Zinc in PDB 4xb8: Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)

The structure of Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc), PDB code: 4xb8 was solved by Q.Chen, Y.Yu, S.A.Li, L.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.99 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.672, 57.269, 129.946, 90.00, 93.65, 90.00
R / Rfree (%)	25.3 / 31.6

The binding sites of Zinc atom in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) (pdb code 4xb8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc), PDB code: 4xb8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)


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 DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:92.3 occ:1.00 OD1 A:ASP95 2.0 78.8 1.0 OD2 A:ASP95 2.0 84.9 1.0 NE2 A:HIS97 2.0 71.3 1.0 O A:HOH505 2.1 0.5 1.0 CG A:ASP95 2.2 69.6 1.0 CE1 A:HIS97 3.0 73.4 1.0 CD2 A:HIS97 3.1 60.2 1.0 ND2 A:ASN12 3.3 52.4 1.0 NH1 A:ARG376 3.4 89.5 1.0 CB A:ASP95 3.6 55.7 1.0 OG A:SER381 4.0 61.8 1.0 ND1 A:HIS97 4.1 53.5 1.0 CG A:HIS97 4.2 47.2 1.0 O A:ASP95 4.4 61.4 1.0 CB A:SER381 4.5 50.4 1.0 NH1 A:ARG13 4.5 47.1 1.0 CG A:ASN12 4.6 51.0 1.0 CZ A:ARG376 4.6 72.1 1.0 CA A:ASP95 4.7 50.6 1.0 C A:ASP95 4.8 0.2 1.0 C A:GLU380 4.9 49.5 1.0 NH2 A:ARG376 4.9 82.4 1.0 O A:GLU380 5.0 57.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)


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 DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:74.1 occ:1.00 OE1 A:GLU383 2.0 60.8 1.0 OE2 A:GLU9 2.0 57.1 1.0 OE1 A:GLU9 2.0 52.1 1.0 O A:GLU383 2.1 75.7 1.0 CD A:GLU9 2.3 61.9 1.0 CD A:GLU383 2.7 58.2 1.0 C A:GLU383 3.1 54.6 1.0 OE2 A:GLU383 3.3 58.4 1.0 CB A:GLU383 3.4 46.1 1.0 CA A:GLU383 3.5 58.8 1.0 N A:GLU383 3.6 60.6 1.0 CG A:GLU383 3.6 43.8 1.0 O A:HOH501 3.6 55.2 1.0 CG A:GLU9 3.9 48.0 1.0 N A:ALA384 4.3 47.5 1.0 CB A:PHE6 4.7 55.2 1.0 CB A:GLU9 4.7 39.7 1.0 CA A:ALA384 4.8 64.7 1.0 C A:ALA382 4.9 43.4 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)


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 DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn409 b:0.4 occ:1.00 OD1 B:ASP111 2.0 0.9 1.0 OE1 A:GLU126 2.0 0.4 1.0 OE2 A:GLU109 2.0 0.4 1.0 OE2 A:GLU126 2.0 0.5 1.0 OD2 B:ASP111 2.0 0.3 1.0 OE1 A:GLU109 2.0 0.9 1.0 CD A:GLU126 2.1 0.8 1.0 CG B:ASP111 2.2 0.9 1.0 CD A:GLU109 2.3 0.7 1.0 CG A:GLU126 3.4 0.5 1.0 CB B:ASP111 3.7 0.4 1.0 CG A:GLU109 3.8 96.6 1.0 CB A:GLU126 3.8 93.9 1.0 O B:ASN112 3.9 92.3 1.0 O B:HOH503 4.1 0.1 1.0 OD1 A:ASP111 4.1 0.8 1.0 CG A:ASP111 4.3 0.0 1.0 CA B:ASP111 4.5 92.7 1.0 CB A:GLU109 4.5 82.0 1.0 N B:ASN112 4.5 76.9 1.0 CB A:ASP111 4.6 0.9 1.0 OE1 B:GLU126 4.7 0.9 1.0 OD2 A:ASP111 4.7 0.0 1.0 C B:ASP111 4.8 82.9 1.0 O A:GLU109 4.9 96.5 1.0 C B:ASN112 5.0 78.1 1.0 ZN A:ZN410 5.0 0.2 1.0 OE1 B:GLU109 5.0 0.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)


