Atomistry » Europium » PDB 1bub-6fkw » 6fkw
Atomistry »
  Europium »
    PDB 1bub-6fkw »
      6fkw »

Europium in PDB 6fkw: Europium-Containing Methanol Dehydrogenase

Enzymatic activity of Europium-Containing Methanol Dehydrogenase

All present enzymatic activity of Europium-Containing Methanol Dehydrogenase:
1.1.2.7; 1.1.2.8;

Protein crystallography data

The structure of Europium-Containing Methanol Dehydrogenase, PDB code: 6fkw was solved by T.Barends, A.Dietl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.27 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.080, 101.180, 107.790, 115.21, 97.53, 91.78
R / Rfree (%) 16.9 / 18.5

Europium Binding Sites:

The binding sites of Europium atom in the Europium-Containing Methanol Dehydrogenase (pdb code 6fkw). This binding sites where shown within 5.0 Angstroms radius around Europium atom.
In total 4 binding sites of Europium where determined in the Europium-Containing Methanol Dehydrogenase, PDB code: 6fkw:
Jump to Europium binding site number: 1; 2; 3; 4;

Europium binding site 1 out of 4 in 6fkw

Go back to Europium Binding Sites List in 6fkw
Europium binding site 1 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 1 of Europium-Containing Methanol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Eu601

b:24.1
occ:0.60
OD2 A:ASP301 2.5 24.4 1.0
O7A A:PQQ602 2.6 21.2 1.0
O5 A:PQQ602 2.6 25.2 1.0
OE1 A:GLU172 2.8 24.1 1.0
OD1 A:ASN256 2.8 21.9 1.0
N6 A:PQQ602 2.8 23.8 1.0
OD1 A:ASP301 2.8 23.2 1.0
OD1 A:ASP299 3.0 22.4 1.0
CG A:ASP301 3.0 21.4 1.0
OE2 A:GLU172 3.1 26.4 1.0
CD A:GLU172 3.3 23.8 1.0
C5 A:PQQ602 3.5 23.1 1.0
C7X A:PQQ602 3.5 22.0 1.0
C6A A:PQQ602 3.7 23.4 1.0
CG A:ASN256 3.7 20.3 1.0
C7 A:PQQ602 3.7 22.1 1.0
CG A:ASP299 3.9 20.1 1.0
OD2 A:ASP299 4.0 22.4 1.0
ND2 A:ASN256 4.4 21.1 1.0
CB A:ASP301 4.5 18.6 1.0
NH2 A:ARG326 4.5 18.9 1.0
CB A:ASN256 4.5 19.4 1.0
CB A:SER255 4.5 16.0 1.0
O7B A:PQQ602 4.7 22.4 1.0
NE1 A:TRP238 4.7 18.4 1.0
CG A:GLU172 4.8 22.6 1.0
CA A:GLY171 4.8 19.2 1.0
N A:ASN256 4.8 16.6 1.0
C4 A:PQQ602 4.9 22.8 1.0
C A:GLY171 4.9 19.7 1.0
CZ2 A:TRP238 4.9 17.5 1.0
OG A:SER255 4.9 17.2 1.0

Europium binding site 2 out of 4 in 6fkw

Go back to Europium Binding Sites List in 6fkw
Europium binding site 2 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 2 of Europium-Containing Methanol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Eu601

b:23.0
occ:0.60
O7A B:PQQ602 2.6 20.9 1.0
O5 B:PQQ602 2.6 23.3 1.0
OD2 B:ASP301 2.6 27.4 1.0
OD1 B:ASN256 2.8 24.2 1.0
OE1 B:GLU172 2.8 25.5 1.0
N6 B:PQQ602 2.8 21.2 1.0
OD1 B:ASP301 2.9 25.6 1.0
OE2 B:GLU172 2.9 28.3 1.0
OD1 B:ASP299 3.0 24.3 1.0
CG B:ASP301 3.1 23.1 1.0
CD B:GLU172 3.2 24.9 1.0
C5 B:PQQ602 3.5 22.1 1.0
C7X B:PQQ602 3.5 20.7 1.0
C6A B:PQQ602 3.6 22.0 1.0
CG B:ASN256 3.6 21.6 1.0
C7 B:PQQ602 3.7 20.9 1.0
CG B:ASP299 3.9 21.8 1.0
OD2 B:ASP299 4.0 23.1 1.0
ND2 B:ASN256 4.4 22.1 1.0
NH2 B:ARG326 4.5 21.1 1.0
CB B:ASN256 4.5 20.2 1.0
CB B:ASP301 4.5 19.9 1.0
CB B:SER255 4.6 17.1 1.0
O7B B:PQQ602 4.7 20.9 1.0
CG B:GLU172 4.7 24.0 1.0
NE1 B:TRP238 4.8 19.9 1.0
N B:ASN256 4.8 17.5 1.0
CA B:GLY171 4.9 20.4 1.0
C4 B:PQQ602 4.9 22.3 1.0
C B:GLY171 4.9 20.9 1.0
CZ2 B:TRP238 5.0 19.2 1.0

