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

Protein crystallography data

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

Yttrium Binding Sites:

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 6ksv

Go back to Yttrium Binding Sites List in 6ksv
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 6ksv

Go back to Yttrium Binding Sites List in 6ksv
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 6ksv

Go back to Yttrium Binding Sites List in 6ksv
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

Reference:

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
Page generated: Wed Dec 16 02:41:17 2020

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