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Magnesium in PDB 4hgr: Crystal Structure of E56A/K67A 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/K67A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron, PDB code: 4hgr 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) 50.72 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.367, 116.765, 75.180, 90.00, 93.09, 90.00
R / Rfree (%) 19 / 24.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E56A/K67A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron (pdb code 4hgr). 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/K67A Mutant of 2-Keto-3-Deoxy-D-Glycero-D- Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron, PDB code: 4hgr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4hgr

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Magnesium binding site 1 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:13.3
occ:1.00
 O A:ASP12 2.1 12.7 1.0
OD2 A:ASP10 2.1 11.0 1.0
O A:HOH327 2.1 15.8 1.0
O A:HOH301 2.1 14.8 1.0
O A:HOH302 2.2 14.5 1.0
OD1 A:ASP103 2.2 14.0 1.0
CG A:ASP10 3.1 12.5 1.0
C A:ASP12 3.2 13.0 1.0
CG A:ASP103 3.2 13.1 1.0
OD1 A:ASP10 3.4 13.3 1.0
OD2 A:ASP103 3.5 17.3 1.0
CB A:ASP12 3.8 11.9 1.0
CA A:ASP12 3.9 13.1 1.0
N A:ASP12 4.0 11.9 1.0
OD2 A:ASP107 4.2 15.3 1.0
O A:HOH329 4.2 16.9 1.0
O A:HOH328 4.2 22.4 1.0
N A:GLY13 4.3 12.2 1.0
CB A:ASP10 4.4 12.2 1.0
O A:HOH325 4.4 14.9 1.0
O A:HOH341 4.4 21.3 1.0
CA A:GLY13 4.5 11.5 1.0
CB A:ASP103 4.6 14.3 1.0
C A:ILE11 4.7 12.2 1.0
CB A:ASP104 4.8 14.4 1.0
N A:ASP103 4.8 11.4 1.0
OD2 A:ASP12 4.9 18.6 1.0
N A:ASP104 4.9 14.3 1.0
CG A:ASP12 4.9 17.2 1.0
N A:ILE11 5.0 11.8 1.0
NZ A:LYS80 5.0 16.3 1.0

Magnesium binding site 2 out of 8 in 4hgr

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Magnesium binding site 2 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:13.7
occ:1.00
 OD1 B:ASP103 2.0 19.4 1.0
OD2 B:ASP10 2.1 14.2 1.0
O B:HOH301 2.2 14.6 1.0
O B:ASP12 2.2 12.6 1.0
O B:HOH316 2.4 16.5 1.0
O B:HOH396 2.9 11.8 1.0
CG B:ASP10 3.1 14.1 1.0
CG B:ASP103 3.1 14.1 1.0
C B:ASP12 3.3 12.2 1.0
OD2 B:ASP103 3.5 19.3 1.0
OD1 B:ASP10 3.5 17.2 1.0
O B:HOH394 3.9 24.1 1.0
O D:HOH382 3.9 23.2 1.0
O D:HOH349 4.0 19.2 1.0
CA B:ASP12 4.1 13.7 1.0
OD2 B:ASP107 4.1 16.9 1.0
CB B:ASP12 4.2 14.0 1.0
N B:ASP12 4.2 10.1 1.0
O B:HOH398 4.2 16.8 1.0
O B:HOH343 4.3 18.7 1.0
N B:GLY13 4.4 11.4 1.0
CB B:ASP10 4.4 12.5 1.0
CB B:ASP103 4.4 16.0 1.0
CB B:ASP104 4.5 17.6 1.0
O B:HOH397 4.6 17.6 1.0
CA B:GLY13 4.6 9.0 1.0
N B:ASP104 4.6 14.1 1.0
N B:ASP103 4.6 14.6 1.0
O B:HOH342 4.7 21.3 1.0
CA B:ASP103 4.9 13.5 1.0
O B:HOH340 4.9 20.8 1.0
CG2 D:THR34 4.9 12.5 1.0
C B:ILE11 5.0 12.5 1.0

