Copper in PDB 7m5c: Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide

The structure of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide, PDB code: 7m5c was solved by G.Singh, A.Aggarwal, T.Moldoveanu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.34 / 3.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.385, 132.215, 89.379, 90, 119.2, 90
R / Rfree (%)	21.3 / 24.9

The binding sites of Copper atom in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide (pdb code 7m5c). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide, PDB code: 7m5c:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:56.0 occ:1.00 NE2 M:HIS164 2.1 64.4 1.0 NE2 A:HIS145 2.1 58.0 1.0 NE2 A:HIS141 2.1 56.9 1.0 CD2 M:HIS164 2.8 60.0 1.0 CE1 A:HIS141 2.9 58.7 1.0 CE1 A:HIS145 2.9 58.4 1.0 CD2 A:HIS145 3.2 54.2 1.0 CD2 A:HIS141 3.2 55.2 1.0 CE1 M:HIS164 3.2 63.0 1.0 CB M:ASP160 3.9 66.1 1.0 CG M:ASP160 4.0 72.6 1.0 CG M:HIS164 4.1 59.7 1.0 ND1 A:HIS141 4.1 58.1 1.0 ND1 A:HIS145 4.1 58.3 1.0 ND1 M:HIS164 4.2 62.3 1.0 CG A:HIS141 4.2 54.3 1.0 CG A:HIS145 4.3 58.8 1.0 OD2 M:ASP160 4.3 75.4 1.0 OD1 M:ASP160 4.5 75.2 1.0 CA M:ASP160 4.8 58.6 1.0 O A:LEU97 4.8 35.9 1.0 O M:ASP160 4.9 64.4 1.0

Copper binding site 2 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu201 b:60.8 occ:1.00 NE2 O:HIS164 2.1 71.5 1.0 NE2 C:HIS145 2.2 62.3 1.0 NE2 C:HIS141 2.4 78.5 1.0 CE1 C:HIS141 2.5 77.9 1.0 CD2 O:HIS164 2.8 67.1 1.0 CE1 C:HIS145 3.1 63.9 1.0 CE1 O:HIS164 3.3 74.4 1.0 CD2 C:HIS145 3.3 59.8 1.0 CD2 C:HIS141 3.7 75.5 1.0 ND1 C:HIS141 3.8 75.1 1.0 CB O:ASP160 3.9 69.4 1.0 CG O:ASP160 4.1 83.2 1.0 CG O:HIS164 4.1 66.1 1.0 OD2 O:ASP160 4.2 88.0 1.0 ND1 O:HIS164 4.3 70.2 1.0 ND1 C:HIS145 4.3 62.7 1.0 CG C:HIS141 4.4 71.8 1.0 CG C:HIS145 4.4 59.6 1.0 OD1 O:ASP160 4.6 90.0 1.0 CA O:ASP160 4.8 54.5 1.0 O C:LEU97 4.9 45.5 1.0 O O:ASP160 5.0 50.8 1.0

Copper binding site 3 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu201 b:43.6 occ:1.00 NE2 E:HIS145 2.0 75.2 1.0 NE2 A:HIS164 2.0 60.5 1.0 NE2 E:HIS141 2.1 67.1 1.0 CE1 E:HIS145 2.8 70.9 1.0 CD2 A:HIS164 3.0 52.6 1.0 CE1 E:HIS141 3.0 66.9 1.0 CE1 A:HIS164 3.0 59.5 1.0 CD2 E:HIS145 3.1 41.3 1.0 CD2 E:HIS141 3.1 67.2 1.0 ND1 E:HIS145 4.0 71.9 1.0 CG A:HIS164 4.1 53.5 1.0 ND1 A:HIS164 4.1 58.1 1.0 ND1 E:HIS141 4.1 68.2 1.0 CG E:HIS145 4.1 42.6 1.0 CG E:HIS141 4.2 65.2 1.0 CB A:ASP160 4.3 57.1 1.0 CG A:ASP160 4.4 67.9 1.0 OD2 A:ASP160 4.6 71.4 1.0 OD1 A:ASP160 4.7 71.4 1.0 O E:LEU97 4.8 46.4 1.0

Copper binding site 4 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ G:Cu201 b:49.2 occ:1.00 NE2 G:HIS141 2.1 70.6 1.0 NE2 G:HIS145 2.1 69.6 1.0 CE1 G:HIS141 2.6 68.9 1.0 CE1 G:HIS145 3.0 70.7 1.0 CD2 G:HIS145 3.2 68.0 1.0 CD2 G:HIS141 3.3 65.2 1.0 ND1 G:HIS141 3.9 68.0 1.0 ND1 G:HIS145 4.1 70.7 1.0 CG G:HIS141 4.2 63.6 1.0 CG G:HIS145 4.3 69.5 1.0

