Zinc in PDB 2akf: Crystal Structure of the Coiled-Coil Domain of Coronin 1

The structure of Crystal Structure of the Coiled-Coil Domain of Coronin 1, PDB code: 2akf was solved by R.A.Kammerer, D.Kostrewa, P.Progias, S.Honnappa, D.Avila, A.Lustig, F.K.Winkler, J.Pieters, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	23.587, 23.569, 46.402, 92.51, 96.85, 119.63
R / Rfree (%)	16 / 19.6

The binding sites of Zinc atom in the Crystal Structure of the Coiled-Coil Domain of Coronin 1 (pdb code 2akf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Coiled-Coil Domain of Coronin 1, PDB code: 2akf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:11.5 occ:0.75 ZN A:ZN1 0.0 11.5 0.8 ZN A:ZN1 1.0 14.3 0.2 OE2 A:GLU435 1.9 13.5 1.0 O A:HOH21 2.0 19.7 1.0 CD A:GLU435 2.7 13.1 1.0 OE1 A:GLU435 2.9 13.1 1.0 O A:HOH16 4.1 20.2 1.0 CG A:GLU435 4.1 12.5 1.0 NE A:ARG438 4.6 11.7 1.0 O A:HOH6 4.7 13.8 1.0 NH2 A:ARG438 4.7 10.4 1.0 CB A:ASN439 4.8 17.2 1.0 OD1 A:ASN439 4.9 25.0 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:14.3 occ:0.25 ZN A:ZN1 0.0 14.3 0.2 ZN A:ZN1 1.0 11.5 0.8 OE2 A:GLU435 2.5 13.5 1.0 OE1 A:GLU435 2.6 13.1 1.0 O A:HOH21 2.8 19.7 1.0 CD A:GLU435 2.8 13.1 1.0 NH2 A:ARG438 3.8 10.4 1.0 NE A:ARG438 4.0 11.7 1.0 O A:HOH6 4.2 13.8 1.0 CG A:GLU435 4.3 12.5 1.0 CZ A:ARG438 4.4 9.5 1.0 O A:HOH16 4.9 20.2 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2 b:17.9 occ:1.00 O B:HOH14 1.9 19.5 1.0 OE1 B:GLU456 2.0 20.9 1.0 ZN B:ZN3 3.0 19.1 0.3 CD B:GLU456 3.0 21.2 1.0 OE2 B:GLU456 3.4 23.3 1.0 ZN B:ZN3 3.4 17.8 0.7 O B:HOH15 4.1 19.9 1.0 OD2 B:ASP452 4.3 19.2 1.0 CG B:GLU456 4.3 20.1 1.0 CB B:GLU456 4.7 18.9 1.0 O B:HOH100 5.0 51.5 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:17.8 occ:0.67 ZN B:ZN3 0.0 17.8 0.7 ZN B:ZN3 1.3 19.1 0.3 OE2 B:GLU456 1.9 23.3 1.0 OD2 B:ASP452 1.9 19.2 1.0 O B:HOH14 2.3 19.5 1.0 CG B:ASP452 2.8 17.9 1.0 CD B:GLU456 2.9 21.2 1.0 OD1 B:ASP452 2.9 22.4 1.0 OE1 B:GLU456 3.2 20.9 1.0 ZN B:ZN2 3.4 17.9 1.0 O B:HOH15 3.5 19.9 1.0 CG B:GLU456 4.1 20.1 1.0 CB B:ASP452 4.2 15.7 1.0 ZN B:ZN4 4.6 22.3 0.7 O B:ASP452 4.7 15.6 1.0 C B:ASP452 4.9 15.4 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn3 b:19.1 occ:0.33 ZN B:ZN3 0.0 19.1 0.3 ZN B:ZN3 1.3 17.8 0.7 O B:HOH14 1.7 19.5 1.0 OD2 B:ASP452 1.8 19.2 1.0 O B:HOH15 2.3 19.9 1.0 OE2 B:GLU456 2.8 23.3 1.0 CG B:ASP452 2.9 17.9 1.0 ZN B:ZN2 3.0 17.9 1.0 OE1 B:GLU456 3.3 20.9 1.0 CD B:GLU456 3.3 21.2 1.0 ZN B:ZN4 3.5 22.3 0.7 OD1 B:ASP452 3.5 22.4 1.0 ZN B:ZN4 4.0 19.3 0.3 CB B:ASP452 4.1 15.7 1.0 O B:HOH90 4.4 25.2 1.0 O B:HOH37 4.7 22.3 1.0 CG B:GLU456 4.7 20.1 1.0 C B:ASP452 4.8 15.4 1.0 O B:ASP452 4.8 15.6 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:22.3 occ:0.67 ZN B:ZN4 0.0 22.3 0.7 ZN B:ZN4 1.4 19.3 0.3 O B:HOH37 1.7 22.3 1.0 O B:HOH90 2.0 25.2 1.0 OE1 B:GLU449 2.1 23.4 1.0 O B:HOH15 2.1 19.9 1.0 CD B:GLU449 3.0 19.8 1.0 OE2 B:GLU449 3.1 23.9 1.0 ZN B:ZN3 3.5 19.1 0.3 OD2 B:ASP452 4.0 19.2 1.0 O B:HOH14 4.1 19.5 1.0 CG B:GLU449 4.4 20.1 1.0 ZN B:ZN3 4.6 17.8 0.7 CG B:ASP452 4.8 17.9 1.0 O B:HOH79 4.9 39.3 1.0 CB B:GLU449 5.0 19.5 1.0 CB B:ASP452 5.0 15.7 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of the Coiled-Coil Domain of Coronin 1


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 the Coiled-Coil Domain of Coronin 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4 b:19.3 occ:0.33 ZN B:ZN4 0.0 19.3 0.3 ZN B:ZN4 1.4 22.3 0.7 O B:HOH90 1.7 25.2 1.0 OE2 B:GLU449 1.8 23.9 1.0 OE1 B:GLU449 1.8 23.4 1.0 O B:HOH15 1.9 19.9 1.0 CD B:GLU449 2.1 19.8 1.0 O B:HOH37 2.8 22.3 1.0 CG B:GLU449 3.6 20.1 1.0 ZN B:ZN3 4.0 19.1 0.3 NE B:ARG453 4.1 22.7 1.0 CG B:ARG453 4.2 20.1 1.0 OD2 B:ASP452 4.3 19.2 1.0 CB B:GLU449 4.5 19.5 1.0 O B:GLU449 4.5 18.0 1.0 O B:HOH14 4.6 19.5 1.0 CA B:GLU449 4.8 18.2 1.0 CD B:ARG453 4.8 21.7 1.0 NH2 B:ARG453 4.8 25.3 1.0 CZ B:ARG453 5.0 23.4 1.0

R.A.Kammerer, D.Kostrewa, P.Progias, S.Honnappa, D.Avila, A.Lustig, F.K.Winkler, J.Pieters, M.O.Steinmetz. A Conserved Trimerization Motif Controls the Topology of Short Coiled Coils Proc.Natl.Acad.Sci.Usa V. 102 13891 2005.
ISSN: ISSN 0027-8424
PubMed: 16172398
DOI: 10.1073/PNAS.0502390102