Magnesium binding site 3 out of 8 in 4hgr

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Magnesium binding site 3 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:14.6
occ:1.00
 O C:HOH369 1.9 18.2 1.0
OD2 C:ASP10 2.0 14.9 1.0
OD1 C:ASP103 2.0 12.9 1.0
O C:HOH302 2.1 14.7 1.0
O C:ASP12 2.1 13.5 1.0
O C:HOH303 2.3 13.9 1.0
CG C:ASP103 3.0 11.2 1.0
CG C:ASP10 3.1 14.1 1.0
C C:ASP12 3.3 12.9 1.0
OD2 C:ASP103 3.3 15.3 1.0
OD1 C:ASP10 3.5 16.3 1.0
OD2 C:ASP107 3.9 13.0 1.0
O C:HOH326 4.1 16.3 1.0
CA C:ASP12 4.1 14.2 1.0
N C:ASP12 4.2 12.6 1.0
CB C:ASP12 4.2 15.4 1.0
O C:HOH318 4.3 24.9 1.0
CB C:ASP10 4.3 11.4 1.0
N C:GLY13 4.3 12.3 1.0
CB C:ASP103 4.3 12.9 1.0
CA C:GLY13 4.5 10.8 1.0
N C:ASP103 4.5 9.4 1.0
NZ C:LYS80 4.7 15.4 1.0
CB C:ASP104 4.7 14.3 1.0
O C:HOH340 4.7 17.2 1.0
N C:ASP104 4.7 11.6 1.0
CA C:ASP103 4.9 13.8 1.0
C C:ILE11 4.9 13.4 1.0
O C:HOH325 4.9 12.2 1.0
CG C:ASP107 4.9 12.7 1.0
C C:ASP103 5.0 15.3 1.0

Magnesium binding site 4 out of 8 in 4hgr

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Magnesium binding site 4 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:12.1
occ:1.00
 O D:HOH398 1.9 11.1 1.0
O D:HOH312 1.9 9.8 1.0
OD2 D:ASP10 2.0 10.1 1.0
OD1 D:ASP103 2.1 14.0 1.0
O D:ASP12 2.1 9.6 1.0
O D:HOH308 2.2 9.2 1.0
CG D:ASP103 3.0 12.6 1.0
CG D:ASP10 3.1 13.6 1.0
C D:ASP12 3.3 12.9 1.0
OD2 D:ASP103 3.4 17.5 1.0
OD1 D:ASP10 3.5 11.4 1.0
O C:HOH311 4.1 16.8 1.0
CA D:ASP12 4.2 11.2 1.0
N D:ASP12 4.2 12.9 1.0
OD2 D:ASP107 4.2 14.4 1.0
CB D:ASP12 4.3 12.3 1.0
N D:GLY13 4.3 11.1 1.0
CB D:ASP10 4.4 12.7 1.0
CB D:ASP103 4.4 9.9 1.0
O D:HOH324 4.4 16.1 1.0
O D:HOH336 4.4 18.2 1.0
O D:HOH316 4.4 14.3 1.0
CA D:GLY13 4.5 9.2 1.0
N D:ASP103 4.5 12.0 1.0
NZ D:LYS80 4.6 13.0 1.0
N D:ASP104 4.7 11.4 1.0
CB D:ASP104 4.8 12.6 1.0
C D:ILE11 4.8 9.2 1.0
CA D:ASP103 4.9 11.0 1.0
OD1 D:ASP107 4.9 15.2 1.0
CG D:ASP107 5.0 13.9 1.0
C D:ASP103 5.0 11.0 1.0

Magnesium binding site 5 out of 8 in 4hgr

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Magnesium binding site 5 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:24.1
occ:1.00
 O E:HOH342 2.0 20.4 1.0
OD2 E:ASP10 2.1 20.5 1.0
O E:HOH301 2.1 16.8 1.0
O E:HOH316 2.4 23.2 1.0
O E:ASP12 2.4 18.6 1.0
CG E:ASP10 2.8 20.4 1.0
OD1 E:ASP10 2.9 21.3 1.0
OD1 E:ASP103 3.1 22.0 1.0
C E:ASP12 3.4 16.8 1.0
O E:HOH348 3.4 28.2 1.0
CB E:ASP12 3.5 20.1 1.0
O E:HOH318 3.6 34.3 1.0
N E:ASP12 3.6 17.4 1.0
CA E:ASP12 3.7 17.3 1.0
CG E:ASP103 4.0 23.6 1.0
O E:HOH315 4.1 26.4 1.0
CB E:ASP10 4.3 17.1 1.0
OD2 E:ASP103 4.3 25.0 1.0
OD2 E:ASP107 4.5 20.2 1.0
C E:ILE11 4.5 18.2 1.0
CG E:ASP12 4.6 21.2 1.0
N E:ILE11 4.6 16.8 1.0
N E:GLY13 4.6 16.9 1.0
OD1 E:ASP12 4.6 22.9 1.0
NZ E:LYS80 4.8 23.3 1.0

