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Potassium in PDB 1egv: Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.

Enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.

All present enzymatic activity of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.:
4.2.1.28;

Protein crystallography data

The structure of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition., PDB code: 1egv was solved by J.Masuda, N.Shibata, 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 / 1.75
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 (%) 15.5 / 21.4

Other elements in 1egv:

The structure of Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition. 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 Klebsella Oxytoca Under the Illuminated Condition. (pdb code 1egv). 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 Klebsella Oxytoca Under the Illuminated Condition., PDB code: 1egv:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 1egv

Go back to Potassium Binding Sites List in 1egv
Potassium binding site 1 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.


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 Klebsella Oxytoca Under the Illuminated Condition. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:9.8
occ:1.00
 OE1 A:GLU221 2.2 10.5 1.0
OE1 A:GLU170 2.3 11.4 1.0
OE1 A:GLN296 2.4 7.3 1.0
O A:SER362 2.4 7.7 1.0
O2 A:PGO602 2.4 10.9 1.0
OE1 A:GLN141 2.4 11.9 1.0
O1 A:PGO602 2.5 10.8 1.0
CD A:GLU221 3.3 14.7 1.0
C2 A:PGO602 3.3 19.5 1.0
CD A:GLU170 3.3 8.3 1.0
C1 A:PGO602 3.3 11.3 1.0
CD A:GLN296 3.4 12.2 1.0
C A:SER362 3.4 8.8 1.0
CD A:GLN141 3.6 13.1 1.0
OE2 A:GLU221 3.7 13.4 1.0
OE2 A:GLU170 3.7 10.0 1.0
NE2 A:GLN296 3.7 12.3 1.0
CB A:SER362 3.9 10.7 1.0
NE2 A:HIS143 4.0 10.2 1.0
NE2 A:GLN141 4.1 8.9 1.0
OD2 A:ASP335 4.2 11.3 1.0
CA A:SER362 4.2 8.4 1.0
OG A:SER362 4.2 10.3 1.0
NE2 A:GLN200 4.2 8.3 1.0
CD2 A:HIS143 4.4 12.8 1.0
N A:GLY363 4.4 10.3 1.0
CG A:GLU221 4.5 11.2 1.0
CA A:GLY363 4.5 7.7 1.0
CG A:GLU170 4.6 8.5 1.0
C3 A:PGO602 4.7 12.6 1.0
CG A:GLN296 4.7 14.4 1.0
CB A:GLU170 4.7 5.6 1.0
CG A:GLN141 4.9 8.6 1.0

Potassium binding site 2 out of 4 in 1egv

Go back to Potassium Binding Sites List in 1egv
Potassium binding site 2 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.


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 Klebsella Oxytoca Under the Illuminated Condition. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:12.5
occ:1.00
 OE1 A:GLU265 2.6 8.7 1.0
O A:GLY261 2.8 11.2 1.0
O A:HOH625 2.8 11.6 1.0
OE1 A:GLU280 2.8 13.8 1.0
O A:HOH727 3.0 12.3 1.0
OG A:SER264 3.0 10.7 1.0
OE2 A:GLU265 3.3 13.2 1.0
CD A:GLU265 3.3 12.0 1.0
SG A:CYS283 3.4 11.3 1.0
C A:GLY261 3.4 11.0 1.0
N A:GLY261 3.8 7.4 1.0
CA A:GLU280 4.0 6.8 1.0
CD A:GLU280 4.1 12.3 1.0
N A:SER262 4.1 8.4 1.0
CB A:SER264 4.1 8.2 1.0
CB A:GLU280 4.2 7.2 1.0
CA A:SER262 4.2 8.7 1.0
CA A:GLY261 4.3 6.3 1.0
N A:SER264 4.4 9.2 1.0
N A:GLU280 4.4 9.3 1.0
CB A:CYS283 4.5 4.7 1.0
N A:GLY263 4.6 8.6 1.0
O A:LEU279 4.6 14.7 1.0
C A:SER262 4.6 11.7 1.0
CB A:SER260 4.6 10.9 1.0
N A:GLY227 4.7 5.6 1.0
C A:LEU279 4.7 10.1 1.0
CG A:GLU265 4.7 11.9 1.0
CG A:GLU280 4.7 9.3 1.0
C A:SER260 4.8 10.5 1.0
CA A:SER264 4.9 9.8 1.0
OE2 A:GLU280 5.0 9.4 1.0

Potassium binding site 3 out of 4 in 1egv

Go back to Potassium Binding Sites List in 1egv
Potassium binding site 3 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.


