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Vanadium in PDB 4hgo: 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic

Protein crystallography data

The structure of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic, PDB code: 4hgo 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) 28.48 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.296, 106.324, 74.147, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24.6

Other elements in 4hgo:

The structure of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic (pdb code 4hgo). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 4 binding sites of Vanadium where determined in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic, PDB code: 4hgo:
Jump to Vanadium binding site number: 1; 2; 3; 4;

Vanadium binding site 1 out of 4 in 4hgo

Go back to Vanadium Binding Sites List in 4hgo
Vanadium binding site 1 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V201

b:45.0
occ:1.00
V A:VN4201 0.0 45.0 1.0
O1 A:VN4201 1.7 22.1 1.0
O2 A:VN4201 1.7 26.5 1.0
O3 A:VN4201 1.7 24.1 1.0
OD2 A:ASP10 2.2 17.3 1.0
O10 A:KDN202 2.5 33.2 1.0
CG A:ASP10 3.1 17.2 1.0
C9 A:KDN202 3.2 38.0 1.0
OD1 A:ASP10 3.4 15.6 1.0
O A:HOH348 3.5 21.3 1.0
MG A:MG200 3.5 21.3 1.0
OG1 A:THR54 3.5 21.0 1.0
NZ A:LYS80 3.7 22.4 1.0
O A:HOH337 3.7 17.2 1.0
OD1 A:ASP12 3.9 21.8 1.0
N A:ASP12 3.9 13.9 1.0
N A:ILE11 4.0 16.5 1.0
N A:GLY55 4.0 24.5 1.0
CA A:THR54 4.2 21.8 1.0
CB A:THR54 4.2 22.6 1.0
CB A:ASP12 4.3 13.4 1.0
CE A:LYS80 4.4 14.8 1.0
O A:ASP12 4.4 14.0 1.0
CB A:ASP10 4.5 16.4 1.0
CG A:ASP12 4.6 21.1 1.0
CA A:ASP12 4.6 15.8 1.0
C7 A:KDN202 4.6 34.8 1.0
C A:THR54 4.7 19.0 1.0
C A:ILE11 4.7 13.8 1.0
O A:LEU53 4.7 16.0 1.0
CA A:ILE11 4.7 12.8 1.0
CA A:ASP10 4.9 15.2 1.0
O A:HOH338 4.9 19.7 1.0
O7 A:KDN202 4.9 35.8 1.0
CB A:ILE11 4.9 15.9 1.0
C A:ASP10 4.9 13.7 1.0
C A:ASP12 5.0 15.9 1.0
O A:HOH306 5.0 21.2 1.0

Vanadium binding site 2 out of 4 in 4hgo

Go back to Vanadium Binding Sites List in 4hgo
Vanadium binding site 2 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V201

b:36.2
occ:1.00
V B:VN4201 0.0 36.2 1.0
O1 B:VN4201 1.7 23.9 1.0
O2 B:VN4201 1.7 21.1 1.0
O3 B:VN4201 1.7 28.8 1.0
OD2 B:ASP10 2.2 20.2 1.0
O10 D:KDN203 2.5 31.9 1.0
CG B:ASP10 3.0 15.3 1.0
OD1 B:ASP10 3.2 16.8 1.0
C9 D:KDN203 3.2 32.3 1.0
MG B:MG200 3.3 19.9 1.0
O B:HOH356 3.5 23.4 1.0
OG1 B:THR54 3.6 18.8 1.0
O B:HOH347 3.6 16.7 1.0
OD2 B:ASP12 3.7 20.2 1.0
NZ B:LYS80 3.8 24.7 1.0
N B:ASP12 3.8 11.6 1.0
CB B:ASP12 4.0 14.4 1.0
N B:ILE11 4.1 11.3 1.0
O B:ASP12 4.2 9.6 1.0
CB B:THR54 4.2 17.6 1.0
N B:GLY55 4.3 14.9 1.0
CA B:THR54 4.3 13.3 1.0
CG B:ASP12 4.3 18.4 1.0
CA B:ASP12 4.4 15.9 1.0
CB B:ASP10 4.4 12.0 1.0
O B:HOH348 4.5 14.8 1.0
C7 D:KDN203 4.6 34.1 1.0
C B:ILE11 4.7 12.3 1.0
CE B:LYS80 4.7 16.1 1.0
C B:ASP12 4.8 10.1 1.0
CA B:ILE11 4.8 11.9 1.0
C B:THR54 4.8 17.7 1.0
O7 D:KDN203 4.8 40.7 1.0
CA B:ASP10 4.9 11.6 1.0
O B:LEU53 4.9 19.1 1.0
C B:ASP10 5.0 11.7 1.0
CB B:ILE11 5.0 14.2 1.0

