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Potassium in PDB 1eex: Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca

Enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca

All present enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca:
4.2.1.28;

Protein crystallography data

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

Resolution Low / High (Å) 30.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.380, 121.400, 207.600, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 22.6

Other elements in 1eex:

The structure of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Potassium Binding Sites:

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

Potassium binding site 1 out of 4 in 1eex

Go back to Potassium Binding Sites List in 1eex
Potassium binding site 1 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca


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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:9.6
occ:1.00
 OE1 A:GLU221 2.2 9.4 1.0
OE1 A:GLU170 2.4 10.2 1.0
O A:SER362 2.4 8.3 1.0
OE1 A:GLN296 2.4 7.3 1.0
OE1 A:GLN141 2.4 12.6 1.0
O2 A:PGO602 2.5 10.4 1.0
O1 A:PGO602 2.5 9.4 1.0
CD A:GLU221 3.3 14.4 1.0
C2 A:PGO602 3.3 19.8 1.0
CD A:GLU170 3.3 9.2 1.0
C1 A:PGO602 3.3 12.0 1.0
CD A:GLN296 3.4 10.0 1.0
C A:SER362 3.4 11.2 1.0
CD A:GLN141 3.5 13.7 1.0
OE2 A:GLU170 3.7 11.3 1.0
OE2 A:GLU221 3.7 13.1 1.0
NE2 A:GLN296 3.7 10.9 1.0
CB A:SER362 3.8 12.3 1.0
NE2 A:HIS143 4.0 11.4 1.0
NE2 A:GLN141 4.1 9.8 1.0
OD2 A:ASP335 4.2 11.8 1.0
OG A:SER362 4.2 9.6 1.0
CA A:SER362 4.2 9.2 1.0
NE2 A:GLN200 4.2 8.1 1.0
CD2 A:HIS143 4.4 12.5 1.0
N A:GLY363 4.4 9.8 1.0
CA A:GLY363 4.5 8.0 1.0
CG A:GLU221 4.5 13.3 1.0
CG A:GLU170 4.6 12.2 1.0
CG A:GLN296 4.7 9.6 1.0
CB A:GLU170 4.7 6.9 1.0
C3 A:PGO602 4.7 11.3 1.0
CG A:GLN141 4.8 8.4 1.0

Potassium binding site 2 out of 4 in 1eex

Go back to Potassium Binding Sites List in 1eex
Potassium binding site 2 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca


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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:12.0
occ:1.00
 OE1 A:GLU265 2.6 8.5 1.0
O A:HOH625 2.8 10.6 1.0
O A:GLY261 2.8 10.0 1.0
OE1 A:GLU280 2.9 12.3 1.0
OG A:SER264 3.0 12.1 1.0
O A:HOH728 3.0 11.3 1.0
OE2 A:GLU265 3.3 14.4 1.0
CD A:GLU265 3.3 12.4 1.0
SG A:CYS283 3.4 11.0 1.0
C A:GLY261 3.5 12.5 1.0
N A:GLY261 3.8 6.6 1.0
CA A:GLU280 4.0 9.5 1.0
CD A:GLU280 4.1 10.2 1.0
N A:SER262 4.1 8.3 1.0
CB A:SER264 4.1 9.3 1.0
CB A:GLU280 4.2 6.5 1.0
CA A:SER262 4.2 7.5 1.0
CA A:GLY261 4.3 6.7 1.0
N A:GLU280 4.4 8.3 1.0
N A:SER264 4.4 10.6 1.0
CB A:CYS283 4.5 5.2 1.0
O A:LEU279 4.6 13.0 1.0
N A:GLY263 4.6 9.1 1.0
C A:SER262 4.6 10.5 1.0
C A:LEU279 4.6 6.6 1.0
N A:GLY227 4.7 6.0 1.0
CB A:SER260 4.7 10.4 1.0
CG A:GLU265 4.7 13.7 1.0
CG A:GLU280 4.7 7.8 1.0
C A:SER260 4.8 11.2 1.0
CA A:SER264 4.9 8.1 1.0
OE2 A:GLU280 5.0 7.9 1.0

Potassium binding site 3 out of 4 in 1eex

Go back to Potassium Binding Sites List in 1eex
Potassium binding site 3 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca


