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Zinc in PDB 5znr: Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide, PDB code: 5znr was solved by X.Lv, J.Du, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.05 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.717, 110.315, 58.643, 90.00, 96.64, 90.00
R / Rfree (%) 20.6 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide (pdb code 5znr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide, PDB code: 5znr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5znr

Go back to Zinc Binding Sites List in 5znr
Zinc binding site 1 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide


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 Ptshl in Complex with An H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:63.6
occ:1.00
ND1 A:HIS165 2.1 64.4 1.0
SG A:CYS142 2.4 0.6 1.0
SG A:CYS144 2.4 0.4 1.0
SG A:CYS168 2.8 97.1 1.0
CB A:CYS142 2.9 58.1 1.0
CE1 A:HIS165 3.1 64.1 1.0
CG A:HIS165 3.1 60.5 1.0
CB A:HIS165 3.4 64.7 1.0
CB A:CYS168 3.4 73.7 1.0
CB A:CYS144 3.8 73.5 1.0
N A:HIS165 3.8 72.3 1.0
N A:CYS144 4.0 74.6 1.0
NE2 A:HIS165 4.2 59.1 1.0
CA A:HIS165 4.2 66.2 1.0
CD2 A:HIS165 4.2 55.9 1.0
N A:LYS143 4.3 78.3 1.0
CA A:CYS142 4.4 68.3 1.0
CA A:CYS144 4.5 74.3 1.0
O A:HIS165 4.6 69.0 1.0
C A:CYS142 4.7 73.0 1.0
CA A:CYS168 4.9 76.9 1.0
O A:TYR141 4.9 57.1 1.0
C A:HIS165 4.9 68.0 1.0
C A:PHE164 5.0 68.3 1.0

Zinc binding site 2 out of 4 in 5znr

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Zinc binding site 2 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide


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 Ptshl in Complex with An H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:98.6
occ:1.00
N A:CYS160 2.1 88.1 1.0
SG A:CYS157 2.3 78.8 1.0
SG A:CYS160 2.4 0.6 1.0
CB A:CYS160 2.4 78.5 1.0
CA A:CYS160 2.7 92.2 1.0
SG A:CYS187 2.8 0.6 1.0
C A:GLY159 3.0 97.4 1.0
SG A:CYS184 3.2 86.9 1.0
CA A:GLY159 3.4 0.2 1.0
CB A:CYS157 3.7 0.4 1.0
O A:CYS157 3.8 0.1 1.0
C A:CYS160 4.0 87.9 1.0
O A:GLY159 4.0 0.4 1.0
N A:GLY159 4.0 0.9 1.0
CB A:CYS184 4.1 0.4 1.0
CB A:CYS187 4.2 0.8 1.0
N A:CYS184 4.2 0.4 1.0
C A:CYS157 4.3 0.3 1.0
N A:SER161 4.4 93.9 1.0
CA A:CYS157 4.7 0.0 1.0
CA A:CYS184 4.7 0.7 1.0
C A:GLU158 4.9 0.1 1.0
O A:CYS160 5.0 90.9 1.0

Zinc binding site 3 out of 4 in 5znr

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Zinc binding site 3 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide


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 Ptshl in Complex with An H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:69.7
occ:1.00
ND1 B:HIS165 2.2 72.3 1.0
SG B:CYS144 2.3 90.7 1.0
SG B:CYS168 2.4 79.3 1.0
SG B:CYS142 2.4 58.4 1.0
CB B:CYS142 3.0 55.9 1.0
CB B:CYS168 3.1 62.8 1.0
CG B:HIS165 3.1 68.9 1.0
CE1 B:HIS165 3.3 73.3 1.0
CB B:HIS165 3.3 64.8 1.0
CB B:CYS144 3.7 68.7 1.0
N B:HIS165 4.0 61.9 1.0
N B:CYS144 4.0 68.2 1.0
CA B:HIS165 4.3 61.0 1.0
CD2 B:HIS165 4.3 69.8 1.0
NE2 B:HIS165 4.3 70.9 1.0
N B:LYS143 4.4 63.7 1.0
CA B:CYS142 4.4 58.2 1.0
CA B:CYS144 4.5 69.3 1.0
CA B:CYS168 4.6 63.4 1.0
C B:CYS142 4.7 61.5 1.0
O B:HIS165 4.8 63.0 1.0
O B:TYR141 4.9 56.7 1.0
N B:CYS168 5.0 58.9 1.0

Zinc binding site 4 out of 4 in 5znr

Go back to Zinc Binding Sites List in 5znr
Zinc binding site 4 out of 4 in the Crystal Structure of Ptshl in Complex with An H3K27ME3 Peptide


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 Ptshl in Complex with An H3K27ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:84.6
occ:1.00
N B:CYS160 2.2 84.6 1.0
SG B:CYS157 2.3 77.7 1.0
SG B:CYS160 2.8 0.6 1.0
CB B:CYS160 2.9 80.2 1.0
SG B:CYS184 3.0 82.0 1.0
CA B:CYS160 3.1 83.6 1.0
C B:GLY159 3.1 88.2 1.0
CA B:GLY159 3.3 93.5 1.0
CB B:CYS157 3.6 71.7 1.0
N B:GLY159 3.8 98.5 1.0
OD1 B:ASN186 3.8 0.9 1.0
CB B:CYS187 3.9 0.9 1.0
O B:GLY159 4.3 90.9 1.0
N B:CYS184 4.3 86.8 1.0
C B:CYS160 4.4 82.3 1.0
SG B:CYS187 4.6 0.1 1.0
CB B:CYS184 4.6 87.7 1.0
N B:SER161 4.6 80.7 1.0
CG B:ASN186 4.8 0.5 1.0
C B:CYS157 4.8 0.9 1.0
O B:CYS184 4.8 97.4 1.0
CA B:CYS157 4.8 70.0 1.0
C B:GLU158 4.9 93.8 1.0
O B:CYS157 4.9 73.8 1.0
CA B:CYS184 5.0 88.4 1.0

Reference:

S.Qian, X.Lv, R.N.Scheid, L.Lu, Z.Yang, W.Chen, R.Liu, M.D.Boersma, J.M.Denu, X.Zhong, J.Du. Dual Recognition of H3K4ME3 and H3K27ME3 By A Plant Histone Reader Shl. Nat Commun V. 9 2425 2018.
ISSN: ESSN 2041-1723
PubMed: 29930355
DOI: 10.1038/S41467-018-04836-Y
Page generated: Wed Dec 16 11:27:33 2020

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