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Zinc in PDB 5yc4: Crystal Structure of AL3 Phd Finger Bound to H3K4ME3

Protein crystallography data

The structure of Crystal Structure of AL3 Phd Finger Bound to H3K4ME3, PDB code: 5yc4 was solved by S.Zhao, B.Zhang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.78 / 2.70
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 30.775, 30.775, 157.333, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of AL3 Phd Finger Bound to H3K4ME3 (pdb code 5yc4). 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 AL3 Phd Finger Bound to H3K4ME3, PDB code: 5yc4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5yc4

Go back to Zinc Binding Sites List in 5yc4
Zinc binding site 1 out of 2 in the Crystal Structure of AL3 Phd Finger Bound to H3K4ME3


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 AL3 Phd Finger Bound to H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:32.8
occ:1.00
ND1 A:HIS31 2.2 32.1 1.0
SG A:CYS34 2.3 30.3 1.0
SG A:CYS7 2.4 28.1 1.0
SG A:CYS10 2.4 28.7 1.0
CG A:HIS31 3.0 28.5 1.0
CB A:CYS7 3.2 26.0 1.0
CE1 A:HIS31 3.2 28.9 1.0
CB A:HIS31 3.3 28.0 1.0
CB A:CYS34 3.4 31.9 1.0
CB A:CYS10 3.4 31.1 1.0
N A:CYS10 3.9 35.5 1.0
N A:HIS31 4.0 30.0 1.0
CD2 A:HIS31 4.2 30.1 1.0
NE2 A:HIS31 4.2 31.3 1.0
CA A:HIS31 4.2 29.2 1.0
CA A:CYS10 4.2 32.0 1.0
CB A:ALA9 4.6 26.9 1.0
CA A:CYS7 4.6 26.6 1.0
CA A:CYS34 4.7 33.0 1.0
C A:ALA9 4.9 36.9 1.0

Zinc binding site 2 out of 2 in 5yc4

Go back to Zinc Binding Sites List in 5yc4
Zinc binding site 2 out of 2 in the Crystal Structure of AL3 Phd Finger Bound to H3K4ME3


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 AL3 Phd Finger Bound to H3K4ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:30.2
occ:1.00
SG A:CYS26 2.3 28.9 1.0
SG A:CYS50 2.4 29.9 1.0
SG A:CYS53 2.4 36.5 1.0
SG A:CYS23 2.5 25.7 1.0
CB A:CYS26 3.2 26.4 1.0
CB A:CYS23 3.3 22.2 1.0
CB A:CYS50 3.3 24.1 1.0
CB A:CYS53 3.4 32.6 1.0
N A:CYS26 3.7 26.5 1.0
N A:CYS50 3.9 29.8 1.0
CA A:CYS26 4.0 28.5 1.0
CA A:CYS50 4.1 29.7 1.0
N A:CYS53 4.3 38.2 1.0
CA A:CYS53 4.5 35.6 1.0
O A:CYS50 4.6 36.8 1.0
CB A:LEU25 4.6 33.2 1.0
C A:CYS50 4.7 33.5 1.0
C A:LEU25 4.7 30.4 1.0
CA A:CYS23 4.7 29.5 1.0
C A:CYS26 4.8 31.2 1.0
N A:GLU27 4.9 32.7 1.0
N A:LEU25 5.0 31.7 1.0

Reference:

S.Zhao, B.Zhang, H.Li. Crystal Structure of AL1 Phd Finger Bound to H3K4ME3 Cell Rep 2018.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2017.12.099
Page generated: Wed Dec 16 11:22:33 2020

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