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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K603

b:12.6
occ:1.00
 OE1 L:GLU170 2.3 12.8 1.0
O L:SER362 2.3 13.2 1.0
OE1 L:GLU221 2.4 16.3 1.0
OE1 L:GLN141 2.4 13.2 1.0
OE1 L:GLN296 2.4 12.1 1.0
O2 L:PGO602 2.5 14.2 1.0
O1 L:PGO602 2.5 11.0 1.0
CD L:GLU170 3.2 18.0 1.0
C2 L:PGO602 3.3 20.7 1.0
C1 L:PGO602 3.3 17.6 1.0
C L:SER362 3.4 12.3 1.0
CD L:GLN296 3.4 14.7 1.0
CD L:GLU221 3.4 14.0 1.0
CD L:GLN141 3.5 9.8 1.0
OE2 L:GLU170 3.6 12.4 1.0
NE2 L:GLN296 3.6 15.8 1.0
OE2 L:GLU221 3.7 11.3 1.0
CB L:SER362 4.0 10.9 1.0
NE2 L:GLN141 4.1 10.2 1.0
OG L:SER362 4.1 9.8 1.0
NE2 L:HIS143 4.1 9.0 1.0
CA L:SER362 4.2 9.5 1.0
OD2 L:ASP335 4.2 12.3 1.0
NE2 L:GLN200 4.2 9.4 1.0
N L:GLY363 4.3 10.8 1.0
CD2 L:HIS143 4.5 8.9 1.0
CA L:GLY363 4.5 8.8 1.0
CG L:GLU170 4.5 17.5 1.0
CG L:GLU221 4.7 11.3 1.0
CG L:GLN296 4.7 9.0 1.0
CB L:GLU170 4.7 14.3 1.0
C3 L:PGO602 4.7 13.1 1.0
CG L:GLN141 4.8 12.7 1.0

Potassium binding site 4 out of 4 in 1eex

Go back to Potassium Binding Sites List in 1eex
Potassium binding site 4 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca


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 the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsiella Oxytoca within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K604

b:15.0
occ:1.00
 OE1 L:GLU265 2.7 10.9 1.0
O L:GLY261 2.7 10.6 1.0
OE1 L:GLU280 2.7 10.0 1.0
O L:HOH624 2.8 10.5 1.0
OG L:SER264 2.9 11.4 1.0
O L:HOH606 3.0 10.2 1.0
SG L:CYS283 3.3 13.4 1.0
CD L:GLU265 3.4 13.4 1.0
OE2 L:GLU265 3.4 9.2 1.0
C L:GLY261 3.4 12.2 1.0
N L:GLY261 3.6 13.1 1.0
CD L:GLU280 4.0 13.2 1.0
CA L:GLU280 4.0 13.1 1.0
N L:SER262 4.1 14.1 1.0
CB L:SER264 4.1 11.6 1.0
CA L:GLY261 4.1 11.1 1.0
CA L:SER262 4.2 11.8 1.0
CB L:GLU280 4.3 10.6 1.0
N L:SER264 4.4 11.8 1.0
N L:GLU280 4.4 10.8 1.0
CB L:CYS283 4.5 7.7 1.0
CB L:SER260 4.5 10.4 1.0
C L:SER262 4.6 13.4 1.0
N L:GLY263 4.6 9.4 1.0
O L:LEU279 4.6 12.8 1.0
C L:SER260 4.7 15.8 1.0
N L:GLY227 4.7 10.5 1.0
C L:LEU279 4.7 13.9 1.0
CG L:GLU280 4.7 10.1 1.0
CG L:GLU265 4.8 9.7 1.0
CA L:SER264 4.8 17.2 1.0
OE2 L:GLU280 4.9 12.2 1.0
CA L:SER260 5.0 7.8 1.0
N1A L:COY601 5.0 14.3 1.0

Reference:

J.Masuda, N.Shibata, Y.Morimoto, T.Toraya, N.Yasuoka. How A Protein Generates A Catalytic Radical From Coenzyme B(12): X-Ray Structure of A Diol-Dehydratase-Adeninylpentylcobalamin Complex. Structure Fold.Des. V. 8 775 2000.
ISSN: ISSN 0969-2126
PubMed: 10903944
DOI: 10.1016/S0969-2126(00)00164-7
Page generated: Mon Aug 12 04:26:10 2024

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