Europium binding site 3 out of 4 in 6fkw

Go back to Europium Binding Sites List in 6fkw
Europium binding site 3 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 3 of Europium-Containing Methanol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Eu601

b:20.5
occ:0.60
O7B C:PQQ602 2.5 20.5 1.0
O5 C:PQQ602 2.5 23.2 1.0
OD2 C:ASP301 2.6 27.9 1.0
OD1 C:ASN256 2.7 23.9 1.0
N6 C:PQQ602 2.7 21.2 1.0
OE1 C:GLU172 2.8 24.0 1.0
OD1 C:ASP301 2.8 30.1 1.0
OD1 C:ASP299 2.9 23.5 1.0
OE2 C:GLU172 2.9 27.1 1.0
CG C:ASP301 3.0 24.3 1.0
CD C:GLU172 3.2 23.9 1.0
C5 C:PQQ602 3.4 22.0 1.0
C7X C:PQQ602 3.5 22.3 1.0
C6A C:PQQ602 3.6 21.9 1.0
C7 C:PQQ602 3.6 21.2 1.0
CG C:ASN256 3.7 21.7 1.0
CG C:ASP299 3.8 21.5 1.0
OD2 C:ASP299 3.9 23.3 1.0
ND2 C:ASN256 4.4 22.2 1.0
CB C:ASP301 4.5 20.8 1.0
NH2 C:ARG326 4.5 19.9 1.0
CB C:ASN256 4.6 20.1 1.0
CB C:SER255 4.6 18.0 1.0
O7A C:PQQ602 4.6 22.1 1.0
NE1 C:TRP238 4.7 19.8 1.0
CG C:GLU172 4.7 22.9 1.0
C4 C:PQQ602 4.8 21.6 1.0
N C:ASN256 4.8 17.5 1.0
CA C:GLY171 4.9 21.3 1.0
C C:GLY171 4.9 21.5 1.0
CZ2 C:TRP238 4.9 19.1 1.0
C8 C:PQQ602 5.0 20.8 1.0

Europium binding site 4 out of 4 in 6fkw

Go back to Europium Binding Sites List in 6fkw
Europium binding site 4 out of 4 in the Europium-Containing Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Europium with other atoms in the Eu binding site number 4 of Europium-Containing Methanol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Eu601

b:42.2
occ:0.60
O5 D:PQQ602 2.4 44.1 1.0
OD2 D:ASP301 2.7 39.3 1.0
N6 D:PQQ602 2.7 44.0 1.0
OE1 D:GLU172 2.8 51.4 1.0
O7B D:PQQ602 2.8 48.0 1.0
OD1 D:ASP299 2.9 44.9 1.0
OE2 D:GLU172 2.9 51.0 1.0
OD1 D:ASP301 3.1 41.9 1.0
CD D:GLU172 3.2 51.1 1.0
CG D:ASP301 3.2 38.9 1.0
OD1 D:ASN256 3.3 44.1 1.0
C5 D:PQQ602 3.3 42.5 1.0
C6A D:PQQ602 3.4 42.5 1.0
OD2 D:ASP299 3.6 42.9 1.0
CG D:ASP299 3.6 42.7 1.0
C7X D:PQQ602 3.6 45.8 1.0
C7 D:PQQ602 3.6 44.0 1.0
CG D:ASN256 3.9 44.8 1.0
NH2 D:ARG326 4.3 34.6 1.0
ND2 D:ASN256 4.3 45.8 1.0
C4 D:PQQ602 4.7 40.7 1.0
CG D:GLU172 4.7 51.6 1.0
CB D:ASP301 4.7 37.4 1.0
CZ2 D:TRP260 4.7 42.9 1.0
CB D:ASN256 4.8 44.4 1.0
O7A D:PQQ602 4.8 45.7 1.0
O D:HOH818 4.9 41.9 1.0
C9A D:PQQ602 4.9 41.7 1.0
NE1 D:TRP260 4.9 44.2 1.0
C8 D:PQQ602 5.0 43.5 1.0
NH1 D:ARG326 5.0 33.5 1.0

Reference:

B.Jahn, A.Pol, H.Lumpe, T.Barends, A.Dietl, C.Hogendoorn, H.Op Den Camp, L.Daumann. Similar But Not the Same: First Kinetic and Structural Analyses of A Methanol Dehydrogenase Containing A Europium Ion in the Active Site. Chembiochem 2018.
ISSN: ESSN 1439-7633
PubMed: 29524328
DOI: 10.1002/CBIC.201800130
Page generated: Sun Dec 13 11:27:57 2020

Last articles

Zn in 7M6U
Zn in 7NNG
Zn in 7NEE
Zn in 7NEU
Zn in 7M3K
Zn in 7KWD
Zn in 7KYH
Zn in 7KNG
Zn in 7KY2
Zn in 7KYF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy