0
N A:ASP110 4.6 16.4 1.0
N A:ASP111 4.6 14.5 1.0
CB A:ASP111 4.7 16.3 1.0
C A:GLY20 4.8 14.3 1.0
O A:HOH302 4.9 18.8 1.0
CA A:ASP110 4.9 14.7 1.0
CG2 A:VAL21 5.0 13.2 1.0

Magnesium binding site 2 out of 4 in 4hgn

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Magnesium binding site 2 out of 4 in the Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron


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 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:17.9
occ:1.00
 OD2 B:ASP17 2.0 20.1 1.0
OD1 B:ASP110 2.0 18.4 1.0
O B:HOH338 2.0 22.1 1.0
O B:HOH321 2.0 17.5 1.0
O B:HOH320 2.1 18.8 1.0
O B:ASP19 2.1 16.9 1.0
CG B:ASP17 3.0 19.2 1.0
CG B:ASP110 3.1 18.2 1.0
C B:ASP19 3.3 17.2 1.0
OD2 B:ASP110 3.5 17.3 1.0
OD1 B:ASP17 3.5 24.4 1.0
OD2 B:ASP114 3.9 18.9 1.0
CA B:ASP19 4.1 18.3 1.0
O B:HOH312 4.2 27.7 1.0
N B:GLY20 4.3 14.6 1.0
CB B:ASP19 4.3 18.6 1.0
N B:ASP19 4.3 17.4 1.0
CB B:ASP17 4.3 17.2 1.0
O B:HOH305 4.4 16.8 1.0
CB B:ASP110 4.4 15.0 1.0
NZ B:LYS87 4.4 26.3 1.0
CA B:GLY20 4.4 15.4 1.0
N B:ASP110 4.5 15.8 1.0
N B:ASP111 4.7 17.4 1.0
CB B:ASP111 4.7 17.1 1.0
CG2 B:VAL21 4.7 15.0 1.0
CG B:ASP114 4.8 21.5 1.0
C B:GLY20 4.9 14.3 1.0
CA B:ASP110 4.9 17.1 1.0
OD1 B:ASP114 4.9 17.9 1.0
O B:HOH309 5.0 25.1 1.0

Magnesium binding site 3 out of 4 in 4hgn

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Magnesium binding site 3 out of 4 in the Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron


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 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:15.8
occ:1.00
 OD2 C:ASP17 1.9 17.0 1.0
OD1 C:ASP110 2.0 14.9 1.0
O C:HOH301 2.0 14.7 1.0
O C:ASP19 2.0 16.1 1.0
O C:HOH348 2.1 17.4 1.0
O C:HOH322 2.1 16.5 1.0
CG C:ASP17 3.0 15.4 1.0
CG C:ASP110 3.1 16.2 1.0
C C:ASP19 3.3 16.0 1.0
OD2 C:ASP110 3.5 18.5 1.0
OD1 C:ASP17 3.5 19.8 1.0
OD2 C:ASP114 4.0 17.9 1.0
CA C:ASP19 4.1 16.8 1.0
N C:GLY20 4.2 15.4 1.0
O C:HOH351 4.2 26.7 1.0
CB C:ASP17 4.3 16.0 1.0
CB C:ASP19 4.3 18.3 1.0
N C:ASP19 4.3 17.4 1.0
CA C:GLY20 4.3 15.3 1.0
CB C:ASP110 4.4 16.2 1.0
O C:HOH306 4.4 19.1 1.0
O C:HOH304 4.5 22.7 1.0
N C:ASP110 4.6 14.9 1.0
NZ C:LYS87 4.7 22.9 1.0
CB C:ASP111 4.7 15.0 1.0
N C:ASP111 4.8 12.8 1.0
C C:GLY20 4.9 14.4 1.0
CG C:ASP114 4.9 14.2 1.0
CA C:ASP110 4.9 14.6 1.0
CG2 C:VAL21 5.0 14.2 1.0
OD1 C:ASP114 5.0 17.1 1.0

Magnesium binding site 4 out of 4 in 4hgn

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Magnesium binding site 4 out of 4 in the Crystal Structure of 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron


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 2-Keto-3-Deoxyoctulosonate 8-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg200

b:18.5
occ:1.00
 OD2 D:ASP17 1.9 21.3 1.0
OD1 D:ASP110 2.0 19.6 1.0
O D:ASP19 2.0 19.5 1.0
O D:HOH370 2.0 21.0 1.0
O D:HOH303 2.1 18.1 1.0
O D:HOH321 2.1 19.8 1.0
CG D:ASP110 3.0 19.4 1.0
CG D:ASP17 3.0 22.2 1.0
C D:ASP19 3.2 19.6 1.0
OD2 D:ASP110 3.4 17.0 1.0
OD1 D:ASP17 3.5 19.9 1.0
OD2 D:ASP114 4.0 19.4 1.0
CA D:ASP19 4.0 20.3 1.0
CB D:ASP19 4.1 21.4 1.0
O D:HOH329 4.2 31.5 1.0
N D:GLY20 4.2 13.7 1.0
N D:ASP19 4.2 19.0 1.0
CB D:ASP17 4.3 18.4 1.0
CB D:ASP110 4.3 19.8 1.0
O D:HOH307 4.4 25.3 1.0
CA D:GLY20 4.4 15.8 1.0
O D:HOH314 4.4 20.8 1.0
N D:ASP110 4.6 16.9 1.0
CB D:ASP111 4.6 20.1 1.0
N D:ASP111 4.7 16.3 1.0
CA D:ASP110 4.9 18.1 1.0
C D:GLY20 4.9 16.2 1.0
CG2 D:VAL21 5.0 15.1 1.0
CG D:ASP114 5.0 19.2 1.0
C D:VAL18 5.0 17.0 1.0

Reference:

K.D.Daughtry, H.Huang, V.Malashkevich, Y.Patskovsky, W.Liu, U.Ramagopal, J.M.Sauder, S.K.Burley, S.C.Almo, D.Dunaway-Mariano, K.N.Allen. Structural Basis For the Divergence of Substrate Specificity and Biological Function Within Had Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis. Biochemistry V. 52 5372 2013.
ISSN: ISSN 0006-2960
PubMed: 23848398
DOI: 10.1021/BI400659K
Page generated: Fri Aug 16 16:17:18 2024

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