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 Klebsella Oxytoca Under the Illuminated Condition. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K603

b:12.7
occ:1.00
 OE1 L:GLU170 2.2 13.7 1.0
O L:SER362 2.3 13.1 1.0
OE1 L:GLU221 2.4 16.2 1.0
OE1 L:GLN141 2.4 13.1 1.0
O2 L:PGO602 2.4 15.6 1.0
OE1 L:GLN296 2.4 11.2 1.0
O1 L:PGO602 2.5 11.2 1.0
CD L:GLU170 3.2 19.1 1.0
C2 L:PGO602 3.3 21.8 1.0
C L:SER362 3.3 14.4 1.0
C1 L:PGO602 3.4 17.6 1.0
CD L:GLU221 3.4 14.1 1.0
CD L:GLN296 3.4 14.0 1.0
CD L:GLN141 3.5 9.3 1.0
OE2 L:GLU170 3.6 12.8 1.0
NE2 L:GLN296 3.7 14.7 1.0
OE2 L:GLU221 3.7 10.0 1.0
CB L:SER362 4.0 9.6 1.0
NE2 L:GLN141 4.1 10.0 1.0
NE2 L:HIS143 4.1 9.4 1.0
OG L:SER362 4.2 9.9 1.0
CA L:SER362 4.2 10.1 1.0
OD2 L:ASP335 4.2 11.4 1.0
NE2 L:GLN200 4.2 10.8 1.0
N L:GLY363 4.3 10.9 1.0
CA L:GLY363 4.5 9.2 1.0
CD2 L:HIS143 4.5 11.2 1.0
CG L:GLU170 4.5 14.8 1.0
CG L:GLU221 4.6 13.3 1.0
CB L:GLU170 4.7 16.6 1.0
C3 L:PGO602 4.7 10.8 1.0
CG L:GLN296 4.7 8.2 1.0
CG L:GLN141 4.8 12.2 1.0

Potassium binding site 4 out of 4 in 1egv

Go back to Potassium Binding Sites List in 1egv
Potassium binding site 4 out of 4 in the Crystal Structure of the Diol Dehydratase-Adeninylpentylcobalamin Complex From Klebsella Oxytoca Under the Illuminated Condition.


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 Klebsella Oxytoca Under the Illuminated Condition. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K604

b:16.3
occ:1.00
 OE1 L:GLU265 2.7 11.5 1.0
OE1 L:GLU280 2.8 11.6 1.0
O L:GLY261 2.8 11.5 1.0
O L:HOH624 2.8 13.0 1.0
OG L:SER264 3.0 10.4 1.0
O L:HOH606 3.0 9.5 1.0
CD L:GLU265 3.4 13.4 1.0
SG L:CYS283 3.4 13.9 1.0
OE2 L:GLU265 3.4 8.2 1.0
C L:GLY261 3.4 11.2 1.0
N L:GLY261 3.7 16.0 1.0
CD L:GLU280 4.0 15.2 1.0
CA L:GLU280 4.0 14.2 1.0
N L:SER262 4.0 15.5 1.0
CB L:SER264 4.1 9.4 1.0
CA L:GLY261 4.2 11.2 1.0
CA L:SER262 4.2 13.9 1.0
CB L:GLU280 4.3 9.7 1.0
N L:GLU280 4.3 10.7 1.0
N L:SER264 4.4 14.1 1.0
CB L:CYS283 4.5 6.7 1.0
CB L:SER260 4.5 12.5 1.0
C L:SER262 4.6 17.9 1.0
N L:GLY263 4.6 12.2 1.0
O L:LEU279 4.6 11.8 1.0
N L:GLY227 4.6 10.8 1.0
C L:LEU279 4.7 17.2 1.0
CG L:GLU280 4.7 12.3 1.0
C L:SER260 4.7 16.6 1.0
CG L:GLU265 4.8 11.6 1.0
CA L:SER264 4.8 16.5 1.0
OE2 L:GLU280 4.9 12.1 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 04:26:24 2024

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