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Magnesium in PDB 4hgq: Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron

Protein crystallography data

The structure of Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron, PDB code: 4hgq 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) 37.10 / 2.28
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.941, 94.116, 161.497, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron (pdb code 4hgq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron, PDB code: 4hgq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4hgq

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Magnesium binding site 1 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:17.3
occ:1.00
 O A:HOH301 1.9 11.8 1.0
O A:ASP12 2.2 9.7 1.0
OD1 A:ASP103 2.2 13.3 1.0
O A:HOH327 2.2 12.5 1.0
OD1 A:ASP10 2.3 14.6 1.0
O A:HOH314 2.4 11.3 1.0
CG A:ASP103 3.1 14.1 1.0
C A:ASP12 3.3 14.3 1.0
CG A:ASP10 3.3 14.3 1.0
OD2 A:ASP103 3.4 12.6 1.0
OD2 A:ASP10 3.8 14.4 1.0
O A:HOH342 4.0 20.2 1.0
OD2 A:ASP107 4.1 13.8 1.0
CA A:ASP12 4.1 9.7 1.0
O B:HOH343 4.1 16.1 1.0
O A:HOH351 4.2 19.0 1.0
CB A:ASP12 4.2 10.0 1.0
N A:GLY13 4.2 12.2 1.0
N A:ASP12 4.3 7.7 1.0
CA A:GLY13 4.4 11.5 1.0
CB A:ASP103 4.5 9.3 1.0
O A:HOH331 4.5 10.0 1.0
CB A:ASP104 4.5 16.0 1.0
CB A:ASP10 4.5 11.0 1.0
N A:ASP103 4.6 11.7 1.0
N A:ASP104 4.7 11.2 1.0
NZ A:LYS80 4.8 8.1 1.0
CA A:ASP103 4.9 12.3 1.0
C A:ASP103 5.0 15.7 1.0

Magnesium binding site 2 out of 8 in 4hgq

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Magnesium binding site 2 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:20.3
occ:1.00
 O B:ASP12 2.1 13.9 1.0
OD1 B:ASP103 2.2 19.3 1.0
O B:HOH308 2.4 20.1 1.0
O B:HOH312 2.4 13.8 1.0
OD1 B:ASP10 2.5 15.8 1.0
CG B:ASP103 2.9 19.3 1.0
OD2 B:ASP103 3.0 23.0 1.0
C B:ASP12 3.3 17.1 1.0
CG B:ASP10 3.6 19.1 1.0
O B:HOH335 3.9 15.9 1.0
O B:HOH357 4.1 21.4 1.0
CB B:ASP12 4.1 12.1 1.0
OD2 B:ASP10 4.1 15.6 1.0
CA B:ASP12 4.1 13.4 1.0
O D:HOH319 4.2 21.4 1.0
N B:GLY13 4.3 15.1 1.0
CA B:GLY13 4.4 14.5 1.0
CB B:ASP103 4.4 19.4 1.0
N B:ASP12 4.4 15.3 1.0
OD2 B:ASP107 4.4 19.6 1.0
CB B:ASP104 4.5 19.6 1.0
O B:HOH331 4.6 21.0 1.0
N B:ASP104 4.7 15.4 1.0
N B:ASP103 4.7 14.4 1.0
O B:HOH301 4.8 7.1 1.0
CB B:ASP10 4.9 14.8 1.0
CA B:ASP103 4.9 19.9 1.0
C B:ASP103 5.0 22.7 1.0

Magnesium binding site 3 out of 8 in 4hgq

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Magnesium binding site 3 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:11.6
occ:1.00
 O C:HOH315 2.0 17.8 1.0
O C:HOH316 2.2 14.7 1.0
OD1 C:ASP103 2.2 14.3 1.0
O C:ASP12 2.2 15.9 1.0
OD1 C:ASP10 2.3 16.0 1.0
CG C:ASP103 3.2 19.2 1.0
CG C:ASP10 3.3 14.4 1.0
C C:ASP12 3.4 14.1 1.0
OD2 C:ASP103 3.5 16.9 1.0
OD2 C:ASP10 3.6 13.4 1.0
O A:HOH349 3.9 24.6 1.0
O C:HOH319 4.1 13.9 1.0
CA C:ASP12 4.1 15.7 1.0
CB C:ASP12 4.1 14.5 1.0
N C:ASP12 4.3 13.3 1.0
OD2 C:ASP107 4.3 18.3 1.0
N C:GLY13 4.4 13.7 1.0
O C:HOH334 4.5 21.6 1.0
CB C:ASP103 4.6 10.1 1.0
CB C:ASP10 4.6 14.6 1.0
CA C:GLY13 4.6 12.8 1.0
N C:ASP103 4.6 10.6 1.0
CB C:ASP104 4.6 13.6 1.0
N C:ASP104 4.8 9.1 1.0
NZ C:LYS80 4.9 8.9 1.0
C C:ILE11 5.0 13.8 1.0
CA C:ASP103 5.0 15.9 1.0

