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Lanthanum in PDB 6oc6: Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone

Protein crystallography data

The structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone, PDB code: 6oc6 was solved by M.Fellner, N.M.Good, N.C.Martinez-Gomez, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.35 / 2.89
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.272, 101.941, 103.691, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.8

Lanthanum Binding Sites:

The binding sites of Lanthanum atom in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone (pdb code 6oc6). This binding sites where shown within 5.0 Angstroms radius around Lanthanum atom.
In total 2 binding sites of Lanthanum where determined in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone, PDB code: 6oc6:
Jump to Lanthanum binding site number: 1; 2;

Lanthanum binding site 1 out of 2 in 6oc6

Go back to Lanthanum Binding Sites List in 6oc6
Lanthanum binding site 1 out of 2 in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 1 of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La701

b:27.2
occ:1.00
O5 A:PQQ702 2.7 21.0 1.0
N6 A:PQQ702 2.7 21.4 1.0
OD2 A:ASP320 2.7 17.1 1.0
OE2 A:GLU192 2.7 33.1 1.0
O7B A:PQQ702 2.7 20.9 1.0
OD1 A:ASP320 2.7 54.7 1.0
OE1 A:GLU192 2.7 54.0 1.0
OD1 A:ASN276 2.7 38.2 1.0
OD1 A:ASP318 2.8 49.9 1.0
CG A:ASP320 3.0 34.7 1.0
CD A:GLU192 3.1 32.1 1.0
CG A:ASN276 3.3 30.8 1.0
C5 A:PQQ702 3.5 24.6 1.0
C7X A:PQQ702 3.5 20.5 1.0
C6A A:PQQ702 3.5 21.6 1.0
CG A:ASP318 3.7 34.2 1.0
C7 A:PQQ702 3.7 19.1 1.0
ND2 A:ASN276 3.7 39.3 1.0
OD2 A:ASP318 3.8 40.7 1.0
CB A:ASN276 4.1 18.3 1.0
CB A:ASP320 4.5 13.9 1.0
O7A A:PQQ702 4.5 24.6 1.0
CG A:GLU192 4.6 16.6 1.0
NH2 A:ARG345 4.6 22.7 1.0
NE1 A:TRP258 4.8 17.0 1.0
C4 A:PQQ702 4.8 31.4 1.0
N A:ASN276 4.8 14.2 1.0
CA A:GLY191 4.9 22.4 1.0
C9A A:PQQ702 4.9 22.1 1.0
C A:GLY191 4.9 17.1 1.0
CZ2 A:TRP258 5.0 16.6 1.0
NE1 A:TRP280 5.0 21.4 1.0
CZ2 A:TRP280 5.0 32.6 1.0
C8 A:PQQ702 5.0 19.2 1.0
N A:GLU192 5.0 19.9 1.0

Lanthanum binding site 2 out of 2 in 6oc6

Go back to Lanthanum Binding Sites List in 6oc6
Lanthanum binding site 2 out of 2 in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone


Mono view


Stereo pair view

A full contact list of Lanthanum with other atoms in the La binding site number 2 of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum and Pyrroloquinoline Quinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La701

b:29.2
occ:1.00
OD1 B:ASP320 2.7 33.2 1.0
OD2 B:ASP320 2.7 39.6 1.0
O7A B:PQQ702 2.7 25.3 1.0
OE2 B:GLU192 2.7 44.0 1.0
O5 B:PQQ702 2.7 32.2 1.0
OD1 B:ASN276 2.7 52.2 1.0
N6 B:PQQ702 2.7 37.4 1.0
OE1 B:GLU192 2.7 62.4 1.0
OD1 B:ASP318 2.8 52.2 1.0
CG B:ASP320 3.1 28.9 1.0
CD B:GLU192 3.1 43.1 1.0
C7X B:PQQ702 3.5 32.6 1.0
C5 B:PQQ702 3.5 39.3 1.0
CG B:ASN276 3.5 51.5 1.0
C6A B:PQQ702 3.5 35.2 1.0
CG B:ASP318 3.6 37.3 1.0
C7 B:PQQ702 3.7 36.2 1.0
OD2 B:ASP318 3.8 24.9 1.0
CB B:ASN276 4.2 21.2 1.0
ND2 B:ASN276 4.3 36.3 1.0
CB B:ASP320 4.5 17.8 1.0
O7B B:PQQ702 4.5 38.7 1.0
CG B:GLU192 4.6 26.1 1.0
NH2 B:ARG345 4.6 26.0 1.0
NE1 B:TRP258 4.8 19.0 1.0
N B:ASN276 4.8 22.9 1.0
CZ2 B:TRP280 4.9 32.1 1.0
C4 B:PQQ702 4.9 42.3 1.0
CA B:GLY191 4.9 30.2 1.0
C9A B:PQQ702 4.9 31.6 1.0
C B:GLY191 5.0 26.4 1.0

Reference:

N.M.Good, M.Fellner, K.Demirer, J.Hu, R.P.Hausinger, N.C.Martinez-Gomez. Lanthanide-Dependent Alcohol Dehydrogenases Require An Essential Aspartate Residue For Metal Coordination and Enzymatic Function J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.RA120.013227
Page generated: Mon Dec 14 03:16:12 2020

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