Zinc in PDB 3sp7: Crystal Structure of Bcl-Xl Bound to BM903

The structure of Crystal Structure of Bcl-Xl Bound to BM903, PDB code: 3sp7 was solved by J.L.Meagher, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.627, 54.891, 79.569, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 18.5

The structure of Crystal Structure of Bcl-Xl Bound to BM903 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Bcl-Xl Bound to BM903 (pdb code 3sp7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Bcl-Xl Bound to BM903, PDB code: 3sp7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Bcl-Xl Bound to BM903


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bcl-Xl Bound to BM903 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn211 b:18.1 occ:0.50 O A:HOH317 1.9 41.1 1.0 OD2 A:ASP11 2.0 21.9 1.0 OE2 A:GLU7 2.0 32.9 0.5 O A:HOH243 2.2 39.4 1.0 CG A:ASP11 2.7 20.7 1.0 OD1 A:ASP11 2.8 23.9 1.0 CD A:GLU7 3.0 39.9 0.5 CG A:GLU7 3.3 15.9 0.5 OE1 A:GLU7 4.1 35.0 0.5 CB A:ASP11 4.2 13.2 1.0 O A:HOH316 4.3 20.9 1.0 O A:HOH238 4.4 37.7 1.0 NZ A:LYS87 4.5 46.0 1.0 CD A:LYS87 4.6 21.8 1.0 O A:GLU7 4.7 13.3 1.0 CB A:GLU7 4.8 13.7 0.5 CB A:GLU7 4.8 14.8 0.5 CG A:GLU7 5.0 26.2 0.5

Zinc binding site 2 out of 4 in the Crystal Structure of Bcl-Xl Bound to BM903


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bcl-Xl Bound to BM903 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn212 b:14.8 occ:0.64 OXT A:ACT501 1.9 20.1 0.9 O A:HOH285 2.1 26.0 1.0 OE1 A:GLU98 2.1 19.6 1.0 OE2 A:GLU98 2.5 21.2 1.0 CD A:GLU98 2.6 21.5 1.0 C A:ACT501 2.9 21.1 0.9 O A:ACT501 3.4 24.0 0.9 NZ A:LYS20 3.7 18.8 1.0 O A:HOH37 4.0 28.4 1.0 O A:HOH307 4.0 31.1 1.0 CG A:GLU98 4.1 15.2 1.0 CE A:LYS20 4.1 18.9 1.0 CH3 A:ACT501 4.1 15.3 0.9 O A:HOH230 4.2 19.2 1.0 O A:HOH57 4.3 29.1 1.0 O A:HOH30 4.5 20.6 1.0 O A:HOH329 4.6 18.9 1.0 O A:HOH63 4.6 28.7 1.0 NH1 A:ARG102 4.8 20.7 1.0 CD2 A:PHE105 5.0 13.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Bcl-Xl Bound to BM903


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Bcl-Xl Bound to BM903 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn213 b:12.5 occ:0.70 O A:ACT503 2.0 27.2 1.0 NE2 A:HIS177 2.0 15.8 1.0 OE2 A:GLU124 2.0 26.2 1.0 OXT A:ACT503 2.6 30.6 1.0 C A:ACT503 2.6 29.7 1.0 CD A:GLU124 2.8 21.2 1.0 OE1 A:GLU124 3.0 33.4 1.0 CD2 A:HIS177 3.0 15.0 1.0 CE1 A:HIS177 3.0 16.7 1.0 CH3 A:ACT503 4.1 30.1 1.0 OH A:TYR120 4.1 12.7 1.0 CG A:HIS177 4.1 14.4 1.0 ND1 A:HIS177 4.2 17.6 1.0 CG A:GLU124 4.2 16.5 1.0 O A:HOH323 4.3 52.3 1.0 CE2 A:TYR120 4.6 11.2 1.0 CZ A:TYR120 4.9 13.0 1.0 NE2 A:GLN121 4.9 40.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Bcl-Xl Bound to BM903


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Bcl-Xl Bound to BM903 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn214 b:34.7 occ:0.50 OE2 A:GLU184 2.1 25.5 1.0 CD A:GLU184 2.9 30.9 1.0 OE1 A:GLU184 3.0 37.1 1.0 O A:HOH257 3.9 28.1 1.0 O A:HOH337 4.0 42.3 1.0 CG A:GLU184 4.4 17.2 1.0 CA A:TRP181 4.6 9.5 1.0 N A:TRP181 4.8 10.8 1.0 CB A:GLU184 4.8 13.5 1.0 CD1 A:TRP181 4.9 12.9 1.0 CB A:TRP181 5.0 10.1 1.0

H.Zhou, J.Chen, J.L.Meagher, A.Aguilar, L.Bai, L.Liu, C.Y.Yang, C.Xin, J.A.Stuckey, S.Wang. Structure-Based Design of A New Class of Potent Bcl-2/Bcl-Xl Inhibitors To Be Published.