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

Protein crystallography data

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

Zinc Binding Sites:

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 5y46

Go back to Zinc Binding Sites List in 5y46
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 5y46

Go back to Zinc Binding Sites List in 5y46
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

Reference:

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
Page generated: Wed Dec 16 11:22:09 2020

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