Zinc in PDB 8spe: Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31

The structure of Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31, PDB code: 8spe was solved by M.S.Miller, A.D.Cowan, P.M.Colman, P.E.Czabotar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.43 / 2.30
Space group	P 31 1
Cell size a, b, c (Å), α, β, γ (°)	141.355, 141.355, 110.191, 90, 90, 120
R / Rfree (%)	22.9 / 25.6

The binding sites of Zinc atom in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 (pdb code 8spe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31, PDB code: 8spe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


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 Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:49.5 occ:1.00 OD2 B:ASP84 2.2 45.4 1.0 OD1 B:ASP84 2.7 48.2 1.0 CG B:ASP84 2.8 47.9 1.0 CB B:ASP86 3.6 50.0 1.0 OD2 B:ASP86 4.1 56.5 1.0 CB B:ASP84 4.3 45.9 1.0 CG B:ASP86 4.4 59.1 1.0 OG B:SER87 4.5 56.4 1.0 CA B:ASP86 4.6 46.1 1.0 C B:ASP86 4.7 44.3 1.0 N B:SER87 4.8 41.8 1.0 CB B:SER87 4.9 39.1 1.0 N B:ASP86 4.9 47.6 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


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 Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:80.2 occ:1.00 OE2 C:GLU69 2.0 66.5 1.0 OD2 Q:ASP102 2.2 58.2 1.0 CD C:GLU69 2.8 59.8 1.0 OE2 D:GLU69 2.9 70.3 1.0 OE1 C:GLU69 3.1 61.2 1.0 OE1 D:GLU69 3.2 66.7 1.0 CG Q:ASP102 3.3 54.5 1.0 CD D:GLU69 3.4 68.2 1.0 CB Q:ASP102 3.7 44.3 1.0 CG C:GLU69 4.1 45.4 1.0 NH2 Q:ARG109 4.1 50.4 1.0 CE R:LYS64 4.2 52.5 1.0 NZ R:LYS64 4.2 46.8 1.0 OD1 Q:ASN104 4.3 59.3 1.0 OD1 Q:ASP102 4.4 53.6 1.0 CG D:GLU69 4.9 61.4 1.0 C2 C:EDO203 4.9 47.5 1.0 O2 C:EDO203 4.9 54.4 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


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 Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:67.4 occ:1.00 OD2 C:ASP53 1.9 62.3 1.0 O C:GLY48 2.0 57.8 1.0 O C:HOH302 2.2 65.0 1.0 C C:GLY48 2.6 58.1 1.0 CA C:GLY48 2.7 58.4 1.0 CG C:ASP53 2.7 55.2 1.0 OD1 C:ASP53 3.0 52.5 1.0 N C:GLY48 3.4 62.9 1.0 N C:PRO49 3.9 56.9 1.0 CB C:ASP53 4.2 46.4 1.0 O C:PRO49 4.3 54.0 1.0 C C:PRO49 4.5 52.6 1.0 CA C:PRO49 4.6 50.3 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