Vanadium binding site 3 out of 4 in 4hgo

Go back to Vanadium Binding Sites List in 4hgo
Vanadium binding site 3 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
C:V201

b:46.4
occ:1.00
V C:VN4201 0.0 46.4 1.0
O1 C:VN4201 1.7 27.8 1.0
O3 C:VN4201 1.7 33.5 1.0
O2 C:VN4201 1.7 30.4 1.0
OD2 C:ASP10 2.2 19.3 1.0
CG C:ASP10 3.1 19.7 1.0
MG C:MG200 3.3 27.3 1.0
OD1 C:ASP10 3.3 16.2 1.0
O C:HOH338 3.3 26.2 1.0
O C:HOH330 3.3 23.4 1.0
NZ C:LYS80 3.7 28.2 1.0
OG1 C:THR54 3.8 28.7 1.0
N C:ASP12 3.8 11.6 1.0
OD1 C:ASP12 3.8 21.9 1.0
N C:ILE11 4.1 18.8 1.0
CB C:ASP12 4.2 14.9 1.0
O C:ASP12 4.3 16.9 1.0
O C:HOH329 4.5 18.7 1.0
CA C:THR54 4.5 27.5 1.0
CA C:ASP12 4.5 14.6 1.0
CB C:THR54 4.5 31.9 1.0
CB C:ASP10 4.5 11.4 1.0
CG C:ASP12 4.5 15.4 1.0
OD1 C:ASN106 4.6 34.2 1.0
N C:GLY55 4.6 24.1 1.0
C C:ILE11 4.7 16.0 1.0
CA C:ILE11 4.8 12.9 1.0
CE C:LYS80 4.8 22.5 1.0
C C:ASP12 4.9 12.9 1.0
O C:LEU53 4.9 23.8 1.0
CA C:ASP10 4.9 12.0 1.0
C C:ASP10 5.0 17.4 1.0

Vanadium binding site 4 out of 4 in 4hgo

Go back to Vanadium Binding Sites List in 4hgo
Vanadium binding site 4 out of 4 in the 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of 2-Keto-3-Deoxy-D-Glycero-D-Galactonononate-9-Phosphate Phosphohydrolase From Bacteroides Thetaiotaomicron in Complex with Transition State Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V202

b:48.1
occ:1.00
V D:VN4202 0.0 48.1 1.0
O2 D:VN4202 1.7 32.8 1.0
O3 D:VN4202 1.7 30.8 1.0
O1 D:VN4202 1.7 32.1 1.0
OD1 D:ASP10 2.4 21.1 1.0
O D:HOH333 3.2 27.6 1.0
CG D:ASP10 3.3 20.6 1.0
MG D:MG201 3.4 21.1 1.0
OD2 D:ASP10 3.5 21.9 1.0
OG1 D:THR54 3.6 26.1 1.0
O D:HOH325 3.7 19.9 1.0
NZ D:LYS80 3.7 32.0 1.0
OD2 D:ASP12 3.8 26.1 1.0
N D:GLY55 4.0 26.1 1.0
N D:ASP12 4.0 15.3 1.0
N D:ILE11 4.2 16.4 1.0
CA D:THR54 4.2 28.6 1.0
CB D:ASP12 4.3 13.2 1.0
CB D:THR54 4.4 25.6 1.0
O D:ASP12 4.5 19.7 1.0
CG D:ASP12 4.6 22.6 1.0
CE D:LYS80 4.6 29.5 1.0
CB D:ASP10 4.6 21.5 1.0
C D:THR54 4.7 25.9 1.0
CA D:ASP12 4.7 14.1 1.0
O D:HOH326 4.8 19.9 1.0
O D:HOH305 4.8 21.2 1.0
C D:ILE11 4.8 14.8 1.0
O D:LEU53 4.8 20.2 1.0
CA D:ILE11 4.9 14.1 1.0
CA D:GLY55 4.9 21.5 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: Thu Oct 29 07:05:30 2020

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