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Neodymium in PDB 7o6z: Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase

Enzymatic activity of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase

All present enzymatic activity of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase:
1.1.2.7;

Protein crystallography data

The structure of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase, PDB code: 7o6z was solved by R.Schmitz, A.Dietl, H.Op Den Camp, T.Barends, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.87, 70.18, 97.23, 90, 91.39, 90
R / Rfree (%) 19.5 / 25.2

Neodymium Binding Sites:

The binding sites of Neodymium atom in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase (pdb code 7o6z). This binding sites where shown within 5.0 Angstroms radius around Neodymium atom.
In total 2 binding sites of Neodymium where determined in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase, PDB code: 7o6z:
Jump to Neodymium binding site number: 1; 2;

Neodymium binding site 1 out of 2 in 7o6z

Go back to Neodymium Binding Sites List in 7o6z
Neodymium binding site 1 out of 2 in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 1 of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Nd801

b:54.5
occ:0.72
OD2 A:ASP347 2.2 60.5 1.0
OE2 A:GLU204 2.3 61.6 1.0
ND2 A:ASN290 2.5 46.5 1.0
OD1 A:ASP345 2.7 48.2 1.0
CG A:ASP347 3.0 55.9 1.0
O A:MOH802 3.0 57.8 1.0
OD1 A:ASP347 3.0 57.3 1.0
O A:HOH998 3.1 56.9 1.0
CD A:GLU204 3.2 56.3 1.0
OE1 A:GLU204 3.5 59.9 1.0
CG A:ASP345 3.5 49.6 1.0
OD2 A:ASP345 3.5 51.3 1.0
CG A:ASN290 3.7 52.1 1.0
C A:MOH802 4.1 55.8 1.0
NH2 A:ARG372 4.3 57.3 1.0
OD2 A:ASP203 4.4 52.1 1.0
CB A:ASP347 4.4 53.7 1.0
OD1 A:ASN290 4.4 58.0 1.0
CB A:ASP203 4.4 53.9 1.0
NH1 A:ARG372 4.5 52.8 1.0
CZ2 A:TRP272 4.5 52.1 1.0
CB A:ASN290 4.5 47.9 1.0
O A:HOH1002 4.5 50.4 1.0
CG A:GLU204 4.6 55.5 1.0
NE1 A:TRP272 4.7 46.7 1.0
CZ A:ARG372 4.8 51.1 1.0
CG A:ASP203 4.9 49.9 1.0
CB A:ASP345 4.9 47.6 1.0
N A:ASN290 4.9 46.1 1.0
CE2 A:TRP272 5.0 46.5 1.0

Neodymium binding site 2 out of 2 in 7o6z

Go back to Neodymium Binding Sites List in 7o6z
Neodymium binding site 2 out of 2 in the Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 2 of Structure of A Neodymium-Containing, XOXF1-Type Methanol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Nd702

b:56.8
occ:0.75
O5 B:PQQ701 2.4 60.1 0.7
OD2 B:ASP347 2.6 58.6 1.0
OE2 B:GLU204 2.7 56.1 1.0
O7B B:PQQ701 2.7 51.4 0.7
OD1 B:ASN290 2.7 57.6 1.0
O B:MOH703 2.7 56.6 1.0
OD1 B:ASP345 2.7 56.5 1.0
OD1 B:ASP347 2.8 58.0 1.0
N6 B:PQQ701 2.8 55.8 0.7
CG B:ASP347 3.0 56.6 1.0
OE1 B:GLU204 3.1 56.5 1.0
CD B:GLU204 3.2 57.7 1.0
C5 B:PQQ701 3.3 58.3 0.7
OD2 B:ASP345 3.3 53.0 1.0
CG B:ASP345 3.4 56.0 1.0
C6A B:PQQ701 3.5 54.5 0.7
C7X B:PQQ701 3.6 56.2 0.7
CG B:ASN290 3.8 57.1 1.0
C7 B:PQQ701 3.9 55.8 0.7
C B:MOH703 4.0 55.7 1.0
OD2 B:ASP203 4.5 54.4 1.0
CB B:ASP347 4.5 51.8 1.0
ND2 B:ASN290 4.5 49.1 1.0
NH2 B:ARG372 4.6 50.9 1.0
C4 B:PQQ701 4.6 58.0 0.7
CB B:ASN290 4.7 52.1 1.0
CG B:GLU204 4.7 54.4 1.0
CB B:ASP203 4.7 51.8 1.0
O7A B:PQQ701 4.8 57.2 0.7
CZ2 B:TRP272 4.8 59.0 1.0
C9A B:PQQ701 4.9 56.3 0.7
CB B:ASP345 4.9 55.6 1.0
NE1 B:TRP272 4.9 54.2 1.0
NE1 B:TRP294 5.0 50.4 1.0
O B:ASP345 5.0 54.9 1.0
O4 B:PQQ701 5.0 56.2 0.7

Reference:

R.Schmitz, H.Op Den Camp. Neodymium As Metal Cofactor For Biological Methanol Oxidation: Structure and Kinetics of A XOXF1-Type Methanol Dehydrogenase To Be Published.
Page generated: Fri Sep 24 16:32:30 2021

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