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Potassium in PDB 5ysh: Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal

Enzymatic activity of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal

All present enzymatic activity of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal:
4.2.1.28;

Protein crystallography data

The structure of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal, PDB code: 5ysh was solved by N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.330, 110.490, 115.480, 92.69, 95.97, 105.44
R / Rfree (%) 16.4 / 19.1

Other elements in 5ysh:

The structure of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal also contains other interesting chemical elements:

Cobalt (Co) 4 atoms
Calcium (Ca) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal (pdb code 5ysh). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal, PDB code: 5ysh:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5ysh

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Potassium binding site 1 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:27.7
occ:1.00
OE2 A:GLU265 2.7 27.6 1.0
O A:GLY261 2.8 23.3 1.0
OE1 A:GLU280 2.8 24.7 1.0
O A:HOH790 3.0 24.5 1.0
O A:HOH723 3.0 25.5 1.0
OG A:SER264 3.1 28.5 1.0
OE1 A:GLU265 3.2 32.0 1.0
CD A:GLU265 3.3 34.6 1.0
SG A:CYS283 3.4 25.2 1.0
C A:GLY261 3.4 18.4 1.0
N A:GLY261 3.7 24.0 1.0
CD A:GLU280 4.0 27.7 1.0
CA A:GLU280 4.0 21.4 1.0
N A:SER262 4.1 21.0 1.0
CA A:GLY261 4.1 18.6 1.0
CB A:SER264 4.1 27.4 1.0
CA A:SER262 4.2 19.0 1.0
CB A:GLU280 4.3 26.8 1.0
N A:GLU280 4.3 21.5 1.0
CB A:CYS283 4.5 25.5 1.0
N A:SER264 4.5 24.0 1.0
CB A:SER260 4.5 20.7 1.0
O A:LEU279 4.5 25.6 1.0
C A:LEU279 4.6 24.8 1.0
N A:GLY263 4.7 24.5 1.0
C A:SER262 4.7 25.2 1.0
C A:SER260 4.7 26.0 1.0
N A:GLY227 4.7 28.9 1.0
CG A:GLU280 4.7 26.2 1.0
CG A:GLU265 4.8 29.7 1.0
CA A:SER264 4.9 29.1 1.0
OE2 A:GLU280 4.9 25.5 1.0

Potassium binding site 2 out of 8 in 5ysh

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Potassium binding site 2 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:35.5
occ:1.00
O A:LEU203 2.6 29.0 1.0
OE1 A:GLU208 2.6 34.4 1.0
O A:THR222 2.8 28.8 1.0
OG1 A:THR222 2.8 25.8 1.0
OE2 A:GLU205 2.8 35.7 1.0
N40 B:B121601 3.5 38.0 1.0
CD A:GLU205 3.5 40.0 1.0
C A:THR222 3.5 29.9 1.0
CD A:GLU208 3.7 37.4 1.0
CB A:THR222 3.7 28.0 1.0
C A:LEU203 3.8 28.1 1.0
OE1 A:GLU205 3.9 32.9 1.0
N A:LEU203 3.9 28.4 1.0
CA A:THR222 4.2 26.2 1.0
CD1 A:ILE223 4.2 33.3 1.0
C38 B:B121601 4.3 40.5 1.0
OE2 A:GLU208 4.4 32.0 1.0
N A:ILE223 4.4 29.9 1.0
CB A:GLU208 4.5 27.8 1.0
CA A:GLU205 4.5 29.8 1.0
CA A:LEU203 4.5 30.7 1.0
O A:HOH703 4.6 28.9 1.0
N A:GLU205 4.6 30.9 1.0
C A:GLU204 4.6 28.6 1.0
CG A:GLU205 4.6 30.2 1.0
CG A:GLU208 4.7 32.6 1.0
O A:HOH714 4.7 24.8 1.0
N A:THR222 4.7 20.2 1.0
CA A:ILE223 4.7 29.1 1.0
C37 B:B121601 4.7 38.0 1.0
C A:SER202 4.8 30.6 1.0
N A:GLU204 4.8 30.9 1.0
CA A:SER202 4.9 23.7 1.0
O A:GLU204 4.9 33.8 1.0
CA A:GLU204 5.0 28.8 1.0
O39 B:B121601 5.0 38.9 1.0

