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Potassium in PDB 1iwb: Crystal Structure of Diol Dehydratase

Enzymatic activity of Crystal Structure of Diol Dehydratase

All present enzymatic activity of Crystal Structure of Diol Dehydratase:
4.2.1.28;

Protein crystallography data

The structure of Crystal Structure of Diol Dehydratase, PDB code: 1iwb was solved by N.Shibata, J.Masuda, Y.Morimoto, N.Yasuoka, T.Toraya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.790, 122.400, 207.590, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 25.6

Other elements in 1iwb:

The structure of Crystal Structure of Diol Dehydratase also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Diol Dehydratase (pdb code 1iwb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Diol Dehydratase, PDB code: 1iwb:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 1iwb

Go back to Potassium Binding Sites List in 1iwb
Potassium binding site 1 out of 6 in the Crystal Structure of Diol Dehydratase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2602

b:15.5
occ:1.00
 OE1 A:GLU170 2.3 17.0 1.0
O A:SER362 2.3 19.1 1.0
OE1 A:GLU221 2.3 21.4 1.0
OE1 A:GLN296 2.4 14.4 1.0
O A:HOH2605 2.4 11.2 1.0
OE1 A:GLN141 2.5 17.6 1.0
O A:HOH2606 2.5 17.2 1.0
CD A:GLU170 3.3 17.7 1.0
C A:SER362 3.4 23.3 1.0
CD A:GLU221 3.4 15.4 1.0
CD A:GLN296 3.4 16.9 1.0
OE2 A:GLU170 3.6 17.1 1.0
CD A:GLN141 3.6 14.6 1.0
NE2 A:GLN296 3.8 14.5 1.0
OE2 A:GLU221 3.8 12.4 1.0
CB A:SER362 3.9 12.5 1.0
NE2 A:HIS143 4.0 12.9 1.0
OD2 A:ASP335 4.1 19.1 1.0
CA A:SER362 4.2 13.1 1.0
OG A:SER362 4.2 15.9 1.0
NE2 A:GLN141 4.2 16.2 1.0
O A:HOH2607 4.2 50.9 1.0
NE2 A:GLN200 4.3 21.7 1.0
N A:GLY363 4.3 19.9 1.0
CD2 A:HIS143 4.4 16.1 1.0
CA A:GLY363 4.5 14.4 1.0
CG A:GLU170 4.6 16.8 1.0
CG A:GLU221 4.6 10.8 1.0
CG A:GLN296 4.7 14.2 1.0
CB A:GLU170 4.7 20.4 1.0
CG A:GLN141 4.9 16.3 1.0

Potassium binding site 2 out of 6 in 1iwb

Go back to Potassium Binding Sites List in 1iwb
Potassium binding site 2 out of 6 in the Crystal Structure of Diol Dehydratase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2603

b:25.4
occ:1.00
 O A:GLY261 2.7 13.9 1.0
OE2 A:GLU265 2.7 13.5 1.0
OE1 A:GLU280 2.9 10.8 1.0
OG A:SER264 3.0 14.3 1.0
O A:HOH2682 3.1 12.5 1.0
O A:HOH2644 3.1 14.5 1.0
OE1 A:GLU265 3.2 16.1 1.0
CD A:GLU265 3.3 13.3 1.0
SG A:CYS283 3.4 19.0 1.0
C A:GLY261 3.5 10.6 1.0
N A:GLY261 3.7 19.5 1.0
CD A:GLU280 4.1 14.7 1.0
CB A:SER264 4.2 11.5 1.0
CA A:GLU280 4.2 14.3 1.0
CA A:GLY261 4.2 14.9 1.0
N A:SER262 4.2 17.4 1.0
CB A:SER260 4.3 18.9 1.0
CA A:SER262 4.4 16.0 1.0
N A:SER264 4.5 16.5 1.0
CB A:GLU280 4.5 15.8 1.0
CB A:CYS283 4.5 7.8 1.0
N A:GLU280 4.5 14.7 1.0
C A:SER260 4.6 13.8 1.0
CG A:GLU265 4.6 12.2 1.0
N A:GLY227 4.7 19.1 1.0
O A:LEU279 4.8 19.0 1.0
C A:LEU279 4.8 16.5 1.0
N A:GLY263 4.8 14.5 1.0
CA A:SER260 4.9 14.4 1.0
OG A:SER260 4.9 28.7 1.0
C A:SER262 4.9 12.7 1.0
CG A:GLU280 4.9 11.9 1.0
CA A:SER264 4.9 15.9 1.0
N A:GLU265 5.0 17.6 1.0