Magnesium binding site 4 out of 8 in 4hgq

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Magnesium binding site 4 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:18.9
occ:1.00
 O D:HOH311 2.1 13.7 1.0
OD2 D:ASP10 2.2 18.7 1.0
O D:HOH345 2.2 22.9 1.0
OD1 D:ASP103 2.3 20.0 1.0
O D:HOH302 2.3 17.6 1.0
O D:ASP12 2.4 17.3 1.0
CG D:ASP10 3.3 18.5 1.0
CG D:ASP103 3.3 22.1 1.0
O D:HOH320 3.5 18.3 1.0
C D:ASP12 3.5 19.8 1.0
OD2 D:ASP103 3.6 21.3 1.0
OD1 D:ASP10 3.7 16.4 1.0
OD2 D:ASP107 3.9 24.0 1.0
CA D:ASP12 4.2 15.0 1.0
CB D:ASP12 4.3 15.2 1.0
N D:ASP12 4.4 12.2 1.0
CB D:ASP104 4.4 17.8 1.0
O D:HOH301 4.5 8.4 1.0
CB D:ASP10 4.6 18.4 1.0
N D:GLY13 4.6 17.7 1.0
N D:ASP103 4.6 21.4 1.0
CB D:ASP103 4.6 19.7 1.0
NZ D:LYS80 4.7 17.5 1.0
CA D:GLY13 4.8 13.4 1.0
N D:ASP104 4.8 18.0 1.0
CG D:ASP107 4.9 24.6 1.0
OD1 D:ASP107 4.9 18.1 1.0

Magnesium binding site 5 out of 8 in 4hgq

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Magnesium binding site 5 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 5 of Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:21.0
occ:1.00
 O E:ASP12 2.2 19.9 1.0
OD1 E:ASP10 2.3 17.9 1.0
O E:HOH322 2.3 24.3 1.0
OD1 E:ASP103 2.3 23.2 1.0
O E:HOH314 2.7 20.1 1.0
CG E:ASP103 3.1 23.4 1.0
OD2 E:ASP103 3.2 20.2 1.0
C E:ASP12 3.3 21.2 1.0
CG E:ASP10 3.4 21.5 1.0
OD2 E:ASP10 3.8 26.4 1.0
O F:HOH371 3.9 35.2 1.0
CB E:ASP12 4.0 20.7 1.0
O E:HOH327 4.0 23.5 1.0
CA E:ASP12 4.0 22.5 1.0
N E:ASP12 4.2 15.9 1.0
N E:GLY13 4.3 17.7 1.0
OD2 E:ASP107 4.3 23.7 1.0
CA E:GLY13 4.5 16.7 1.0
CB E:ASP103 4.5 17.0 1.0
CB E:ASP104 4.6 19.7 1.0
CB E:ASP10 4.6 20.8 1.0
O E:HOH317 4.8 12.7 1.0
N E:ASP103 4.9 19.4 1.0
CG2 F:THR34 4.9 22.7 1.0
N E:ASP104 4.9 19.1 1.0
C E:ILE11 5.0 20.7 1.0