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 Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:85.4 occ:1.00 OD1 D:ASP86 2.0 82.7 1.0 OD2 I:ASP86 2.1 74.1 1.0 OD1 D:ASP84 2.2 70.4 1.0 CG D:ASP86 2.8 79.1 1.0 OD2 D:ASP86 2.9 84.8 1.0 CG D:ASP84 3.2 67.6 1.0 NH2 I:ARG94 3.2 57.8 1.0 CG I:ASP86 3.3 70.8 1.0 OD2 D:ASP84 3.4 72.6 1.0 CZ I:ARG94 3.8 60.0 1.0 OD1 I:ASP86 3.9 70.5 1.0 NE I:ARG94 4.2 61.5 1.0 CB D:ASP86 4.2 70.7 1.0 CB I:ASP86 4.4 67.5 1.0 N D:ASP86 4.5 61.2 1.0 NH1 I:ARG94 4.6 47.4 1.0 CB D:ASP84 4.6 62.9 1.0 CA D:ASP86 4.8 68.0 1.0 CA D:ASP84 4.9 58.7 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:70.5 occ:1.00 OE2 I:GLU69 1.9 46.2 1.0 OE2 J:GLU69 2.0 70.4 1.0 CD J:GLU69 2.7 57.5 1.0 OE1 J:GLU69 2.8 61.1 1.0 CD I:GLU69 2.9 54.7 1.0 OE1 I:GLU69 3.3 55.3 1.0 NH2 I:ARG65 3.9 50.2 1.0 CG J:GLU69 4.1 56.4 1.0 O1 J:EDO202 4.1 60.6 1.0 O2 J:EDO202 4.1 49.2 1.0 C2 J:EDO202 4.2 56.8 1.0 CG I:GLU69 4.3 44.7 1.0 C1 J:EDO202 4.8 55.8 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn201 b:105.4 occ:1.00 OD2 J:ASP86 2.0 97.3 1.0 OD1 J:ASP84 2.0 89.0 1.0 CG J:ASP86 2.7 88.7 1.0 CG J:ASP84 2.9 82.5 1.0 CB J:ASP86 3.0 80.6 1.0 OD2 J:ASP84 3.0 83.0 1.0 OD1 J:ASP86 3.7 90.9 1.0 N J:ASP86 3.9 69.0 1.0 CA J:ASP86 4.1 80.4 1.0 CB J:ASP84 4.3 66.4 1.0 N J:THR85 4.7 63.9 1.0 CA J:ASP84 4.8 65.8 1.0 C J:ASP84 4.9 65.0 1.0 C J:ASP86 4.9 75.3 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn201 b:63.5 occ:1.00 OD2 M:ASP53 2.0 53.5 1.0 O M:GLY48 2.1 50.3 1.0 O M:HOH303 2.1 63.1 1.0 C M:GLY48 2.8 54.3 1.0 CG M:ASP53 2.8 52.8 1.0 CA M:GLY48 2.9 51.4 1.0 OD1 M:ASP53 2.9 51.6 1.0 N M:GLY48 3.6 57.6 1.0 OG a:SER101 3.9 54.1 1.0 N M:PRO49 4.1 53.8 1.0 CB M:ASP53 4.3 45.0 1.0 O M:PRO49 4.4 49.4 1.0 O a:SER101 4.5 51.9 1.0 C M:PRO49 4.6 49.3 1.0 C a:SER101 4.6 56.4 1.0 CB a:SER101 4.6 54.8 1.0 CA a:ASP102 4.7 52.6 1.0 N a:ASP102 4.8 53.4 1.0 CA M:PRO49 4.8 48.5 1.0 O M:HOH302 4.9 52.0 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ c:Zn201 b:54.4 occ:1.00 OE2 c:GLU69 2.0 47.1 1.0 CD c:GLU69 2.9 41.0 1.0 OE1 c:GLU69 3.1 39.4 1.0 CD c:ARG65 4.2 48.9 1.0 CG c:GLU69 4.3 43.6 1.0 CG c:ARG65 4.6 46.2 1.0 NE c:ARG65 4.9 48.8 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Bax Core Domain BH3-Groove Dimer - Tetrameric Fraction P31 within 5.0Å range: probe atom residue distance (Å) B Occ h:Zn201 b:152.4 occ:1.00 OD2 h:ASP86 2.5 177.6 1.0 OD2 h:ASP84 2.6 180.3 1.0 OD1 h:ASP84 2.8 184.2 1.0 CG h:ASP84 3.0 184.9 1.0 CG h:ASP86 3.7 177.8 1.0 CB h:ASP84 4.4 183.5 1.0 OD1 h:ASP86 4.6 177.5 1.0 CB h:ASP86 4.6 168.2 1.0 CA h:ASP84 4.9 181.5 1.0

M.S.Miller, A.D.Cowan, J.M.Brouwer, S.T.Smyth, L.Peng, A.Z.Wardak, R.T.Uren, C.Luo, M.J.Roy, S.Shah, Z.Tan, G.E.Reid, P.M.Colman, P.E.Czabotar. Sequence Differences Between Bax and Bak Core Domains Manifest As Differences in Their Interactions with Lipids. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 38088212
DOI: 10.1111/FEBS.17031