Potassium binding site 3 out of 6 in 1iwb

Go back to Potassium Binding Sites List in 1iwb
Potassium binding site 3 out of 6 in the Crystal Structure of Diol Dehydratase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2604

b:21.5
occ:1.00
 O A:THR222 2.5 24.3 1.0
O A:LEU203 2.6 22.3 1.0
OE1 A:GLU208 2.6 13.5 1.0
OE1 A:GLU205 2.6 22.0 1.0
OG1 A:THR222 2.8 16.1 1.0
C A:THR222 3.4 19.4 1.0
N40 B:B121601 3.5 28.0 1.0
CD A:GLU205 3.5 23.6 1.0
CD A:GLU208 3.7 20.9 1.0
OE2 A:GLU205 3.7 20.0 1.0
C A:LEU203 3.7 15.8 1.0
CB A:THR222 3.8 10.2 1.0
CD1 A:ILE223 3.9 15.6 1.0
N A:LEU203 4.0 20.9 1.0
CA A:THR222 4.1 14.0 1.0
C38 B:B121601 4.2 29.8 1.0
N A:ILE223 4.2 15.7 1.0
O A:HOH2683 4.3 23.5 1.0
N A:GLU205 4.3 14.4 1.0
CA A:GLU205 4.4 15.4 1.0
OE2 A:GLU208 4.4 17.4 1.0
CB A:GLU208 4.4 22.1 1.0
CA A:LEU203 4.5 17.9 1.0
C A:GLU204 4.5 11.8 1.0
O A:HOH2679 4.5 17.8 1.0
CG A:GLU205 4.6 16.0 1.0
CA A:ILE223 4.6 16.5 1.0
CG A:GLU208 4.6 20.6 1.0
N A:THR222 4.7 15.4 1.0
C37 B:B121601 4.7 17.5 1.0
N A:GLU204 4.8 18.1 1.0
O A:GLU204 4.8 19.8 1.0
O39 B:B121601 4.9 24.9 1.0
C A:SER202 4.9 21.4 1.0
CA A:GLU204 4.9 15.5 1.0

Potassium binding site 4 out of 6 in 1iwb

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Potassium binding site 4 out of 6 in the Crystal Structure of Diol Dehydratase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K3602

b:16.8
occ:1.00
 OE1 L:GLU221 2.2 21.2 1.0
O L:HOH3605 2.3 18.0 1.0
OE1 L:GLU170 2.3 16.8 1.0
O L:SER362 2.4 14.7 1.0
O L:HOH3606 2.4 11.5 1.0
OE1 L:GLN296 2.4 14.9 1.0
OE1 L:GLN141 2.4 16.0 1.0
CD L:GLU221 3.2 19.1 1.0
CD L:GLU170 3.3 21.6 1.0
C L:SER362 3.4 11.3 1.0
CD L:GLN296 3.4 22.0 1.0
CD L:GLN141 3.6 18.3 1.0
OE2 L:GLU221 3.6 18.4 1.0
OE2 L:GLU170 3.7 21.2 1.0
NE2 L:GLN296 3.8 17.2 1.0
CB L:SER362 3.9 16.0 1.0
NE2 L:GLN141 4.1 23.6 1.0
NE2 L:HIS143 4.1 20.3 1.0
OG L:SER362 4.2 16.2 1.0
CA L:SER362 4.2 13.4 1.0
O L:HOH3607 4.2 42.7 1.0
OD2 L:ASP335 4.3 16.8 1.0
NE2 L:GLN200 4.3 19.9 1.0
N L:GLY363 4.4 13.3 1.0
CD2 L:HIS143 4.4 22.4 1.0
CG L:GLU221 4.5 20.1 1.0
CA L:GLY363 4.5 12.3 1.0
CG L:GLU170 4.6 24.5 1.0
CB L:GLU170 4.8 21.1 1.0
CG L:GLN296 4.8 8.1 1.0
CG L:GLN141 4.8 13.5 1.0