Magnesium binding site 6 out of 8 in 4hgq

Go back to Magnesium Binding Sites List in 4hgq
Magnesium binding site 6 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 6 of Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:23.7
occ:1.00
 O F:HOH305 1.8 20.1 1.0
O F:ASP12 2.3 19.1 1.0
O F:HOH313 2.3 22.0 1.0
OD1 F:ASP10 2.4 18.0 1.0
OD1 F:ASP103 2.4 20.1 1.0
C F:ASP12 3.2 20.3 1.0
CG F:ASP103 3.3 22.4 1.0
OD2 F:ASP103 3.4 28.8 1.0
CG F:ASP10 3.4 22.5 1.0
CB F:ASP12 3.7 17.8 1.0
OD2 F:ASP10 3.8 21.0 1.0
O H:HOH318 3.9 25.4 1.0
CA F:ASP12 3.9 17.4 1.0
O F:HOH335 4.0 28.0 1.0
N F:ASP12 4.2 16.2 1.0
N F:GLY13 4.2 17.2 1.0
CA F:GLY13 4.4 17.1 1.0
OD2 F:ASP107 4.6 26.2 1.0
CB F:ASP104 4.7 26.4 1.0
CB F:ASP103 4.7 22.0 1.0
CB F:ASP10 4.7 18.4 1.0
O F:HOH301 4.8 12.5 1.0
CG2 H:THR34 4.8 15.7 1.0
O F:HOH318 4.8 24.5 1.0
C F:ILE11 4.9 18.6 1.0
CG F:ASP12 4.9 21.1 1.0

Magnesium binding site 7 out of 8 in 4hgq

Go back to Magnesium Binding Sites List in 4hgq
Magnesium binding site 7 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 7 of Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg201

b:21.6
occ:1.00
 O G:HOH303 1.9 23.5 1.0
OD1 G:ASP10 2.2 26.4 1.0
O G:ASP12 2.2 21.0 1.0
OD1 G:ASP103 2.3 20.3 1.0
O G:HOH320 2.4 22.0 1.0
O G:HOH314 2.8 30.8 1.0
CG G:ASP103 3.3 21.3 1.0
CG G:ASP10 3.3 25.3 1.0
C G:ASP12 3.3 22.9 1.0
OD2 G:ASP103 3.5 23.0 1.0
OD2 G:ASP10 3.7 26.1 1.0
O E:HOH335 3.7 32.5 1.0
O G:HOH313 4.0 25.8 1.0
CA G:ASP12 4.0 20.8 1.0
N G:ASP12 4.0 20.4 1.0
CB G:ASP12 4.1 20.6 1.0
O G:HOH338 4.2 31.5 1.0
OD2 G:ASP107 4.2 30.9 1.0
N G:GLY13 4.4 20.5 1.0
O G:HOH301 4.5 11.1 1.0
CB G:ASP10 4.6 21.3 1.0
CB G:ASP103 4.6 22.8 1.0
CB G:ASP104 4.7 26.6 1.0
CA G:GLY13 4.7 18.2 1.0
NZ G:LYS80 4.7 22.1 1.0
C G:ILE11 4.8 24.6 1.0
N G:ASP103 4.9 18.3 1.0
OD1 G:ASP107 5.0 26.4 1.0

Magnesium binding site 8 out of 8 in 4hgq

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Magnesium binding site 8 out of 8 in the Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-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 8 of Crystal Structure of E56A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg201

b:24.9
occ:1.00
 O H:HOH304 2.3 19.1 1.0
O H:HOH341 2.3 26.6 1.0
O H:ASP12 2.4 23.1 1.0
OD2 H:ASP10 2.4 25.0 1.0
OD1 H:ASP103 2.5 24.4 1.0
O H:HOH317 2.5 31.5 1.0
CG H:ASP10 3.4 24.9 1.0
C H:ASP12 3.4 20.6 1.0
CG H:ASP103 3.5 30.9 1.0
O G:HOH340 3.5 29.6 1.0
O H:HOH325 3.6 20.4 1.0
OD1 H:ASP10 3.6 19.1 1.0
OD2 H:ASP103 3.7 22.8 1.0
CB H:ASP12 3.9 24.3 1.0
O H:HOH321 3.9 22.9 1.0
CA H:ASP12 4.0 23.2 1.0
O H:HOH315 4.1 26.2 1.0
N H:ASP12 4.3 22.3 1.0
O H:HOH301 4.3 12.0 1.0
N H:GLY13 4.4 16.6 1.0
OD2 H:ASP107 4.6 27.5 1.0
CA H:GLY13 4.7 19.8 1.0
CB H:ASP10 4.7 23.5 1.0
CB H:ASP104 4.8 22.9 1.0
NZ H:LYS80 4.8 23.0 1.0
CB H:ASP103 4.8 21.2 1.0
OD2 H:ASP12 4.9 25.6 1.0
C H:ILE11 4.9 22.3 1.0
CG H:ASP12 5.0 26.0 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 16:17:37 2024

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