Zinc in PDB 5wo3: Chaperone Spy Bound to IM7 (IM7 Un-Modeled)

The structure of Chaperone Spy Bound to IM7 (IM7 Un-Modeled), PDB code: 5wo3 was solved by S.Horowitz, P.Koldewey, R.Martin, J.C.A.Bardwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.21 / 1.87
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	43.150, 43.150, 260.159, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.3

The structure of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled) (pdb code 5wo3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled), PDB code: 5wo3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:29.6 occ:1.00 HN1 A:IMD210 1.4 40.0 1.0 OE2 A:GLU120 1.8 34.5 1.0 N1 A:IMD210 2.0 33.4 1.0 H2 A:IMD210 2.0 32.3 1.0 ND1 B:HIS65 2.1 35.8 1.0 C2 A:IMD210 2.2 26.9 1.0 CL A:CL205 2.3 54.2 1.0 CD A:GLU120 2.8 43.5 1.0 CE1 B:HIS65 3.0 34.0 1.0 HE1 B:HIS65 3.1 40.9 1.0 CG B:HIS65 3.2 34.3 1.0 C5 A:IMD210 3.3 36.3 1.0 OE1 A:GLU120 3.3 41.1 1.0 HD1 A:PHE119 3.3 41.0 1.0 HB2 B:HIS65 3.4 40.7 1.0 HB3 B:HIS65 3.5 40.7 1.0 N3 A:IMD210 3.6 32.8 1.0 CB B:HIS65 3.6 34.0 1.0 O B:HOH310 3.9 52.0 1.0 HA B:ARG62 3.9 42.5 1.0 H5 A:IMD210 3.9 43.5 1.0 C4 A:IMD210 4.0 23.0 1.0 CD1 A:PHE119 4.1 34.2 1.0 HG2 A:GLU120 4.1 43.2 1.0 CG A:GLU120 4.1 36.0 1.0 NE2 B:HIS65 4.2 32.8 1.0 HA A:GLU120 4.3 45.6 1.0 HE1 A:PHE119 4.3 41.0 1.0 HE B:ARG62 4.3 57.4 1.0 CD2 B:HIS65 4.3 36.6 1.0 HN3 A:IMD210 4.3 39.3 1.0 HG3 B:ARG62 4.3 58.4 1.0 HB3 A:PHE119 4.5 37.6 1.0 CE1 A:PHE119 4.6 34.2 1.0 HG3 A:GLU120 4.7 43.2 1.0 C5 B:IMD202 4.8 34.6 1.0 N1 B:IMD202 4.8 30.8 1.0 CA B:ARG62 4.8 35.4 1.0 C4 B:IMD202 4.9 34.0 1.0 C2 B:IMD202 4.9 28.4 1.0 O B:HOH324 4.9 44.3 1.0 N3 B:IMD202 4.9 23.6 1.0 HE2 B:HIS65 4.9 39.4 1.0 CA A:GLU120 5.0 38.0 1.0

Zinc binding site 2 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:29.0 occ:1.00 OE1 A:GLU86 2.1 30.3 1.0 CD A:GLU86 2.7 26.9 1.0 OE2 A:GLU86 2.7 23.8 1.0 O A:HOH331 3.9 34.4 1.0 O A:HOH315 4.2 24.4 1.0 CG A:GLU86 4.2 28.2 1.0 HB3 A:GLU86 4.4 30.8 1.0 HB2 A:GLU86 4.5 30.8 1.0 HB1 A:ALA83 4.6 31.7 1.0 CB A:GLU86 4.6 25.6 1.0 HG3 A:GLU86 4.6 33.8 1.0 HG2 A:GLU86 4.7 33.8 1.0

