Atomistry » Potassium » PDB 1d7v-1gmk » 1egv
Atomistry »
  Potassium »
    PDB 1d7v-1gmk »
      1egv »

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

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