Yttrium in PDB 8pun: Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12

The structure of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12, PDB code: 8pun was solved by N.Polidori, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 2.30
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	187.712, 187.712, 129.317, 90, 90, 90
R / Rfree (%)	18 / 20.5

The structure of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Yttrium atom in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 (pdb code 8pun). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 7 binding sites of Yttrium where determined in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12, PDB code: 8pun:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7;

Yttrium binding site 1 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y404 b:93.5 occ:1.00 OE1 A:GLU315 2.9 76.2 1.0 OE2 A:GLU315 3.0 91.4 1.0 CD A:GLU315 3.3 66.0 1.0 OE1 C:GLU283 4.4 66.4 1.0 CG A:GLU315 4.7 50.4 1.0 OE2 C:GLU283 4.7 65.5 1.0 CD C:GLU283 5.0 63.9 1.0

Yttrium binding site 2 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Y405 b:39.2 occ:1.00 OE1 A:GLU150 2.7 46.5 1.0 OD1 A:ASP151 2.7 46.7 1.0 O A:HOH634 2.9 40.3 1.0 O A:HOH579 2.9 53.9 1.0 CG A:ASP151 3.5 38.6 1.0 CD A:GLU150 3.6 57.0 1.0 OD2 A:ASP151 3.7 45.4 1.0 OE2 A:GLU150 3.8 53.5 1.0 O A:HOH635 4.0 48.6 1.0 OG A:SER148 4.0 37.9 1.0 CH2 A:TRP130 4.5 60.0 1.0 CZ3 A:TRP130 4.5 56.6 1.0 CB A:ASP151 4.9 40.2 1.0 N A:ASP151 5.0 45.0 1.0

Yttrium binding site 3 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Y405 b:37.2 occ:1.00 OD1 B:ASP151 2.7 41.5 1.0 OE1 B:GLU150 2.7 43.5 1.0 O B:HOH659 2.9 43.4 1.0 O B:HOH633 2.9 46.2 1.0 O B:HOH669 3.0 40.6 1.0 CD B:GLU150 3.5 48.4 1.0 CG B:ASP151 3.5 37.6 1.0 OE2 B:GLU150 3.6 52.1 1.0 OD2 B:ASP151 3.7 43.6 1.0 OG B:SER148 4.0 35.8 1.0 O B:HOH657 4.0 49.7 1.0 CH2 B:TRP130 4.4 64.7 1.0 CZ3 B:TRP130 4.6 55.0 1.0 CB B:ASP151 4.9 41.0 1.0 N B:ASP151 4.9 38.0 1.0 CG B:GLU150 4.9 43.2 1.0

Yttrium binding site 4 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Y406 b:88.3 occ:1.00 OE2 B:GLU315 2.9 66.1 1.0 OE1 B:GLU315 3.0 78.4 1.0 CD B:GLU315 3.3 55.0 1.0 OE1 D:GLU283 4.1 64.4 1.0 CG B:GLU315 4.7 45.9 1.0 OE2 D:GLU283 4.7 58.0 1.0 CD D:GLU283 4.9 57.9 1.0

Yttrium binding site 5 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Y403 b:84.3 occ:1.00 OE2 C:GLU315 2.9 76.3 1.0 OE1 C:GLU315 3.0 77.9 1.0 O A:HOH566 3.0 66.3 1.0 O C:HOH648 3.1 68.9 1.0 O1 A:PEG406 3.2 68.8 1.0 CD C:GLU315 3.2 63.6 1.0 C1 A:PEG406 3.7 75.2 1.0 OE1 A:GLU283 4.0 66.5 1.0 OE2 A:GLU283 4.6 70.2 1.0 CG C:GLU315 4.6 47.9 1.0 CD A:GLU283 4.8 61.0 1.0

Yttrium binding site 6 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Y403 b:120.6 occ:1.00 OE1 D:GLU153 3.0 55.7 0.5 OE2 D:GLU150 3.3 93.4 1.0 CD D:GLU153 3.8 48.8 0.5 CG D:GLU150 3.8 74.5 1.0 CD D:GLU150 4.0 91.0 1.0 OE2 D:GLU153 4.0 53.0 0.5 CG D:GLU153 4.8 41.3 0.5

Yttrium binding site 7 out of 7 in the Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 7 of Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 within 5.0Å range: probe atom residue distance (Å) B Occ D:Y405 b:84.1 occ:1.00 OE2 D:GLU315 2.9 76.4 1.0 OE1 D:GLU315 3.0 78.5 1.0 CD D:GLU315 3.2 62.7 1.0 O1 B:PGE403 4.0 62.4 0.7 OE1 B:GLU283 4.1 67.5 1.0 OE2 B:GLU283 4.6 65.3 1.0 CG D:GLU315 4.6 49.8 1.0 CD B:GLU283 4.8 57.5 1.0

N.Polidori, K.Gruber. Old Yellow Enzyme From the Thermophilic Ferrovum Sp. JA12 To Be Published.