Potassium binding site 5 out of 6 in 1iwb

Go back to Potassium Binding Sites List in 1iwb
Potassium binding site 5 out of 6 in the Crystal Structure of Diol Dehydratase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K3603

b:24.9
occ:1.00
 O L:GLY261 2.7 16.7 1.0
OE1 L:GLU280 2.8 17.7 1.0
O L:HOH3609 2.8 20.6 1.0
OE2 L:GLU265 3.0 21.4 1.0
OG L:SER264 3.0 15.8 1.0
O L:HOH3676 3.0 17.3 1.0
OE1 L:GLU265 3.4 26.1 1.0
SG L:CYS283 3.4 19.8 1.0
C L:GLY261 3.4 19.2 1.0
CD L:GLU265 3.5 29.1 1.0
N L:GLY261 3.7 20.6 1.0
CD L:GLU280 4.0 22.1 1.0
CB L:SER264 4.1 22.2 1.0
CA L:GLY261 4.1 21.9 1.0
N L:SER262 4.2 21.0 1.0
CA L:GLU280 4.2 16.8 1.0
CA L:SER262 4.3 21.7 1.0
N L:SER264 4.4 22.2 1.0
CB L:GLU280 4.4 18.9 1.0
CB L:CYS283 4.5 11.2 1.0
CB L:SER260 4.5 18.2 1.0
C L:SER260 4.6 24.6 1.0
N L:GLY227 4.6 20.3 1.0
N L:GLU280 4.6 18.4 1.0
C L:SER262 4.7 14.8 1.0
N L:GLY263 4.8 15.8 1.0
O L:LEU279 4.8 21.6 1.0
CG L:GLU280 4.8 26.7 1.0
CA L:SER264 4.9 20.9 1.0
C L:LEU279 4.9 17.4 1.0
OE2 L:GLU280 4.9 12.9 1.0
CA L:SER260 4.9 19.5 1.0
N L:GLU265 5.0 16.4 1.0
CG L:GLU265 5.0 22.8 1.0

Potassium binding site 6 out of 6 in 1iwb

Go back to Potassium Binding Sites List in 1iwb
Potassium binding site 6 out of 6 in the Crystal Structure of Diol Dehydratase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Diol Dehydratase within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K3604

b:25.8
occ:1.00
 OE1 L:GLU208 2.5 19.5 1.0
O L:THR222 2.6 21.4 1.0
O L:LEU203 2.7 13.9 1.0
OG1 L:THR222 2.7 16.8 1.0
OE1 L:GLU205 3.0 21.0 1.0
N40 E:B121602 3.3 24.0 1.0
C L:THR222 3.4 24.9 1.0
CD L:GLU208 3.5 22.7 1.0
CD L:GLU205 3.6 32.2 1.0
OE2 L:GLU205 3.7 24.9 1.0
CB L:THR222 3.8 15.5 1.0
C L:LEU203 3.9 19.9 1.0
N L:LEU203 4.0 29.0 1.0
CD1 L:ILE223 4.0 25.9 1.0
CA L:THR222 4.1 16.3 1.0
C38 E:B121602 4.2 19.8 1.0
OE2 L:GLU208 4.2 21.1 1.0
N L:ILE223 4.3 13.4 1.0
O L:HOH3614 4.4 17.3 1.0
CB L:GLU208 4.4 17.2 1.0
O L:HOH3675 4.5 14.0 1.0
C L:GLU204 4.5 18.9 1.0
CA L:LEU203 4.5 22.7 1.0
N L:GLU205 4.5 19.4 1.0
CG L:GLU208 4.6 21.4 1.0
CA L:GLU205 4.6 16.9 1.0
N L:THR222 4.6 13.6 1.0
CA L:ILE223 4.7 14.1 1.0
C37 E:B121602 4.7 22.5 1.0
O L:GLU204 4.7 21.9 1.0
CG L:GLU205 4.8 25.0 1.0
C L:SER202 4.8 22.1 1.0
N L:GLU204 4.9 20.2 1.0
O39 E:B121602 4.9 24.3 1.0
CA L:SER202 4.9 20.2 1.0

Reference:

N.Shibata, J.Masuda, Y.Morimoto, N.Yasuoka, T.Toraya. Substrate-Induced Conformational Change of A Coenzyme B12-Dependent Enzyme: Crystal Structure of the Substrate-Free Form of Diol Dehydratase Biochemistry V. 41 12607 2002.
ISSN: ISSN 0006-2960
PubMed: 12379103
DOI: 10.1021/BI026104Z
Page generated: Sun Dec 13 22:43:46 2020

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