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 DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn410 b:0.2 occ:1.00 OD1 A:ASP111 2.0 0.8 1.0 CD B:GLU126 2.0 0.1 1.0 OE1 B:GLU126 2.0 0.9 1.0 OE2 B:GLU126 2.0 0.9 1.0 OE1 B:GLU109 2.0 0.0 1.0 OD2 A:ASP111 2.0 0.0 1.0 OE2 B:GLU109 2.0 0.8 1.0 CD B:GLU109 2.2 0.2 1.0 CG A:ASP111 2.3 0.0 1.0 CG B:GLU126 3.2 0.6 1.0 CG B:GLU109 3.6 0.8 1.0 OD1 B:ASP111 3.7 0.9 1.0 O A:ASN112 3.7 90.0 1.0 CB A:ASP111 3.8 0.9 1.0 CB B:GLU109 4.1 0.5 1.0 OE2 A:GLU126 4.4 0.5 1.0 CG B:ASP111 4.4 0.9 1.0 CB B:GLU126 4.5 90.6 1.0 CA A:ASP111 4.5 92.5 1.0 N A:ASN112 4.5 87.4 1.0 O A:HOH503 4.6 0.5 1.0 C A:ASP111 4.8 89.9 1.0 C A:ASN112 4.8 83.8 1.0 CB B:ASP111 4.8 0.4 1.0 ZN A:ZN409 5.0 0.4 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)


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 DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:0.4 occ:1.00 CG B:ASP95 1.8 0.1 1.0 OD1 B:ASP95 2.0 0.4 1.0 OD2 B:ASP95 2.0 0.9 1.0 NE2 B:HIS97 2.0 0.1 1.0 O B:HOH505 2.1 94.8 1.0 CE1 B:HIS97 2.6 0.2 1.0 CB B:ASP95 2.7 95.2 1.0 CD2 B:HIS97 3.2 0.3 1.0 ND1 B:HIS97 3.8 0.2 1.0 NE B:ARG376 4.1 88.9 1.0 O B:GLU380 4.1 99.9 1.0 CG B:HIS97 4.1 98.8 1.0 CA B:ASP95 4.1 0.9 1.0 N B:GLU380 4.5 0.2 1.0 NH2 B:ARG376 4.5 94.8 1.0 O B:ASP378 4.6 99.4 1.0 C B:ASP95 4.7 0.5 1.0 CZ B:ARG376 4.7 90.2 1.0 C B:GLU380 4.8 97.7 1.0 CA B:GLN379 4.8 0.7 1.0 O B:ASP95 4.9 0.7 1.0 CD B:ARG376 4.9 85.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc)


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 DSCAM1 Isoform 9.44, N-Terminal Four Ig Domains (with Zinc) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:0.1 occ:1.00 OE1 B:GLU9 2.0 0.3 1.0 OE2 B:GLU9 2.0 0.5 1.0 OE1 B:GLU383 2.0 0.9 1.0 O B:GLU383 2.0 0.6 1.0 CD B:GLU9 2.3 0.0 1.0 C B:GLU383 3.0 0.9 1.0 CD B:GLU383 3.2 0.3 1.0 O B:HOH504 3.5 1.0 1.0 CA B:GLU383 3.6 0.6 1.0 CB B:GLU383 3.7 0.7 1.0 N B:GLU383 3.8 0.2 1.0 CG B:GLU9 3.8 0.1 1.0 N B:ALA384 4.0 0.5 1.0 CG B:GLU383 4.0 0.7 1.0 NH1 B:ARG94 4.1 0.7 1.0 OE2 B:GLU383 4.1 0.6 1.0 CB B:PHE6 4.3 0.9 1.0 CA B:ALA384 4.3 0.7 1.0 CD2 B:PHE6 4.6 0.5 1.0 CB B:GLU9 4.6 0.2 1.0 CG B:PHE6 4.8 0.9 1.0

S.A.Li, L.Cheng, Y.Yu, Q.Chen. Structural Basis of DSCAM1 Homodimerization: Insights Into Context Constraint For Protein Recognition Sci Adv V. 2 01118 2016.
ISSN: ESSN 2375-2548
PubMed: 27386517
DOI: 10.1126/SCIADV.1501118