Magnesium binding site 6 out of 8 in 4hgr

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Magnesium binding site 6 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:16.6
occ:1.00
 O F:HOH301 1.8 19.2 1.0
OD1 F:ASP103 2.0 19.4 1.0
O F:ASP12 2.1 13.7 1.0
O F:HOH302 2.1 17.6 1.0
OD2 F:ASP10 2.2 17.3 1.0
O F:HOH352 2.3 15.2 1.0
CG F:ASP103 2.9 19.4 1.0
OD2 F:ASP103 3.1 15.5 1.0
CG F:ASP10 3.3 17.4 1.0
C F:ASP12 3.3 12.6 1.0
OD1 F:ASP10 3.7 14.4 1.0
O F:HOH322 3.7 18.4 1.0
OD2 F:ASP107 4.1 17.4 1.0
O F:HOH327 4.1 18.6 1.0
CA F:ASP12 4.1 14.1 1.0
CB F:ASP12 4.2 14.3 1.0
O F:HOH311 4.2 19.2 1.0
N F:ASP12 4.3 14.0 1.0
CB F:ASP103 4.3 16.8 1.0
N F:GLY13 4.3 12.1 1.0
CB F:ASP104 4.4 18.5 1.0
CA F:GLY13 4.5 12.3 1.0
CB F:ASP10 4.5 16.1 1.0
N F:ASP103 4.7 18.9 1.0
N F:ASP104 4.7 15.2 1.0
O F:HOH310 4.8 14.8 1.0
CA F:ASP103 4.9 17.4 1.0
CG2 H:THR34 4.9 15.2 1.0
C F:ASP103 5.0 18.0 1.0

Magnesium binding site 7 out of 8 in 4hgr

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Magnesium binding site 7 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:19.2
occ:1.00
 O G:ASP12 1.9 14.1 1.0
O G:HOH302 2.0 18.3 1.0
OD2 G:ASP10 2.1 14.6 1.0
OD1 G:ASP103 2.2 13.6 1.0
O G:HOH303 2.3 19.9 1.0
O G:HOH320 2.4 17.0 1.0
C G:ASP12 3.0 15.2 1.0
CG G:ASP103 3.1 18.2 1.0
CG G:ASP10 3.1 14.4 1.0
OD2 G:ASP103 3.3 18.0 1.0
OD1 G:ASP10 3.5 13.8 1.0
CB G:ASP12 3.7 16.3 1.0
CA G:ASP12 3.7 15.3 1.0
N G:ASP12 4.0 12.6 1.0
N G:GLY13 4.0 15.0 1.0
O G:HOH333 4.2 24.1 1.0
OD2 G:ASP107 4.3 16.7 1.0
CA G:GLY13 4.3 16.4 1.0
CB G:ASP10 4.5 13.2 1.0
CB G:ASP103 4.5 15.6 1.0
C G:ILE11 4.7 14.4 1.0
N G:ASP103 4.8 13.4 1.0
O G:HOH312 4.8 19.9 1.0
O G:HOH306 4.9 21.3 1.0
CB G:ASP104 4.9 15.4 1.0
C G:GLY13 5.0 15.8 1.0
O G:HOH351 5.0 26.1 1.0

Magnesium binding site 8 out of 8 in 4hgr

Go back to Magnesium Binding Sites List in 4hgr
Magnesium binding site 8 out of 8 in the Crystal Structure of E56A/K67A 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/K67A 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:18.6
occ:1.00
 OD2 H:ASP10 2.0 18.9 1.0
O H:ASP12 2.1 14.5 1.0
O H:HOH315 2.2 18.9 1.0
OD1 H:ASP103 2.2 20.6 1.0
O H:HOH324 2.4 19.1 1.0
O H:HOH322 2.9 22.0 1.0
CG H:ASP10 3.1 18.1 1.0
C H:ASP12 3.2 16.0 1.0
CG H:ASP103 3.3 17.5 1.0
OD1 H:ASP10 3.4 16.5 1.0
OD2 H:ASP103 3.7 18.9 1.0
O H:HOH319 3.7 26.8 1.0
CB H:ASP12 3.9 18.4 1.0
CA H:ASP12 3.9 15.0 1.0
N H:ASP12 4.0 14.4 1.0
OD2 H:ASP107 4.3 18.5 1.0
N H:GLY13 4.3 14.2 1.0
CB H:ASP10 4.4 14.0 1.0
O H:HOH301 4.4 20.5 1.0
O H:HOH330 4.4 21.5 1.0
CB H:ASP103 4.5 14.9 1.0
O H:HOH321 4.6 16.9 1.0
CA H:GLY13 4.6 13.0 1.0
N H:ASP103 4.6 15.8 1.0
CB H:ASP104 4.7 18.6 1.0
NZ H:LYS80 4.8 20.1 1.0
C H:ILE11 4.8 15.3 1.0
N H:ASP104 4.9 16.8 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 16:17:57 2024

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