Neodymium in PDB 8fns: X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7

The structure of X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7, PDB code: 8fns was solved by J.J.Jung, C.-Y.Lin, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.18 / 1.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.099, 44.398, 82.316, 90, 90, 90
R / Rfree (%)	14.5 / 15.2

The binding sites of Neodymium atom in the X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7 (pdb code 8fns). This binding sites where shown within 5.0 Angstroms radius around Neodymium atom.
In total 4 binding sites of Neodymium where determined in the X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7, PDB code: 8fns:
Jump to Neodymium binding site number: 1; 2; 3; 4;

Neodymium binding site 1 out of 4 in the X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 1 of X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Nd201 b:15.6 occ:1.00 OD1 A:ASP35 2.4 17.3 1.0 OD1 A:ASP39 2.4 16.8 1.0 O A:HOH326 2.4 18.6 1.0 OD1 A:ASP37 2.5 18.0 1.0 O A:THR41 2.5 16.1 1.0 O A:HOH345 2.5 16.9 1.0 OE1 A:GLU46 2.5 15.2 1.0 OE2 A:GLU46 2.6 16.0 1.0 OD2 A:ASP39 2.8 17.6 1.0 CG A:ASP39 2.9 17.3 1.0 CD A:GLU46 2.9 15.7 1.0 CG A:ASP37 3.5 18.5 1.0 CG A:ASP35 3.5 17.2 1.0 C A:THR41 3.6 15.7 1.0 OD2 A:ASP37 3.8 18.7 1.0 OD2 A:ASP35 4.3 17.3 1.0 CB A:ASP39 4.4 17.7 1.0 OG1 A:THR41 4.4 16.5 1.0 N A:THR41 4.4 16.1 1.0 CB A:ASP35 4.4 17.2 1.0 CG A:GLU46 4.4 16.0 1.0 N A:ASP43 4.5 15.5 1.0 N A:ILE42 4.5 15.7 1.0 CA A:ASP35 4.5 17.7 1.0 O A:HOH422 4.5 27.5 1.0 CA A:ILE42 4.5 15.7 1.0 N A:ASP39 4.6 17.6 1.0 CA A:THR41 4.6 15.8 1.0 N A:ASP37 4.8 18.9 1.0 CB A:ASP37 4.8 19.2 1.0 OD2 A:ASP43 4.8 17.4 1.0 CG A:ASP43 4.9 16.9 1.0 C A:ILE42 4.9 15.9 1.0 CA A:ASP39 4.9 17.5 1.0 O A:HOH387 4.9 26.9 1.0 C A:ASP35 4.9 18.4 1.0 N A:LYS38 5.0 19.5 1.0

Neodymium binding site 2 out of 4 in the X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 2 of X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Nd202 b:23.9 occ:0.99 OD1 A:ASP59 2.4 28.5 1.0 OD1 A:ASP63 2.4 28.9 1.0 O A:THR65 2.5 24.8 1.0 O A:HOH322 2.5 27.7 1.0 OE2 A:GLU70 2.6 24.1 1.0 OE1 A:GLU70 2.6 23.0 1.0 O A:HOH328 2.6 26.1 1.0 OD1 A:ASP61 2.6 33.9 1.0 OD2 A:ASP63 2.6 31.1 1.0 CG A:ASP63 2.9 30.4 1.0 CD A:GLU70 2.9 24.4 1.0 CG A:ASP61 3.5 34.9 1.0 CG A:ASP59 3.6 28.7 1.0 OD2 A:ASP61 3.7 35.0 1.0 C A:THR65 3.7 24.0 1.0 OG1 A:THR65 4.3 26.2 1.0 OD2 A:ASP59 4.3 29.7 1.0 CB A:ASP63 4.3 31.9 1.0 CG A:GLU70 4.4 26.5 1.0 CA A:LEU66 4.5 24.1 1.0 N A:THR65 4.5 24.6 1.0 N A:LEU66 4.5 24.3 1.0 CB A:ASP59 4.5 27.7 1.0 CA A:THR65 4.6 23.7 1.0 O A:HOH312 4.7 39.7 1.0 CA A:ASP59 4.7 28.2 1.0 N A:ASP63 4.7 32.6 1.0 O A:HOH319 4.9 58.3 1.0 N A:ASP67 4.9 25.9 1.0 CB A:ASP61 4.9 36.6 1.0 CA A:ASP63 5.0 32.0 1.0

