Zinc in PDB 5k6v: Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2

The structure of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2, PDB code: 5k6v was solved by X.Jin, K.M.Goodman, S.Mannepalli, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.74 / 3.21
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.189, 158.189, 53.525, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.4

The binding sites of Zinc atom in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 (pdb code 5k6v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2, PDB code: 5k6v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn507 b:81.9 occ:1.00 ND1 A:HIS18 2.6 54.9 1.0 CE1 A:HIS18 3.1 63.5 1.0 CG A:HIS18 3.6 57.6 1.0 NE2 A:HIS18 4.1 67.7 1.0 CB A:HIS18 4.2 38.7 1.0 CD2 A:HIS18 4.4 64.1 1.0 ND2 A:ASN22 4.6 57.5 1.0 CA A:HIS18 4.9 38.0 1.0

Zinc binding site 2 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn508 b:0.7 occ:1.00 O A:HOH603 2.6 37.9 1.0 OD2 A:ASP376 2.6 65.1 1.0 OD1 A:ASP376 3.0 74.9 1.0 CG A:ASP376 3.1 70.0 1.0 CB A:ASP376 4.5 62.3 1.0

Zinc binding site 3 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn509 b:1.0 occ:1.00 OD2 A:ASP186 2.4 0.3 1.0 CD2 A:HIS190 2.9 1.0 1.0 CG A:ASP186 3.1 1.0 1.0 CB A:HIS190 3.3 0.9 1.0 CG A:HIS190 3.4 0.6 1.0 OD1 A:ASP186 3.6 0.0 1.0 N A:HIS190 3.7 0.8 1.0 O A:THR187 3.8 1.0 1.0 CA A:HIS190 4.0 0.3 1.0 CB A:ASP186 4.1 0.9 1.0 NE2 A:HIS190 4.1 0.4 1.0 CE1 A:HIS108 4.2 0.9 1.0 O A:GLN106 4.2 84.8 1.0 N A:THR189 4.5 0.9 1.0 O A:ASP186 4.6 0.7 1.0 C A:THR189 4.6 0.0 1.0 ND1 A:HIS190 4.7 0.6 1.0 CB A:THR189 4.7 0.3 1.0 C A:ASP186 4.7 0.7 1.0 ND1 A:HIS108 4.8 0.4 1.0 C A:THR187 4.8 0.1 1.0 CA A:THR189 4.9 0.7 1.0

Zinc binding site 4 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn510 b:0.4 occ:1.00 CD2 A:HIS108 3.0 0.3 1.0 CG A:HIS108 3.6 0.5 1.0 CB A:HIS108 3.6 85.9 1.0 CA A:HIS108 3.8 76.0 1.0 N A:ALA109 3.8 55.5 1.0 ND2 A:ASN220 4.0 72.3 1.0 CE A:MET193 4.2 88.6 1.0 NE2 A:HIS108 4.2 0.5 1.0 C A:HIS108 4.4 56.5 1.0 CG2 A:ILE196 4.4 81.2 1.0 CG A:ASN220 4.7 60.6 1.0 ND1 A:HIS108 4.8 0.4 1.0 CB A:ALA109 4.9 53.2 1.0 CD1 A:ILE196 4.9 74.0 1.0 CA A:ALA109 5.0 51.9 1.0

Zinc binding site 5 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:81.2 occ:1.00 NE2 A:HIS180 2.3 49.1 1.0 OD2 A:ASP99 2.4 80.7 1.0 CE1 A:HIS180 3.0 49.4 1.0 CG A:ASP99 3.1 70.5 1.0 CD2 A:HIS180 3.4 58.5 1.0 CB A:ASP99 3.5 48.8 1.0 OD1 A:ASP99 4.2 87.5 1.0 ND1 A:HIS180 4.2 48.7 1.0 CD2 A:PHE178 4.4 45.0 1.0 CG A:HIS180 4.4 48.1 1.0 CB A:PHE178 4.5 42.1 1.0 CG A:PHE178 4.9 42.6 1.0 CA A:ASP99 5.0 48.2 1.0

Zinc binding site 6 out of 6 in the Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sidekick-1 Immunoglobulin Domains 1-4, Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:0.3 occ:1.00 CE1 A:HIS243 3.1 0.1 1.0 NE2 A:HIS243 3.4 0.1 1.0 ND1 A:HIS243 4.0 0.2 1.0 CD2 A:HIS243 4.5 0.6 1.0 CG A:HIS243 4.8 87.5 1.0

K.M.Goodman, M.Yamagata, X.Jin, S.Mannepalli, P.S.Katsamba, G.Ahlsen, A.P.Sergeeva, B.Honig, J.R.Sanes, L.Shapiro. Molecular Basis of Sidekick-Mediated Cell-Cell Adhesion and Specificity. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27644106
DOI: 10.7554/ELIFE.19058