Ytterbium in PDB 1pk0: Crystal Structure of the EF3-Cam Complexed with Pmeapp

All present enzymatic activity of Crystal Structure of the EF3-Cam Complexed with Pmeapp:
4.6.1.1;

The structure of Crystal Structure of the EF3-Cam Complexed with Pmeapp, PDB code: 1pk0 was solved by Y.Shen, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.98 / 3.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	116.263, 165.759, 342.409, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 30.2

The structure of Crystal Structure of the EF3-Cam Complexed with Pmeapp also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Ytterbium atom in the Crystal Structure of the EF3-Cam Complexed with Pmeapp (pdb code 1pk0). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Crystal Structure of the EF3-Cam Complexed with Pmeapp, PDB code: 1pk0:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 the EF3-Cam Complexed with Pmeapp within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb901 b:77.5 occ:1.00 OD2 A:ASP493 2.3 20.0 1.0 C5' A:EMA1999 2.6 37.2 1.0 NE2 A:HIS577 2.6 20.7 1.0 OD2 A:ASP491 2.7 31.6 1.0 OD1 A:ASP491 2.8 30.6 1.0 CG A:ASP493 3.0 18.7 1.0 OD1 A:ASP493 3.0 17.7 1.0 CG A:ASP491 3.1 29.5 1.0 O5' A:EMA1999 3.1 35.5 1.0 O3A A:EMA1999 3.4 35.7 1.0 CD2 A:HIS577 3.5 19.2 1.0 PA A:EMA1999 3.6 36.9 1.0 CE1 A:HIS577 3.6 23.5 1.0 O1A A:EMA1999 3.7 38.3 1.0 O A:HOH7 4.0 5.5 1.0 O A:LYS346 4.3 20.3 1.0 CB A:ASP493 4.4 19.7 1.0 CB A:ASP491 4.5 27.4 1.0 C4' A:EMA1999 4.5 40.0 1.0 PB A:EMA1999 4.7 33.7 1.0 ND1 A:HIS577 4.7 22.6 1.0 CG A:HIS577 4.7 18.6 1.0 CA A:ASP493 4.8 20.1 1.0 O2B A:EMA1999 4.9 36.9 1.0 O3B A:EMA1999 4.9 33.7 1.0 O2A A:EMA1999 4.9 38.0 1.0 CD A:LYS346 5.0 24.3 1.0

Ytterbium binding site 2 out of 3 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 the EF3-Cam Complexed with Pmeapp within 5.0Å range: probe atom residue distance (Å) B Occ B:Yb902 b:82.8 occ:1.00 OD2 B:ASP493 2.2 24.4 1.0 CE1 B:HIS577 2.5 33.4 1.0 C5' B:EMA2999 2.5 60.9 1.0 OD2 B:ASP491 2.6 27.4 1.0 NE2 B:HIS577 2.9 33.4 1.0 CG B:ASP493 3.0 21.9 1.0 O5' B:EMA2999 3.1 57.7 1.0 OD1 B:ASP491 3.1 27.8 1.0 OD1 B:ASP493 3.1 21.5 1.0 CG B:ASP491 3.1 23.3 1.0 PA B:EMA2999 3.6 61.4 1.0 ND1 B:HIS577 3.6 34.8 1.0 O3A B:EMA2999 3.6 59.1 1.0 O1A B:EMA2999 3.7 63.6 1.0 O B:LYS346 4.0 24.8 1.0 CD2 B:HIS577 4.2 33.6 1.0 CB B:ASP493 4.3 20.6 1.0 O B:HOH12 4.4 13.5 1.0 C4' B:EMA2999 4.5 55.7 1.0 CG B:HIS577 4.5 32.6 1.0 CB B:ASP491 4.5 21.3 1.0 CA B:ASP493 4.7 20.3 1.0 PB B:EMA2999 4.9 58.4 1.0 O2A B:EMA2999 4.9 60.0 1.0

Ytterbium binding site 3 out of 3 in the Crystal Structure of the EF3-Cam Complexed with Pmeapp


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 the EF3-Cam Complexed with Pmeapp within 5.0Å range: probe atom residue distance (Å) B Occ C:Yb903 b:86.7 occ:1.00 OD2 C:ASP493 2.5 21.6 1.0 OD2 C:ASP491 2.5 30.4 1.0 NE2 C:HIS577 2.7 27.2 1.0 C5' C:EMA3999 2.8 64.3 1.0 OD1 C:ASP491 2.8 30.0 1.0 CG C:ASP491 3.0 27.9 1.0 CD2 C:HIS577 3.1 14.9 1.0 CG C:ASP493 3.1 21.0 1.0 OD1 C:ASP493 3.2 23.2 1.0 O1A C:EMA3999 3.4 63.7 1.0 O5' C:EMA3999 3.5 63.9 1.0 PA C:EMA3999 3.7 64.0 1.0 CE1 C:HIS577 3.9 30.4 1.0 O C:HOH14 4.0 1.2 1.0 O3A C:EMA3999 4.1 60.0 1.0 O C:LYS346 4.1 24.9 1.0 CB C:ASP491 4.4 27.1 1.0 CG C:HIS577 4.4 17.8 1.0 CB C:ASP493 4.5 21.4 1.0 ND1 C:HIS577 4.7 24.4 1.0 C4' C:EMA3999 4.9 66.0 1.0 CA C:ASP493 5.0 20.9 1.0

Y.Shen, N.L.Zhukovskaya, M.I.Zimmer, S.Soelaiman, P.Bergson, C.R.Wang, C.S.Gibbs, W.J.Tang. Selective Inhibition of Anthrax Edema Factor By Adefovir, A Drug For Chronic Hepatitis B Virus Infection. Proc.Natl.Acad.Sci.Usa V. 101 3242 2004.
ISSN: ISSN 0027-8424
PubMed: 14978283
DOI: 10.1073/PNAS.0306552101