Ytterbium in PDB 6oww: Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium

The structure of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium, PDB code: 6oww was solved by E.W.Titus, F.H.Deiter, C.Shi, N.Jura, R.C.Deo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	214.34 / 3.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.832, 86.015, 214.340, 90.00, 89.91, 90.00
R / Rfree (%)	29 / 34

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 63;

Binding sites:

The binding sites of Ytterbium atom in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium (pdb code 6oww). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 63 binding sites of Ytterbium where determined in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium, PDB code: 6oww:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Ytterbium binding site 1 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb401 b:0.3 occ:0.87 OE1 A:GLU187 2.5 0.7 1.0 OE2 A:GLU184 2.6 0.1 1.0 OE2 A:GLU187 3.1 0.0 1.0 CD A:GLU187 3.2 0.7 1.0 OE1 A:GLU184 3.3 0.8 1.0 CD A:GLU184 3.4 0.1 1.0 NZ A:LYS180 4.5 0.4 1.0 CG A:GLU187 4.6 0.5 1.0 CG A:GLU184 4.8 0.9 1.0 OD1 A:ASP120 4.9 0.6 1.0 CD B:LYS47 5.0 0.8 1.0

Ytterbium binding site 2 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb402 b:0.0 occ:0.77 OE1 A:GLU110 2.8 0.8 1.0 OE2 A:GLU110 3.2 0.2 1.0 OE1 A:GLU124 3.2 0.1 1.0 CD A:GLU110 3.4 0.7 1.0 CB A:ASP109 3.7 0.3 1.0 OD2 A:ASP109 3.8 0.4 1.0 CG A:ASP109 4.0 0.8 1.0 CD A:GLU124 4.1 0.5 1.0 OE2 A:GLU124 4.2 0.7 1.0 OH A:TYR115 4.4 0.9 1.0 CG A:GLU110 4.9 0.1 1.0 CA A:ASP109 4.9 0.8 1.0 N A:GLU110 4.9 0.5 1.0 OD1 A:ASP109 4.9 1.0 1.0

Ytterbium binding site 3 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb403 b:0.9 occ:0.65 OD1 A:ASP351 3.3 99.3 1.0 OD2 A:ASP351 3.3 0.2 1.0 CG A:ASP351 3.6 0.6 1.0 OE2 A:GLU357 3.8 0.9 1.0 OE1 A:GLU357 3.8 0.2 1.0 CD A:GLU357 4.2 0.8 1.0 O A:LEU352 4.3 0.4 1.0 O A:ASP351 4.6 0.8 1.0

Ytterbium binding site 4 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb404 b:0.9 occ:0.80 OE2 A:GLU124 2.7 0.7 1.0 CE2 A:PHE258 3.3 0.3 1.0 CD A:GLU110 3.6 0.7 1.0 CG A:GLU110 3.7 0.1 1.0 OD1 A:ASP126 3.8 0.4 1.0 OE2 A:GLU110 3.8 0.2 1.0 CZ A:PHE258 3.8 0.6 1.0 CD A:GLU124 3.9 0.5 1.0 OG A:SER113 3.9 0.3 1.0 OE1 A:GLU110 4.0 0.8 1.0 CD2 A:PHE258 4.1 0.6 1.0 CB A:GLU110 4.3 0.9 1.0 OE1 A:GLU124 4.7 0.1 1.0 CG A:GLU124 4.7 0.0 1.0 CG A:ASP126 4.9 0.0 1.0

Ytterbium binding site 5 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb405 b:93.0 occ:0.53 OE1 A:GLU174 3.6 97.8 1.0 OE2 A:GLU174 3.7 89.4 1.0 CB B:ASP144 3.9 95.4 1.0 CD A:GLU174 4.0 92.0 1.0 OD2 B:ASP144 4.2 81.8 1.0 CG B:ASP144 4.5 88.9 1.0 YB A:YB406 4.7 0.6 0.6

Ytterbium binding site 6 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb406 b:0.6 occ:0.61 CB A:ASP144 3.7 0.8 1.0 OD2 A:ASP144 3.8 98.8 1.0 OE1 B:GLU174 3.8 93.2 1.0 OE2 B:GLU174 3.9 90.3 1.0 CD B:GLU174 4.1 89.4 1.0 CG A:ASP144 4.2 0.3 1.0 YB A:YB405 4.7 93.0 0.5 CA A:ASP144 4.9 0.7 1.0

Ytterbium binding site 7 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb407 b:0.5 occ:0.45 OD1 A:ASP310 2.9 98.4 1.0 O3 A:SO4410 3.4 0.7 1.0 O1 A:SO4410 3.7 0.2 1.0 CG A:ASP310 4.0 90.8 1.0 S A:SO4410 4.2 0.9 1.0 OD2 A:ASP310 4.4 85.8 1.0 NH2 A:ARG251 4.5 90.8 1.0

Ytterbium binding site 8 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb408 b:94.7 occ:0.50 O A:SER208 2.3 0.3 1.0 C A:SER208 3.5 0.7 1.0 OE2 A:GLU213 3.6 0.2 1.0 CB A:SER208 3.9 90.1 1.0 OD2 A:ASP215 3.9 91.4 1.0 OD1 A:ASP215 4.2 91.0 1.0 CA A:SER208 4.3 98.6 1.0 CD A:GLU213 4.4 0.1 1.0 OE1 A:GLU213 4.4 99.6 1.0 CG A:ASP215 4.5 93.7 1.0 O A:LEU207 4.5 91.1 1.0 N A:LEU209 4.5 0.6 1.0 CA A:LEU209 4.7 1.0 1.0

Ytterbium binding site 9 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 9 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb409 b:0.7 occ:1.00 OD1 A:ASP348 2.5 0.6 1.0 OD2 A:ASP350 3.1 0.5 1.0 CG A:ASP348 3.5 0.6 1.0 CG A:ASP350 4.0 0.8 1.0 OD2 A:ASP348 4.0 0.4 1.0 CB A:ASP350 4.1 0.8 1.0 N A:ASP350 4.6 92.5 1.0 CB A:ASP348 4.6 0.9 1.0 CA A:ASP348 4.8 95.1 1.0 CA A:ASP350 5.0 94.8 1.0

Ytterbium binding site 10 out of 63 in the Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 10 of Crystal Structure of A Human Cardiac Calsequestrin Filament Complexed with Ytterbium within 5.0Å range: probe atom residue distance (Å) B Occ B:Yb401 b:0.4 occ:0.92 OE1 B:GLU187 2.3 0.5 1.0 OE2 B:GLU184 2.8 89.1 1.0 CD B:GLU187 3.1 86.8 1.0 OE2 B:GLU187 3.3 79.5 1.0 OE1 B:GLU184 3.4 82.6 1.0 CD B:GLU184 3.5 84.5 1.0 NZ B:LYS180 4.5 86.0 1.0 CG B:GLU187 4.6 90.5 1.0 CD A:LYS47 4.7 0.0 1.0 OD1 B:ASP120 4.7 0.2 1.0 CG B:GLU184 4.9 83.2 1.0 CB B:GLU187 5.0 88.2 1.0

E.W.Titus, F.H.Deiter, C.Shi, J.Wojciak, M.Scheinman, N.Jura, R.C.Deo. The Structure of A Calsequestrin Filament Reveals Mechanisms of Familial Arrhythmia. Nat.Struct.Mol.Biol. 2020.
ISSN: ESSN 1545-9985
PubMed: 33046906
DOI: 10.1038/S41594-020-0510-9