Zinc binding site 3 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:44.3 occ:1.00 OD1 A:ASP71 2.0 40.5 1.0 O A:HOH370 2.5 45.2 1.0 CG A:ASP71 2.7 41.6 1.0 OD2 A:ASP71 2.9 35.9 1.0 O A:HOH334 4.0 37.6 1.0 CB A:ASP71 4.2 35.1 1.0 HB3 A:ASP71 4.4 42.1 1.0 HB2 A:ASP71 4.5 42.1 1.0 HG23 A:THR72 4.6 40.8 1.0 O A:HOH329 4.6 40.4 1.0 H A:ASP71 4.9 41.2 1.0 O A:HOH387 5.0 51.1 1.0

Zinc binding site 4 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:52.2 occ:1.00 OE1 A:GLU44 2.2 39.7 1.0 O A:HOH304 2.3 42.2 1.0 CD A:GLU44 3.0 41.9 1.0 OE2 A:GLU44 3.0 48.9 1.0 HG2 A:GLN41 3.5 36.0 1.0 HA A:GLN41 3.9 33.2 1.0 O A:HOH357 4.2 31.3 1.0 HG3 A:GLN40 4.3 33.0 1.0 CG A:GLN41 4.3 30.0 1.0 HG3 A:GLN41 4.3 36.0 1.0 CG A:GLU44 4.4 37.2 1.0 HB2 A:GLU44 4.5 41.1 1.0 CA A:GLN41 4.8 27.7 1.0 HE21 A:GLN40 4.8 42.9 1.0 HE21 A:GLN41 4.8 40.2 1.0 CB A:GLU44 4.9 34.3 1.0 HG3 A:GLU44 4.9 44.7 1.0 HB3 A:GLU44 4.9 41.1 1.0 HG2 A:GLU44 4.9 44.7 1.0 CB A:GLN41 5.0 27.7 1.0

Zinc binding site 5 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:0.8 occ:1.00 HG12 B:ILE68 1.7 40.7 1.0 HB2 A:GLN100 1.7 25.7 0.5 HB2 A:GLN100 1.8 25.5 0.5 HB3 A:GLN100 2.0 25.5 0.5 OE1 A:GLN100 2.0 25.1 0.5 HB3 A:GLN100 2.0 25.7 0.5 HD13 B:ILE68 2.1 40.1 1.0 CB A:GLN100 2.2 21.3 0.5 CB A:GLN100 2.2 21.4 0.5 HD11 B:ILE68 2.2 40.1 1.0 CD1 B:ILE68 2.3 33.4 1.0 CG1 B:ILE68 2.4 33.9 1.0 CD A:GLN100 2.5 26.6 0.5 HG3 A:GLN100 2.5 33.9 0.5 CG A:GLN100 2.8 28.0 0.5 CG A:GLN100 2.9 28.3 0.5 HG13 B:ILE68 3.1 40.7 1.0 HG23 B:ILE68 3.1 42.6 1.0 HD12 B:ILE68 3.3 40.1 1.0 HG21 B:ILE68 3.3 42.6 1.0 HA A:MET97 3.4 21.4 1.0 CB B:ILE68 3.4 32.5 1.0 HG2 A:GLN100 3.4 33.6 0.5 HG3 A:GLN100 3.5 33.6 0.5 CG2 B:ILE68 3.5 35.5 1.0 NE2 A:GLN100 3.5 35.3 0.5 CA A:GLN100 3.6 24.7 0.5 CA A:GLN100 3.6 23.4 0.5 HG2 A:GLN100 3.6 33.9 0.5 HE22 A:GLN100 3.8 42.4 0.5 CD A:GLN100 3.8 33.8 0.5 OE1 A:GLN100 3.9 35.3 0.5 C A:GLN100 3.9 19.5 1.0 HA B:ILE68 3.9 28.4 1.0 H A:ASN101 4.0 26.0 1.0 H A:GLN100 4.1 26.1 1.0 O A:MET97 4.1 21.7 1.0 HB B:ILE68 4.1 39.0 1.0 N A:ASN101 4.1 21.6 1.0 HA A:GLN100 4.2 28.1 1.0 CA A:MET97 4.3 17.9 1.0 CA B:ILE68 4.3 23.7 1.0 O A:LEU96 4.3 38.2 1.0 N A:GLN100 4.4 21.7 1.0 HG22 B:ILE68 4.4 42.6 1.0 HG2 A:MET97 4.5 32.3 1.0 O A:GLN100 4.5 21.8 1.0 C A:MET97 4.6 18.9 1.0 HZ A:PHE115 4.7 43.4 1.0 HG3 B:MET64 4.8 47.3 1.0

