Atomistry » Potassium » PDB 1gup-1k4c » 1iwb
Atomistry »
  Potassium »
    PDB 1gup-1k4c »
      1iwb »

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

Go back to Potassium Binding Sites List in 1iwb
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: Mon Aug 12 04:34:33 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