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Yttrium in PDB 4phg: Crystal Structure of YPT7 Covalently Modified with Gtp

Protein crystallography data

The structure of Crystal Structure of YPT7 Covalently Modified with Gtp, PDB code: 4phg was solved by D.Koch, D.Wiegandt, S.Vieweg, F.Hofmann, Y.Wu, A.Itzen, M.P.Mueller, R.S.Goody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.01 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.970, 53.160, 46.910, 90.00, 106.35, 90.00
R / Rfree (%) 17.5 / 23.4

Other elements in 4phg:

The structure of Crystal Structure of YPT7 Covalently Modified with Gtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of YPT7 Covalently Modified with Gtp (pdb code 4phg). 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 YPT7 Covalently Modified with Gtp, PDB code: 4phg:
Jump to Yttrium binding site number: 1; 2; 3;

Yttrium binding site 1 out of 3 in 4phg

Go back to Yttrium Binding Sites List in 4phg
Yttrium binding site 1 out of 3 in the Crystal Structure of YPT7 Covalently Modified with Gtp


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 YPT7 Covalently Modified with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y203

b:30.8
occ:1.00
OD1 A:ASP31 2.2 30.6 1.0
O A:HOH306 2.4 27.1 1.0
OD2 A:ASP31 2.5 24.7 1.0
CG A:ASP31 2.6 26.5 1.0
CB A:ASP31 4.1 27.3 1.0
OD2 A:ASP166 4.3 27.7 1.0
OD1 A:ASP166 4.5 28.4 1.0
O A:ARG27 4.6 25.2 1.0
O A:TYR28 4.6 24.4 1.0
CG A:ASP166 4.9 26.0 1.0
CA A:ASP31 4.9 26.3 1.0

Yttrium binding site 2 out of 3 in 4phg

Go back to Yttrium Binding Sites List in 4phg
Yttrium binding site 2 out of 3 in the Crystal Structure of YPT7 Covalently Modified with Gtp


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 YPT7 Covalently Modified with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y204

b:31.1
occ:1.00
O A:HOH301 1.9 42.8 1.0
OE1 A:GLU106 2.4 33.3 1.0
OE2 A:GLU69 2.5 40.0 1.0
OE2 A:GLU106 2.5 28.2 1.0
OE1 A:GLU69 2.8 53.5 1.0
O A:HOH308 2.8 42.9 1.0
CD A:GLU106 2.8 28.6 1.0
CD A:GLU69 3.0 45.4 1.0
CG A:GLU106 4.3 27.6 1.0
CG A:GLU69 4.4 44.8 1.0
NE2 A:HIS110 4.8 43.1 1.0

Yttrium binding site 3 out of 3 in 4phg

Go back to Yttrium Binding Sites List in 4phg
Yttrium binding site 3 out of 3 in the Crystal Structure of YPT7 Covalently Modified with Gtp


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 YPT7 Covalently Modified with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y205

b:37.8
occ:1.00
OE1 A:GLU117 2.3 48.3 1.0
CD A:GLU117 3.4 50.8 1.0
CG A:GLU117 4.1 52.5 1.0
OE2 A:GLU117 4.4 52.5 1.0

Reference:

D.Koch, D.Wiegandt, S.Vieweg, F.Hofmann, Y.Wu, A.Itzen, M.P.Mueller, R.S.Goody. Crystal Structure of YPT7 Covalently Modified with Gtp To Be Published.
Page generated: Wed Dec 16 02:41:14 2020

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