Potassium binding site 3 out of 8 in 5ysh

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Potassium binding site 3 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:22.0
occ:1.00
OE2 D:GLU265 2.7 22.6 1.0
OE1 D:GLU280 2.7 21.0 1.0
O D:GLY261 2.8 17.2 1.0
O D:HOH802 2.8 21.2 1.0
O D:HOH752 3.0 21.5 1.0
OG D:SER264 3.2 24.5 1.0
OE1 D:GLU265 3.4 23.6 1.0
CD D:GLU265 3.4 25.5 1.0
SG D:CYS283 3.4 20.4 1.0
C D:GLY261 3.4 17.8 1.0
N D:GLY261 3.6 21.0 1.0
CD D:GLU280 3.9 22.8 1.0
CA D:GLU280 4.1 17.6 1.0
N D:SER262 4.1 15.4 1.0
CA D:GLY261 4.1 17.0 1.0
CA D:SER262 4.2 14.9 1.0
CB D:SER264 4.2 21.7 1.0
CB D:GLU280 4.3 22.4 1.0
CB D:SER260 4.5 15.5 1.0
N D:GLU280 4.5 18.5 1.0
N D:SER264 4.5 23.3 1.0
CB D:CYS283 4.5 17.4 1.0
O D:LEU279 4.6 20.9 1.0
C D:SER260 4.6 19.4 1.0
N D:GLY227 4.7 20.6 1.0
C D:SER262 4.7 16.3 1.0
CG D:GLU280 4.7 19.4 1.0
C D:LEU279 4.7 20.0 1.0
N D:GLY263 4.7 20.1 1.0
CG D:GLU265 4.9 26.2 1.0
OE2 D:GLU280 4.9 18.0 1.0
CA D:SER260 4.9 14.6 1.0
N1 D:5AD605 5.0 25.9 1.0
CA D:SER264 5.0 20.4 1.0

Potassium binding site 4 out of 8 in 5ysh

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Potassium binding site 4 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:27.9
occ:1.00
O D:LEU203 2.6 18.4 1.0
OE1 D:GLU208 2.7 18.1 1.0
O D:THR222 2.7 19.3 1.0
OE1 D:GLU205 2.8 21.9 1.0
OG1 D:THR222 2.8 17.4 1.0
O D:HOH768 3.1 43.2 1.0
N40 E:B121601 3.2 28.9 1.0
CD D:GLU205 3.5 25.4 1.0
C D:THR222 3.5 22.3 1.0
CB D:THR222 3.8 18.7 1.0
OE2 D:GLU205 3.8 24.1 1.0
CD D:GLU208 3.8 20.7 1.0
C D:LEU203 3.8 21.4 1.0
N D:LEU203 3.9 18.6 1.0
C38 E:B121601 4.1 29.9 1.0
CD1 D:ILE223 4.2 19.9 1.0
CA D:THR222 4.2 15.0 1.0
N D:ILE223 4.4 16.8 1.0
CA D:GLU205 4.4 22.4 1.0
O D:HOH749 4.5 18.0 1.0
OE2 D:GLU208 4.5 17.6 1.0
CB D:GLU208 4.5 17.2 1.0
CA D:LEU203 4.5 17.2 1.0
CG D:GLU205 4.6 20.6 1.0
N D:GLU205 4.6 17.8 1.0
CA D:ILE223 4.6 13.2 1.0
C D:GLU204 4.6 19.6 1.0
C37 E:B121601 4.6 21.4 1.0
O D:HOH704 4.7 19.5 1.0
N D:THR222 4.7 13.1 1.0
CG D:GLU208 4.7 14.9 1.0
O D:GLU204 4.8 18.9 1.0
C D:SER202 4.8 18.9 1.0
N D:GLU204 4.9 15.4 1.0
O39 E:B121601 4.9 30.6 1.0
CA D:SER202 4.9 15.7 1.0
CB D:GLU205 5.0 21.8 1.0