Zinc binding site 6 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:23.9 occ:1.00 HN3 B:IMD202 1.2 28.3 1.0 N3 B:IMD202 1.9 23.6 1.0 CL A:CL206 2.2 58.9 1.0 H4 B:IMD202 2.3 40.8 1.0 C4 B:IMD202 2.4 34.0 1.0 C2 B:IMD202 3.3 28.4 1.0 H2 B:IMD202 3.7 34.1 1.0 C5 B:IMD202 3.8 34.6 1.0 N1 B:IMD202 4.1 30.8 1.0 HN3 A:IMD210 4.5 39.3 1.0 N3 A:IMD210 4.5 32.8 1.0 H5 B:IMD202 4.5 41.5 1.0 C2 A:IMD210 4.7 26.9 1.0 H2 A:IMD210 4.9 32.3 1.0 C4 A:IMD210 4.9 23.0 1.0 HE1 B:HIS65 4.9 40.9 1.0 HB3 A:ASN116 5.0 25.6 1.0

Zinc binding site 7 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:0.6 occ:1.00 HE A:ARG62 2.2 50.5 0.5 NE A:ARG62 2.2 42.0 0.5 CZ A:ARG62 2.2 42.2 0.5 NH1 A:ARG62 2.3 41.5 0.5 HH11 A:ARG62 2.3 49.7 0.5 HH12 A:ARG62 2.9 49.7 0.5 NH2 A:ARG62 3.1 39.8 0.5 CD A:ARG62 3.2 36.0 0.5 HD2 A:ARG62 3.2 43.2 0.5 O A:HOH359 3.4 42.7 1.0 HD3 A:ARG62 3.4 43.2 0.5 HH21 A:ARG62 3.5 47.8 0.5 HD2 A:ARG62 3.5 43.5 0.5 HH22 A:ARG62 3.5 47.8 0.5 HE A:ARG62 4.0 48.0 0.5 HG3 A:ARG62 4.2 45.7 0.5 CD A:ARG62 4.3 36.2 0.5 O A:HOH305 4.5 31.9 1.0 NE A:ARG62 4.5 40.0 0.5 CG A:ARG62 4.6 38.4 0.5 CG A:ARG62 4.6 38.1 0.5 HB3 A:ARG62 4.6 37.8 0.5 HB3 A:ARG62 4.7 37.8 0.5 HB2 A:ARG62 4.8 37.8 0.5 HG2 A:GLU59 4.8 76.1 1.0 HG3 A:ARG62 4.9 46.0 0.5 HB2 A:ARG62 4.9 37.8 0.5 CB A:ARG62 5.0 31.5 0.5 CB A:ARG62 5.0 31.5 0.5

Zinc binding site 8 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:30.5 occ:0.40 ZN B:ZN203 0.0 30.5 0.4 ZN B:ZN203 1.7 29.4 0.6 H2 B:IMD202 2.2 34.1 1.0 OD1 B:ASP66 2.5 43.2 1.0 OD2 B:ASP66 2.9 46.4 1.0 CG B:ASP66 2.9 40.7 1.0 C2 B:IMD202 3.0 28.4 1.0 H5 A:IMD210 3.0 43.5 1.0 HN1 B:IMD202 3.0 36.9 1.0 H4 A:IMD210 3.1 27.6 1.0 N1 B:IMD202 3.3 30.8 1.0 C5 A:IMD210 3.5 36.3 1.0 C4 A:IMD210 3.6 23.0 1.0 N3 B:IMD202 4.2 23.6 1.0 CB B:ASP66 4.3 38.1 1.0 HB3 B:ASP66 4.5 45.7 1.0 HA B:ASP66 4.6 34.9 1.0 C5 B:IMD202 4.7 34.6 1.0 HN3 B:IMD202 4.7 28.3 1.0 N1 A:IMD210 4.7 33.4 1.0 N3 A:IMD210 4.8 32.8 1.0 HG3 B:ARG62 4.9 58.4 1.0 HB2 B:ASP66 4.9 45.7 1.0 CA B:ASP66 5.0 29.1 1.0

