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Potassium in PDB 8tda: Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2

Protein crystallography data

The structure of Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2, PDB code: 8tda was solved by A.C.Lazarski, L.J.Worrall, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.15 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.939, 80.018, 103.148, 90, 90, 90
R / Rfree (%) 17.6 / 21.3

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2 (pdb code 8tda). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2, PDB code: 8tda:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 8tda

Go back to Potassium Binding Sites List in 8tda
Potassium binding site 1 out of 4 in the Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:21.1
occ:1.00
 OE1 A:GLN273 2.5 20.2 1.0
OE2 A:GLU164 2.5 28.8 1.0
OE1 A:GLN166 2.6 19.3 1.0
O A:SER135 2.6 17.8 1.0
OD1 A:ASN134 2.6 22.6 1.0
O A:HOH573 2.8 32.5 1.0
C A:SER135 3.5 17.5 1.0
O A:HOH427 3.5 27.6 1.0
CD A:GLN273 3.6 18.7 1.0
CD A:GLN166 3.6 18.6 1.0
CG A:ASN134 3.7 20.3 1.0
CD A:GLU164 3.8 22.3 1.0
NE2 A:GLN273 4.0 19.8 1.0
NE2 A:GLN166 4.0 21.8 1.0
ND2 A:ASN134 4.1 22.1 1.0
CA A:SER135 4.2 17.8 1.0
N A:SER135 4.2 17.9 1.0
N A:GLY136 4.3 17.6 1.0
CA A:GLY136 4.4 17.1 1.0
OE1 A:GLU164 4.4 24.9 1.0
CD2 A:HIS275 4.4 20.6 1.0
O A:VAL167 4.5 19.0 1.0
O A:HOH440 4.6 35.1 1.0
CG A:GLU164 4.7 20.9 1.0
CG A:HIS275 4.8 19.7 1.0
N A:VAL167 4.8 17.2 1.0
CG A:GLN273 4.9 17.5 1.0
C A:ASN134 4.9 19.8 1.0
CB A:HIS275 4.9 17.9 1.0
O A:HOH624 5.0 40.1 1.0
CG A:GLN166 5.0 18.2 1.0
CD1 A:TYR190 5.0 22.1 1.0

Potassium binding site 2 out of 4 in 8tda

Go back to Potassium Binding Sites List in 8tda
Potassium binding site 2 out of 4 in the Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K302

b:30.2
occ:1.00
 O A:HOH561 2.7 31.4 1.0
O A:HOH574 2.8 30.6 1.0
O A:TRP75 2.8 19.6 1.0
O A:PHE72 2.9 21.9 1.0
O A:HOH662 2.9 43.1 1.0
O A:HOH500 3.1 32.2 1.0
C A:PHE72 3.7 21.1 1.0
CG2 A:VAL83 4.0 24.6 1.0
C A:TRP75 4.0 19.3 1.0
CB A:PHE72 4.0 21.3 1.0
N A:TRP75 4.2 19.1 1.0
N A:GLY74 4.4 19.5 1.0
N A:ASN73 4.5 22.4 1.0
CA A:ASN73 4.5 22.3 1.0
CA A:PHE72 4.5 21.3 1.0
O A:HOH555 4.6 34.2 1.0
O A:HOH568 4.6 32.9 1.0
CA A:TRP75 4.6 18.9 1.0
O A:HOH534 4.7 25.9 1.0
C A:ASN73 4.8 21.1 1.0

Potassium binding site 3 out of 4 in 8tda

Go back to Potassium Binding Sites List in 8tda
Potassium binding site 3 out of 4 in the Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:20.6
occ:1.00
 O B:HOH536 2.3 32.6 1.0
OD1 B:ASN134 2.4 21.8 1.0
OE1 B:GLN273 2.4 20.3 1.0
OE1 B:GLN166 2.4 18.6 1.0
O B:SER135 2.4 18.6 1.0
OE2 B:GLU164 2.5 24.1 1.0
C B:SER135 3.4 18.3 1.0
CD B:GLN273 3.5 18.8 1.0
CD B:GLN166 3.5 19.1 1.0
CD B:GLU164 3.5 21.0 1.0
CG B:ASN134 3.5 20.9 1.0
O B:HOH417 3.7 24.6 1.0
OE1 B:GLU164 3.8 22.8 1.0
NE2 B:GLN166 3.9 18.8 1.0
NE2 B:GLN273 3.9 20.0 1.0
ND2 B:ASN134 4.1 21.2 1.0
N B:SER135 4.1 17.7 1.0
CA B:SER135 4.1 17.9 1.0
N B:GLY136 4.3 17.8 1.0
CA B:GLY136 4.4 17.1 1.0
O B:VAL167 4.4 19.9 1.0
CD2 B:HIS275 4.6 21.7 1.0
N B:VAL167 4.7 17.5 1.0
C B:ASN134 4.8 19.6 1.0
CG B:GLU164 4.8 19.7 1.0
CG B:GLN166 4.8 18.7 1.0
CG B:GLN273 4.8 17.0 1.0
CB B:ASN134 4.8 20.5 1.0
CA B:GLN166 4.9 17.5 1.0
CG B:HIS275 4.9 19.7 1.0

Potassium binding site 4 out of 4 in 8tda

Go back to Potassium Binding Sites List in 8tda
Potassium binding site 4 out of 4 in the Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Bacteroides Thetaiotaomicron 3-Keto-2-Hydroxy-Glucal- Hydratase BT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K302

b:29.9
occ:1.00
 O B:HOH497 2.8 30.5 1.0
O B:TRP75 2.8 19.7 1.0
O B:PHE72 2.8 20.7 1.0
O B:HOH628 3.0 47.2 1.0
O B:HOH597 3.0 29.5 1.0
O B:HOH500 3.0 30.4 1.0
C B:PHE72 3.7 21.3 1.0
CG2 B:VAL83 4.0 22.4 1.0
C B:TRP75 4.0 18.7 1.0
CB B:PHE72 4.0 19.2 1.0
N B:TRP75 4.2 17.6 1.0
N B:GLY74 4.3 20.3 1.0
CA B:ASN73 4.3 20.6 1.0
N B:ASN73 4.4 21.9 1.0
CA B:PHE72 4.5 20.5 1.0
CA B:TRP75 4.6 18.2 1.0
O B:HOH541 4.7 33.6 1.0
C B:ASN73 4.7 20.1 1.0
O B:HOH524 4.8 26.5 1.0

Reference:

S.A.Nasseri, A.C.Lazarski, I.L.Lemmer, C.Y.Zhang, E.Brencher, H.Chen, L.Sim, D.Panwar, L.Betschart, L.J.Worrall, H.Brumer, N.C.J.Strynadka, S.G.Withers. An Alternative Broad-Specificity Pathway For Glycan Breakdown in Bacteria Nature 2024.
ISSN: ESSN 1476-4687
Page generated: Tue Aug 13 00:56:33 2024

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