Potassium binding site 5 out of 8 in 5ysh

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Potassium binding site 5 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K602

b:30.9
occ:1.00
O G:GLY261 2.7 26.0 1.0
OE2 G:GLU265 2.8 33.4 1.0
OE1 G:GLU280 2.8 26.4 1.0
O G:HOH748 3.0 33.8 1.0
O G:HOH714 3.0 28.5 1.0
OG G:SER264 3.0 27.9 1.0
OE1 G:GLU265 3.3 30.8 1.0
C G:GLY261 3.4 33.1 1.0
CD G:GLU265 3.4 31.6 1.0
SG G:CYS283 3.4 31.7 1.0
N G:GLY261 3.6 34.4 1.0
CD G:GLU280 4.0 29.2 1.0
N G:SER262 4.1 22.9 1.0
CA G:GLU280 4.1 24.4 1.0
CA G:GLY261 4.1 35.0 1.0
CB G:SER264 4.2 31.6 1.0
CA G:SER262 4.2 24.2 1.0
CB G:GLU280 4.3 26.5 1.0
N G:GLU280 4.4 26.0 1.0
N G:SER264 4.5 27.9 1.0
CB G:SER260 4.5 27.8 1.0
CB G:CYS283 4.6 25.6 1.0
N G:GLY227 4.7 30.7 1.0
C G:SER260 4.7 35.4 1.0
N G:GLY263 4.7 26.6 1.0
O G:LEU279 4.7 29.1 1.0
C G:SER262 4.7 23.5 1.0
C G:LEU279 4.7 28.6 1.0
CG G:GLU280 4.8 32.0 1.0
CG G:GLU265 4.8 26.7 1.0
CA G:SER264 4.9 28.9 1.0
OE2 G:GLU280 4.9 31.4 1.0
CA G:SER260 5.0 29.1 1.0
N1 G:5AD605 5.0 45.6 1.0

Potassium binding site 6 out of 8 in 5ysh

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Potassium binding site 6 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K603

b:36.3
occ:1.00
O G:LEU203 2.6 35.6 1.0
OE1 G:GLU208 2.6 38.7 1.0
O G:THR222 2.6 33.6 1.0
OG1 G:THR222 2.8 33.0 1.0
OE2 G:GLU205 2.9 37.7 1.0
C G:THR222 3.5 34.1 1.0
N40 H:B121601 3.5 37.7 1.0
CD G:GLU205 3.6 43.2 1.0
CD G:GLU208 3.7 43.7 1.0
C G:LEU203 3.8 37.6 1.0
CB G:THR222 3.8 31.9 1.0
OE1 G:GLU205 3.8 39.7 1.0
N G:LEU203 3.9 36.9 1.0
CD1 G:ILE223 4.0 30.8 1.0
CA G:THR222 4.1 31.5 1.0
C38 H:B121601 4.3 39.3 1.0
O G:HOH749 4.3 36.2 1.0
N G:ILE223 4.4 30.3 1.0
CB G:GLU208 4.4 36.2 1.0
OE2 G:GLU208 4.5 38.9 1.0
CA G:LEU203 4.5 33.1 1.0
CA G:GLU205 4.5 35.4 1.0
N G:GLU205 4.5 35.9 1.0
C G:GLU204 4.6 39.5 1.0
O G:HOH702 4.6 32.5 1.0
CA G:ILE223 4.6 32.9 1.0
N G:THR222 4.7 27.2 1.0
CG G:GLU208 4.7 42.3 1.0
CG G:GLU205 4.7 35.0 1.0
C G:SER202 4.8 35.9 1.0
O G:GLU204 4.8 38.0 1.0
N G:GLU204 4.8 33.6 1.0
C37 H:B121601 4.8 36.7 1.0
CA G:SER202 4.9 36.0 1.0
O39 H:B121601 5.0 40.9 1.0
CA G:GLU204 5.0 35.5 1.0

