Zinc in PDB 5y46: Crystal Structure of A Collagen-Like Peptide with Interruption Sequence

The structure of Crystal Structure of A Collagen-Like Peptide with Interruption Sequence, PDB code: 5y46 was solved by T.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.95 / 1.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	20.650, 25.290, 53.980, 90.00, 93.06, 90.00
R / Rfree (%)	10.6 / 13

The binding sites of Zinc atom in the Crystal Structure of A Collagen-Like Peptide with Interruption Sequence (pdb code 5y46). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Collagen-Like Peptide with Interruption Sequence, PDB code: 5y46:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Collagen-Like Peptide with Interruption Sequence


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 A Collagen-Like Peptide with Interruption Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:4.8 occ:0.82 O A:HOH207 2.0 11.5 1.0 O A:HOH242 2.0 5.7 1.0 O A:GLY1 2.1 8.2 1.0 N A:GLY1 2.1 6.8 1.0 O A:HOH240 2.2 7.7 1.0 O B:HOH239 2.2 6.4 1.0 C A:GLY1 2.8 8.0 1.0 CA A:GLY1 2.9 8.4 1.0 N A:PRO2 4.1 10.1 1.0 N B:GLY1 4.2 4.8 1.0 O A:HOH244 4.4 7.3 1.0 O A:HOH236 4.5 10.1 1.0 CA B:GLY1 4.5 5.1 1.0 CA A:PRO2 4.8 9.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Collagen-Like Peptide with Interruption Sequence


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 A Collagen-Like Peptide with Interruption Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:3.7 occ:0.93 OXT B:ACT101 2.0 5.4 1.0 N B:GLY1 2.0 4.8 1.0 N C:GLY1 2.1 4.6 1.0 O B:GLY1 2.2 4.1 1.0 C B:ACT101 2.7 5.3 1.0 O B:ACT101 2.8 6.3 1.0 C B:GLY1 2.9 4.1 1.0 CA C:GLY1 3.0 4.0 1.0 CA B:GLY1 3.0 5.1 1.0 O A:HOH203 3.8 9.9 1.0 O C:HOH138 4.0 9.7 1.0 CH3 B:ACT101 4.2 6.2 1.0 O A:PRO2 4.2 8.0 1.0 O B:HOH239 4.2 6.4 1.0 N B:PRO2 4.2 4.4 1.0 O B:HOH235 4.3 4.8 1.0 C C:GLY1 4.4 3.5 1.0 O C:GLY1 4.8 4.2 1.0 O B:PRO2 4.9 4.1 1.0 CA B:PRO2 4.9 4.0 0.5

T.Xu, C.Z.Zhou, J.Xiao, J.Liu. Unique Conformation in A Natural Interruption Sequence of Type Xix Collagen Revealed By Its High-Resolution Crystal Structure. Biochemistry V. 57 1087 2018.
ISSN: ISSN 1520-4995
PubMed: 29376320
DOI: 10.1021/ACS.BIOCHEM.7B01010