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Lanthanum in PDB 6oc5: Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum

Protein crystallography data

The structure of Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum, PDB code: 6oc5 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) 48.61 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.320, 87.952, 202.134, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28

Lanthanum Binding Sites:

The binding sites of Lanthanum atom in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum (pdb code 6oc5). 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, PDB code: 6oc5:
Jump to Lanthanum binding site number: 1; 2;

Lanthanum binding site 1 out of 2 in 6oc5

Go back to Lanthanum Binding Sites List in 6oc5
Lanthanum binding site 1 out of 2 in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:La701

b:65.7
occ:1.00
OD1 A:ASN276 2.7 66.3 1.0
OE2 A:GLU192 2.7 73.1 1.0
OE1 A:GLU192 2.7 73.8 1.0
O A:HOH804 2.8 59.0 1.0
OD1 A:ASP320 2.8 62.5 1.0
OD2 A:ASP320 2.8 59.2 1.0
OD1 A:ASP318 2.8 62.8 1.0
CG A:ASP320 3.1 61.0 1.0
CD A:GLU192 3.1 73.6 1.0
CG A:ASN276 3.2 67.8 1.0
OD2 A:ASP318 3.2 61.9 1.0
CG A:ASP318 3.4 63.4 1.0
CB A:ASN276 3.8 68.3 1.0
ND2 A:ASN276 3.8 69.2 1.0
CB A:ASP320 4.5 61.7 1.0
N A:ASN276 4.6 66.8 1.0
CG A:GLU192 4.6 74.0 1.0
CA A:GLY191 4.6 71.8 1.0
NE1 A:TRP258 4.7 56.8 1.0
NH2 A:ARG345 4.7 60.2 1.0
C A:GLY191 4.7 72.2 1.0
CZ2 A:TRP258 4.7 55.6 1.0
N A:GLU192 4.7 72.6 1.0
CA A:ASN276 4.9 68.5 1.0
CB A:ASP318 4.9 66.0 1.0
NE1 A:TRP280 4.9 69.7 1.0

Lanthanum binding site 2 out of 2 in 6oc5

Go back to Lanthanum Binding Sites List in 6oc5
Lanthanum binding site 2 out of 2 in the Lanthanide-Dependent Methanol Dehydrogenase Xoxf From Methylobacterium Extorquens, in Complex with Lanthanum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:La701

b:71.4
occ:0.59
O B:HOH803 2.7 69.7 1.0
OD1 B:ASP318 2.7 78.7 1.0
OE2 B:GLU192 2.8 85.9 1.0
OD2 B:ASP320 2.8 65.7 1.0
OE1 B:GLU192 2.8 78.7 1.0
OD1 B:ASP320 2.8 72.0 1.0
OD1 B:ASN276 2.9 72.0 1.0
CG B:ASP320 3.1 68.9 1.0
CD B:GLU192 3.1 83.5 1.0
OD2 B:ASP318 3.2 79.4 1.0
CG B:ASP318 3.3 80.3 1.0
CG B:ASN276 3.4 75.1 1.0
ND2 B:ASN276 3.9 76.6 1.0
CB B:ASN276 4.3 77.8 1.0
CB B:ASP320 4.5 69.3 1.0
CG B:GLU192 4.6 87.1 1.0
NH2 B:ARG345 4.6 71.1 1.0
CZ2 B:TRP258 4.7 66.0 1.0
NE1 B:TRP280 4.7 88.0 1.0
CZ2 B:TRP280 4.8 89.3 1.0
NE1 B:TRP258 4.8 61.5 1.0
CB B:ASP318 4.8 83.2 1.0
NH1 B:ARG345 4.9 68.0 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 03:14:36 2020

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