Copper binding site 5 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ I:Cu201 b:51.4 occ:1.00 NE2 C:HIS164 2.0 62.7 1.0 NE2 I:HIS145 2.0 85.1 1.0 NE2 I:HIS141 2.1 97.7 1.0 CE1 I:HIS145 2.7 91.3 1.0 CD2 C:HIS164 2.9 59.8 1.0 CE1 C:HIS164 2.9 60.1 1.0 CD2 I:HIS141 3.0 95.4 1.0 CE1 I:HIS141 3.1 99.9 1.0 CD2 I:HIS145 3.1 86.0 1.0 ND1 I:HIS145 3.9 91.0 1.0 ND1 C:HIS164 4.0 61.7 1.0 CG C:HIS164 4.1 59.1 1.0 CG I:HIS145 4.1 84.5 1.0 ND1 I:HIS141 4.1 97.5 1.0 CG I:HIS141 4.2 91.9 1.0 CB C:ASP160 4.2 82.6 1.0 CG C:ASP160 4.2 89.3 1.0 OD1 C:ASP160 4.4 92.0 1.0 O I:LEU97 4.6 58.0 1.0 OD2 C:ASP160 4.7 91.8 1.0 O I:GLN101 4.7 77.7 1.0 CA C:ASP160 4.8 65.4 1.0

Copper binding site 6 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ M:Cu201 b:73.0 occ:1.00 NE2 M:HIS145 2.0 115.6 1.0 NE2 M:HIS141 2.1 112.7 1.0 CE1 M:HIS145 2.8 115.6 1.0 CE1 M:HIS141 3.0 110.2 1.0 CD2 M:HIS141 3.1 105.7 1.0 CD2 M:HIS145 3.2 109.7 1.0 ND1 M:HIS145 4.0 114.8 1.0 ND1 M:HIS141 4.1 105.5 1.0 CG M:HIS141 4.2 101.1 1.0 CG M:HIS145 4.2 110.3 1.0 O M:LEU97 4.6 65.8 1.0 O M:LEU100 5.0 75.5 1.0

Copper binding site 7 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ O:Cu201 b:70.0 occ:1.00 NE2 O:HIS145 2.1 103.8 1.0 NE2 O:HIS141 2.2 95.1 1.0 CE1 O:HIS141 2.2 87.7 1.0 CE1 O:HIS145 3.0 104.3 1.0 CD2 O:HIS145 3.1 99.4 1.0 CD2 O:HIS141 3.5 86.9 1.0 ND1 O:HIS141 3.5 84.8 1.0 ND1 O:HIS145 4.1 103.5 1.0 CG O:HIS141 4.1 82.4 1.0 CG O:HIS145 4.2 98.3 1.0 O O:LEU97 5.0 47.3 1.0

Copper binding site 8 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ Q:Cu201 b:54.9 occ:1.00 NE2 Q:HIS145 2.1 88.5 1.0 NE2 Q:HIS141 2.1 77.6 1.0 CE1 Q:HIS145 2.9 90.5 1.0 CE1 Q:HIS141 3.1 80.2 1.0 CD2 Q:HIS141 3.2 76.6 1.0 CD2 Q:HIS145 3.2 86.7 1.0 ND1 Q:HIS145 4.1 90.2 1.0 ND1 Q:HIS141 4.2 78.5 1.0 CG Q:HIS141 4.3 75.1 1.0 CG Q:HIS145 4.3 87.4 1.0 O Q:LEU97 4.6 63.5 1.0 O Q:LEU100 4.9 58.1 1.0

Copper binding site 9 out of 9 in the Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Human Bak in Complex with Wt Bak BH3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ S:Cu201 b:62.5 occ:1.00 NE2 S:HIS145 2.2 89.3 1.0 NE2 S:HIS141 2.2 67.4 1.0 CE1 S:HIS145 2.9 94.3 1.0 CE1 S:HIS141 3.0 66.8 1.0 CD2 S:HIS145 3.3 91.3 1.0 CD2 S:HIS141 3.4 65.0 1.0 ND1 S:HIS145 4.1 95.0 1.0 ND1 S:HIS141 4.2 65.7 1.0 CG S:HIS145 4.3 91.4 1.0 CG S:HIS141 4.4 65.0 1.0

G.Singh, C.D.Guibao, J.Seetharaman, A.Aggarwal, C.R.Grace, D.E.Mcnamara, S.Vaithiyalingam, M.B.Waddell, T.Moldoveanu. Structural Basis of Bak Activation in Mitochondrial Apoptosis Initiation. Nat Commun V. 13 250 2022.
ISSN: ESSN 2041-1723
PubMed: 35017502
DOI: 10.1038/S41467-021-27851-Y