Yttrium in PDB 6ksv: Crystal Structure of Sure with D-Leu

The structure of Crystal Structure of Sure with D-Leu, PDB code: 6ksv was solved by R.Zhai, T.Mori, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.09 / 2.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.370, 152.060, 64.540, 90.00, 113.08, 90.00
R / Rfree (%)	20 / 27.9

The binding sites of Yttrium atom in the Crystal Structure of Sure with D-Leu (pdb code 6ksv). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 3 binding sites of Yttrium where determined in the Crystal Structure of Sure with D-Leu, PDB code: 6ksv:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in the Crystal Structure of Sure with D-Leu


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Sure with D-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Y605 b:92.3 occ:1.00 OD2 A:ASP86 3.5 66.2 1.0 OD1 A:ASP83 3.8 60.1 1.0 CG A:ASP83 4.3 61.1 1.0 CB A:ASP83 4.4 50.6 1.0 CG A:ASP86 4.4 66.8 1.0 CB A:ASP86 4.5 64.9 1.0

Yttrium binding site 2 out of 3 in the Crystal Structure of Sure with D-Leu


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Sure with D-Leu within 5.0Å range: probe atom residue distance (Å) B Occ A:Y606 b:83.6 occ:1.00 OE1 A:GLU126 2.6 74.1 1.0 OE2 A:GLU123 2.7 72.9 1.0 OE1 A:GLU123 2.7 67.8 1.0 OE2 A:GLU126 2.8 69.5 1.0 CD A:GLU126 3.0 70.3 1.0 CD A:GLU123 3.1 72.4 1.0 O A:HOH702 3.4 58.3 1.0 CG A:GLU126 4.3 65.8 1.0 CG A:GLU123 4.6 64.3 1.0 N A:ASP125 4.8 57.8 1.0 OD2 A:ASP125 4.9 67.6 1.0 O A:GLU123 4.9 63.9 1.0

Yttrium binding site 3 out of 3 in the Crystal Structure of Sure with D-Leu


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Crystal Structure of Sure with D-Leu within 5.0Å range: probe atom residue distance (Å) B Occ B:Y504 b:87.7 occ:1.00 OE1 B:GLU126 2.4 77.2 1.0 OE1 B:GLU123 2.9 74.6 1.0 OE2 B:GLU123 3.0 77.9 1.0 CD B:GLU123 3.3 75.1 1.0 OD1 B:ASP125 3.3 67.6 1.0 CD B:GLU126 3.6 72.2 1.0 CG B:GLU126 4.2 62.3 1.0 CG B:ASP125 4.4 71.6 1.0 OE2 B:GLU126 4.6 78.6 1.0 CG B:GLU123 4.7 73.2 1.0 CB B:GLU126 4.8 66.1 1.0 OD2 B:ASP125 4.9 71.5 1.0 N B:ASP125 4.9 67.5 1.0

K.Matsuda, R.Zhai, T.Mori, M.Kobayashi, A.Sano, I.Abe, T.Wakimoto. Heterochiral Coupling in Non-Ribosomal Peptide Macrolactamization Nat Catal 2020.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-020-0456-7