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

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

Go back to Magnesium Binding Sites List in 4hgr
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

Go back to Magnesium Binding Sites List in 4hgr
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

Go back to Magnesium Binding Sites List in 4hgr
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

Go back to Magnesium Binding Sites List in 4hgr
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

Go back to Magnesium Binding Sites List in 4hgr
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

Go back to Magnesium Binding Sites List in 4hgr
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

Go back to Magnesium Binding Sites List in 4hgr
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy