Atomistry » Magnesium » PDB 4h9l-4hli » 4hgn
Atomistry »
  Magnesium »
    PDB 4h9l-4hli »
      4hgn »

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

Go back to Magnesium Binding Sites List in 4hgn
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

Go back to Magnesium Binding Sites List in 4hgn
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

Go back to Magnesium Binding Sites List in 4hgn
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

Go back to Magnesium Binding Sites List in 4hgn
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy