Zinc in PDB 6o38: Structure of A Chaperone-Substrate Complex

The structure of Structure of A Chaperone-Substrate Complex, PDB code: 6o38 was solved by D.V.Urusova, N.H.Tolia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.79 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	110.747, 118.489, 129.583, 108.94, 103.97, 100.10
R / Rfree (%)	22.5 / 24

The binding sites of Zinc atom in the Structure of A Chaperone-Substrate Complex (pdb code 6o38). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Chaperone-Substrate Complex, PDB code: 6o38:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of A Chaperone-Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Chaperone-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:55.4 occ:1.00 NE2 A:HIS508 2.1 55.5 1.0 NE2 A:HIS502 2.1 53.6 1.0 OD1 G:ASP170 2.1 70.5 1.0 NE2 A:HIS498 2.2 55.2 1.0 OD2 G:ASP170 2.3 68.7 1.0 CG G:ASP170 2.5 70.5 1.0 CE1 A:HIS508 2.7 56.7 1.0 CD2 A:HIS502 3.0 53.2 1.0 CE1 A:HIS502 3.1 53.6 1.0 CD2 A:HIS498 3.1 54.8 1.0 CE1 A:HIS498 3.2 54.3 1.0 CD2 A:HIS508 3.2 54.6 1.0 ND1 A:HIS508 3.9 56.8 1.0 CB G:ASP170 4.0 73.5 1.0 CG A:HIS502 4.1 53.0 1.0 CG A:HIS508 4.2 55.5 1.0 ND1 A:HIS502 4.2 53.3 1.0 CG A:HIS498 4.3 53.6 1.0 ND1 A:HIS498 4.3 53.4 1.0 O G:ASP170 4.4 79.8 1.0 C G:ASP170 4.4 78.8 1.0 OE1 A:GLU499 4.6 56.1 1.0 O G:GLN171 4.7 75.1 1.0 CA G:ASP170 4.7 77.8 1.0 N G:GLN171 4.8 79.2 1.0 C G:GLN171 4.8 77.2 1.0 OE2 A:GLU499 5.0 56.9 1.0

Zinc binding site 2 out of 6 in the Structure of A Chaperone-Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Chaperone-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:45.8 occ:1.00 NE2 B:HIS508 2.0 48.1 1.0 NE2 B:HIS502 2.1 45.3 1.0 NE2 B:HIS498 2.2 46.2 1.0 OD1 H:ASP170 2.2 59.2 1.0 OD2 H:ASP170 2.3 57.7 1.0 CG H:ASP170 2.5 59.1 1.0 CE1 B:HIS508 2.7 49.2 1.0 CD2 B:HIS502 3.0 45.1 1.0 CD2 B:HIS498 3.1 46.4 1.0 CE1 B:HIS498 3.1 45.1 1.0 CE1 B:HIS502 3.1 45.3 1.0 CD2 B:HIS508 3.2 47.0 1.0 ND1 B:HIS508 3.9 48.8 1.0 CB H:ASP170 4.1 61.5 1.0 CG B:HIS508 4.2 47.5 1.0 CG B:HIS502 4.2 44.9 1.0 ND1 B:HIS498 4.2 44.6 1.0 ND1 B:HIS502 4.2 45.0 1.0 CG B:HIS498 4.2 45.6 1.0 O H:ASP170 4.4 67.3 1.0 C H:ASP170 4.5 66.5 1.0 O H:GLN171 4.7 64.1 1.0 OE2 B:GLU499 4.7 47.7 1.0 C H:GLN171 4.7 65.9 1.0 CA H:ASP170 4.8 65.1 1.0 N H:GLN171 4.8 67.1 1.0 N H:GLU172 5.0 66.1 1.0

Zinc binding site 3 out of 6 in the Structure of A Chaperone-Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Chaperone-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:50.8 occ:1.00 NE2 C:HIS508 2.0 54.4 1.0 NE2 C:HIS502 2.0 49.2 1.0 OD2 K:ASP170 2.1 61.4 1.0 OD1 K:ASP170 2.3 61.8 1.0 NE2 C:HIS498 2.3 52.0 1.0 CG K:ASP170 2.4 61.3 1.0 CE1 C:HIS508 2.6 55.1 1.0 CD2 C:HIS502 3.0 49.2 1.0 CE1 C:HIS502 3.1 48.3 1.0 CD2 C:HIS508 3.2 53.1 1.0 CD2 C:HIS498 3.2 52.7 1.0 CE1 C:HIS498 3.2 51.1 1.0 ND1 C:HIS508 3.8 54.5 1.0 CB K:ASP170 4.0 61.1 1.0 CG C:HIS508 4.1 53.2 1.0 CG C:HIS502 4.1 48.1 1.0 ND1 C:HIS502 4.2 47.7 1.0 ND1 C:HIS498 4.3 51.1 1.0 CG C:HIS498 4.3 52.1 1.0 C K:ASP170 4.4 64.1 1.0 O K:ASP170 4.5 65.4 1.0 O K:GLN171 4.6 65.3 1.0 C K:GLN171 4.7 66.7 1.0 N K:GLN171 4.7 64.6 1.0 CA K:ASP170 4.7 62.5 1.0 OE2 C:GLU499 4.8 53.9 1.0 N K:GLU172 4.9 68.9 1.0

Zinc binding site 4 out of 6 in the Structure of A Chaperone-Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Chaperone-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:43.7 occ:1.00 NE2 D:HIS502 2.0 44.1 1.0 NE2 D:HIS508 2.1 48.4 1.0 OD2 L:ASP170 2.1 55.1 1.0 OD1 L:ASP170 2.2 56.0 1.0 NE2 D:HIS498 2.2 46.2 1.0 CG L:ASP170 2.5 55.4 1.0 CE1 D:HIS508 2.7 49.1 1.0 CD2 D:HIS502 2.9 43.5 1.0 CE1 D:HIS502 3.1 44.2 1.0 CD2 D:HIS498 3.1 46.0 1.0 CE1 D:HIS498 3.1 45.6 1.0 CD2 D:HIS508 3.2 47.8 1.0 ND1 D:HIS508 3.9 49.0 1.0 CB L:ASP170 4.0 56.0 1.0 CG D:HIS502 4.1 43.2 1.0 CG D:HIS508 4.1 48.2 1.0 ND1 D:HIS502 4.2 43.8 1.0 ND1 D:HIS498 4.2 45.1 1.0 CG D:HIS498 4.3 45.3 1.0 C L:ASP170 4.4 59.1 1.0 O L:ASP170 4.4 60.4 1.0 O L:GLN171 4.6 62.3 1.0 CA L:ASP170 4.7 57.9 1.0 C L:GLN171 4.7 63.9 1.0 N L:GLN171 4.8 62.2 1.0 OE2 D:GLU499 4.8 47.5 1.0

Zinc binding site 5 out of 6 in the Structure of A Chaperone-Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Chaperone-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn601 b:43.5 occ:1.00 NE2 E:HIS508 2.1 43.6 1.0 NE2 E:HIS502 2.1 43.3 1.0 NE2 E:HIS498 2.1 43.4 1.0 OD2 M:ASP170 2.2 64.5 1.0 OD1 M:ASP170 2.2 64.0 1.0 CG M:ASP170 2.5 64.7 1.0 CE1 E:HIS508 2.8 44.8 1.0 CD2 E:HIS502 3.0 42.9 1.0 CD2 E:HIS498 3.0 43.6 1.0 CE1 E:HIS498 3.1 42.5 1.0 CE1 E:HIS502 3.1 43.2 1.0 CD2 E:HIS508 3.2 42.8 1.0 ND1 E:HIS508 3.9 45.0 1.0 CB M:ASP170 4.0 66.3 1.0 ND1 E:HIS498 4.2 42.0 1.0 CG E:HIS502 4.2 42.5 1.0 CG E:HIS498 4.2 42.8 1.0 ND1 E:HIS502 4.2 42.8 1.0 CG E:HIS508 4.2 43.8 1.0 O M:ASP170 4.5 68.1 1.0 C M:ASP170 4.5 68.4 1.0 CE E:MSE527 4.5 41.2 1.0 OE2 E:GLU499 4.6 47.5 1.0 O M:GLN171 4.7 69.3 1.0 C M:GLN171 4.8 69.8 1.0 CA M:ASP170 4.8 67.8 1.0 N M:GLN171 4.9 69.5 1.0

Zinc binding site 6 out of 6 in the Structure of A Chaperone-Substrate Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Chaperone-Substrate Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn601 b:55.3 occ:1.00 NE2 F:HIS508 2.1 57.5 1.0 NE2 F:HIS502 2.2 53.9 1.0 NE2 F:HIS498 2.3 55.0 1.0 OD1 N:ASP170 2.5 75.2 1.0 OD2 N:ASP170 2.5 73.2 1.0 CE1 F:HIS508 2.6 58.2 1.0 CG N:ASP170 2.8 74.7 1.0 CD2 F:HIS502 3.1 54.1 1.0 CD2 F:HIS498 3.2 55.2 1.0 CE1 F:HIS502 3.2 53.5 1.0 CE1 F:HIS498 3.2 54.2 1.0 CD2 F:HIS508 3.3 56.5 1.0 ND1 F:HIS508 3.9 57.7 1.0 CG F:HIS508 4.2 56.7 1.0 CG F:HIS502 4.2 53.8 1.0 ND1 F:HIS502 4.3 53.3 1.0 CB N:ASP170 4.3 76.2 1.0 ND1 F:HIS498 4.3 54.0 1.0 CG F:HIS498 4.3 54.6 1.0 O N:ASP170 4.7 83.3 1.0 O N:GLN171 4.7 79.5 1.0 OE2 F:GLU499 4.7 59.5 1.0 C N:ASP170 4.7 81.9 1.0 C N:GLN171 4.7 82.0 1.0 N N:GLU172 4.9 83.2 1.0 N N:GLN171 5.0 82.4 1.0

D.V.Urusova, R.L.Kinsella, N.D.Salinas, M.F.Haurat, M.F.Feldman, N.H.Tolia. The Structure Ofacinetobacter-Secreted Protease Cpaa Complexed with Its Chaperone Cpab Reveals A Novel Mode of A T2SS Chaperone-Substrate Interaction. J.Biol.Chem. V. 294 13344 2019.
ISSN: ESSN 1083-351X
PubMed: 31320476
DOI: 10.1074/JBC.RA119.009805