Potassium binding site 7 out of 8 in 5ysh

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Potassium binding site 7 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K602

b:34.8
occ:1.00
O J:GLY261 2.7 39.6 1.0
OE2 J:GLU280 2.8 41.6 1.0
OE2 J:GLU265 2.8 43.5 1.0
O J:HOH739 2.8 43.8 1.0
O J:HOH786 2.9 45.0 1.0
OG J:SER264 3.0 43.9 1.0
C J:GLY261 3.3 42.0 1.0
OE1 J:GLU265 3.4 43.0 1.0
SG J:CYS283 3.4 43.0 1.0
CD J:GLU265 3.4 48.7 1.0
N J:GLY261 3.7 41.5 1.0
CD J:GLU280 4.0 45.5 1.0
CA J:GLU280 4.1 41.2 1.0
N J:SER262 4.1 34.9 1.0
CA J:GLY261 4.1 41.0 1.0
CB J:SER264 4.1 48.4 1.0
CA J:SER262 4.3 35.2 1.0
CB J:GLU280 4.3 44.4 1.0
N J:GLU280 4.4 39.6 1.0
N J:SER264 4.5 40.1 1.0
CB J:CYS283 4.5 40.3 1.0
O J:LEU279 4.6 40.7 1.0
CB J:SER260 4.6 45.0 1.0
C J:LEU279 4.7 40.0 1.0
C J:SER260 4.7 43.9 1.0
N J:GLY227 4.7 47.0 1.0
C J:SER262 4.7 36.1 1.0
CG J:GLU280 4.8 47.2 1.0
N J:GLY263 4.8 39.4 1.0
N6 J:5AD605 4.9 60.8 1.0
CG J:GLU265 4.9 43.5 1.0
CA J:SER264 4.9 43.0 1.0
OE1 J:GLU280 4.9 39.4 1.0

Potassium binding site 8 out of 8 in 5ysh

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Potassium binding site 8 out of 8 in the Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Diol Dehydratase - Alpha/T172A Mutant Complexed with Adocbl, Aerobically-Prepared Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K603

b:54.4
occ:1.00
O J:LEU203 2.7 58.8 1.0
OE2 J:GLU208 2.7 49.6 1.0
O J:THR222 2.7 44.2 1.0
OG1 J:THR222 2.9 44.8 1.0
OE1 J:GLU205 3.0 54.6 1.0
O39 K:B121601 3.2 70.1 1.0
C J:THR222 3.5 53.1 1.0
CD J:GLU205 3.6 54.0 1.0
CB J:THR222 3.8 42.9 1.0
C J:LEU203 3.8 59.2 1.0
CD J:GLU208 3.8 51.8 1.0
N J:LEU203 3.9 49.6 1.0
OE2 J:GLU205 4.0 48.9 1.0
CD1 J:ILE223 4.0 51.7 1.0
CA J:THR222 4.1 45.3 1.0
C38 K:B121601 4.2 71.2 1.0
N J:ILE223 4.4 48.1 1.0
CB J:GLU208 4.5 50.6 1.0
O J:HOH710 4.5 41.3 1.0
CA J:GLU205 4.5 52.3 1.0
CA J:LEU203 4.5 52.9 1.0
N J:GLU205 4.6 52.3 1.0
C J:GLU204 4.6 52.2 1.0
OE1 J:GLU208 4.6 46.4 1.0
N J:THR222 4.7 41.8 1.0
CG J:GLU205 4.7 54.9 1.0
CA J:ILE223 4.7 48.8 1.0
C J:SER202 4.7 46.2 1.0
CG J:GLU208 4.7 49.3 1.0
CA J:SER202 4.8 44.9 1.0
C37 K:B121601 4.8 70.5 1.0
O J:GLU204 4.8 52.6 1.0
N J:GLU204 4.9 50.9 1.0

Reference:

N.Shibata, Y.Sueyoshi, Y.Higuchi, T.Toraya. Direct Participation of A Peripheral Side Chain of A Corrin Ring in Coenzyme B12CATALYSIS. Angew. Chem. Int. Ed. Engl. V. 57 7830 2018.
ISSN: ESSN 1521-3773
PubMed: 29797764
DOI: 10.1002/ANIE.201803591
Page generated: Mon Dec 14 00:15:12 2020

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