Zinc binding site 9 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:29.4 occ:0.60 ZN B:ZN203 0.0 29.4 0.6 ZN B:ZN203 1.7 30.5 0.4 H5 A:IMD210 2.1 43.5 1.0 H4 A:IMD210 2.4 27.6 1.0 OD2 B:ASP66 2.4 46.4 1.0 C5 A:IMD210 2.7 36.3 1.0 OD1 B:ASP66 2.8 43.2 1.0 C4 A:IMD210 2.8 23.0 1.0 CG B:ASP66 2.9 40.7 1.0 H2 B:IMD202 3.0 34.1 1.0 HG3 B:ARG62 3.4 58.4 1.0 HG2 B:ARG62 3.4 58.4 1.0 C2 B:IMD202 3.8 28.4 1.0 HN1 B:IMD202 3.8 36.9 1.0 CG B:ARG62 3.8 48.7 1.0 N1 A:IMD210 4.0 33.4 1.0 N3 A:IMD210 4.1 32.8 1.0 N1 B:IMD202 4.1 30.8 1.0 HD3 B:ARG62 4.2 65.3 1.0 O B:ARG62 4.2 31.5 1.0 CB B:ASP66 4.4 38.1 1.0 CD B:ARG62 4.6 54.4 1.0 HN1 A:IMD210 4.6 40.0 1.0 C2 A:IMD210 4.7 26.9 1.0 HB2 B:ASP66 4.7 45.7 1.0 HN3 A:IMD210 4.8 39.3 1.0 HB3 B:ASP66 4.8 45.7 1.0 C B:ARG62 4.8 42.9 1.0 H B:ASP66 4.9 33.5 1.0 HB3 B:HIS65 4.9 40.7 1.0 N3 B:IMD202 5.0 23.6 1.0

Zinc binding site 10 out of 13 in the Chaperone Spy Bound to IM7 (IM7 Un-Modeled)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Chaperone Spy Bound to IM7 (IM7 Un-Modeled) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:47.2 occ:1.00 HZ1 B:LYS90 1.6 43.4 1.0 HZ3 B:LYS90 2.0 43.4 1.0 NZ B:LYS90 2.1 36.1 1.0 OE2 B:GLU87 2.6 50.2 1.0 OE1 B:GLU87 2.8 30.8 1.0 HZ2 B:LYS90 2.8 43.4 1.0 HE2 B:LYS90 2.9 46.3 1.0 CE B:LYS90 3.1 38.6 1.0 CD B:GLU87 3.1 40.5 1.0 O B:HOH333 3.3 53.0 1.0 HE3 B:LYS90 3.6 46.3 1.0 O B:HOH364 4.2 47.9 1.0 HD3 B:LYS90 4.2 36.6 1.0 CD B:LYS90 4.3 30.5 1.0 CG B:GLU87 4.6 39.1 1.0 HD2 B:LYS90 4.8 36.6 1.0 HG3 B:GLU87 4.9 47.0 1.0

S.Horowitz, L.Salmon, P.Koldewey, L.S.Ahlstrom, R.Martin, S.Quan, P.V.Afonine, H.Van Den Bedem, L.Wang, Q.Xu, R.C.Trievel, C.L.Brooks, J.C.Bardwell. Visualizing Chaperone-Assisted Protein Folding. Nat. Struct. Mol. Biol. V. 23 691 2016.
ISSN: ESSN 1545-9985
PubMed: 27239796
DOI: 10.1038/NSMB.3237