Neodymium binding site 3 out of 4 in the X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 3 of X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Nd203 b:20.6 occ:1.00 OD1 A:ASP84 2.4 25.3 1.0 O A:HOH320 2.4 23.8 1.0 OD1 A:ASP88 2.5 25.0 1.0 O A:HOH331 2.5 22.5 1.0 OD1 A:ASP86 2.5 23.1 1.0 O A:THR90 2.5 24.2 1.0 OE1 A:GLU95 2.5 18.1 1.0 OE2 A:GLU95 2.6 18.6 1.0 OD2 A:ASP88 2.7 25.1 1.0 CG A:ASP88 2.9 25.6 1.0 CD A:GLU95 2.9 18.2 1.0 CG A:ASP86 3.4 23.3 1.0 CG A:ASP84 3.5 25.2 1.0 OD2 A:ASP86 3.7 22.4 1.0 C A:THR90 3.7 23.8 1.0 OD2 A:ASP84 4.0 26.2 1.0 OG1 A:THR90 4.3 25.0 1.0 CB A:ASP88 4.4 27.0 1.0 CG A:GLU95 4.5 18.0 1.0 N A:THR90 4.5 25.2 1.0 CA A:LEU91 4.5 23.0 1.0 N A:LEU91 4.5 23.3 1.0 CB A:ASP84 4.6 23.5 1.0 O A:HOH434 4.6 36.0 1.0 CA A:THR90 4.6 24.3 1.0 N A:ASP92 4.7 21.8 1.0 N A:ASP88 4.7 28.1 1.0 CA A:ASP84 4.8 22.6 1.0 CB A:ASP86 4.8 25.0 1.0 OD2 A:ASP92 4.8 22.2 1.0 O A:HOH373 4.9 27.6 1.0 N A:ASP86 4.9 25.2 1.0 CA A:ASP88 5.0 27.8 1.0

Neodymium binding site 4 out of 4 in the X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7


Mono view


Stereo pair view

A full contact list of Neodymium with other atoms in the Nd binding site number 4 of X-Ray Crystal Structure of Methylorubrum Extorquens AM1 Lanmodulin (Lanm) with Neodymium (III) Bound at pH 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Nd204 b:17.5 occ:1.00 OD1 A:ASN108 2.4 16.8 1.0 O A:HOH342 2.5 20.5 1.0 OE2 A:GLU119 2.5 20.6 1.0 O A:HOH337 2.5 22.1 1.0 O A:THR114 2.5 17.8 1.0 OD1 A:ASP112 2.5 18.7 1.0 OE1 A:GLU119 2.6 18.9 1.0 OD2 A:ASP112 2.6 19.2 1.0 OD2 A:ASP110 2.6 20.7 1.0 OD1 A:ASP110 2.7 20.4 1.0 CG A:ASP112 2.9 19.1 1.0 CD A:GLU119 2.9 19.6 1.0 CG A:ASP110 3.0 20.8 1.0 CG A:ASN108 3.5 16.7 1.0 C A:THR114 3.7 17.1 1.0 ND2 A:ASN108 4.0 16.7 1.0 CB A:ASP112 4.4 19.4 1.0 OG1 A:THR114 4.4 18.5 1.0 CG A:GLU119 4.4 19.3 1.0 O A:HOH316 4.5 32.6 1.0 O A:HOH310 4.6 29.7 1.0 CA A:ILE115 4.6 16.5 1.0 CB A:ASP110 4.6 21.4 1.0 N A:ILE115 4.6 16.2 1.0 N A:THR114 4.6 17.4 1.0 CA A:THR114 4.7 17.2 1.0 OD2 A:ASP116 4.7 19.6 1.0 N A:ASP116 4.8 17.5 1.0 CB A:ASN108 4.8 16.7 1.0 N A:ASP112 4.9 19.5 1.0 CG A:ASP116 5.0 18.8 1.0

J.A.Mattocks, J.J.Jung, C.Y.Lin, Z.Dong, N.H.Yennawar, E.R.Featherston, C.S.Kang-Yun, T.A.Hamilton, D.M.Park, A.K.Boal, J.A.Cotruvo. Enhanced Rare-Earth Separation with A Metal-Sensitive Lanmodulin Dimer Nature V. 618 87 2023.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-05945-5