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Zinc in PDB 5fb0: Crystal Structure of A Phd Finger Bound to Histone H3 T3PH Peptide

Protein crystallography data

The structure of Crystal Structure of A Phd Finger Bound to Histone H3 T3PH Peptide, PDB code: 5fb0 was solved by H.Li, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.14 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.830, 99.160, 53.716, 90.00, 93.17, 90.00
R / Rfree (%) 22.4 / 27.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH Peptide (pdb code 5fb0). 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 A Phd Finger Bound to Histone H3 T3PH Peptide, PDB code: 5fb0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5fb0

Go back to Zinc Binding Sites List in 5fb0
Zinc binding site 1 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:39.1
occ:1.00
ND1 A:HIS725 2.2 44.8 1.0
SG A:CYS708 2.3 48.9 1.0
SG A:CYS728 2.5 36.4 1.0
SG A:CYS705 2.6 33.2 1.0
CB A:CYS705 3.0 30.1 1.0
CG A:HIS725 3.0 37.3 1.0
CE1 A:HIS725 3.1 42.9 1.0
CB A:CYS728 3.1 31.0 1.0
CB A:HIS725 3.4 35.4 1.0
CB A:CYS708 3.7 41.8 1.0
N A:CYS708 4.0 33.0 1.0
N A:HIS725 4.0 45.1 1.0
NE2 A:HIS725 4.1 45.8 1.0
CD2 A:HIS725 4.1 45.9 1.0
CA A:HIS725 4.3 45.5 1.0
CA A:CYS708 4.4 36.2 1.0
CA A:CYS705 4.5 27.4 1.0
CA A:CYS728 4.6 44.8 1.0
CB A:VAL707 4.7 45.0 1.0

Zinc binding site 2 out of 4 in 5fb0

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Zinc binding site 2 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:38.7
occ:1.00
SG A:CYS720 2.3 42.8 1.0
SG A:CYS742 2.3 34.6 1.0
SG A:CYS717 2.4 40.5 1.0
SG A:CYS745 2.4 41.5 1.0
CB A:CYS720 3.1 41.2 1.0
CB A:CYS717 3.3 40.2 1.0
CB A:CYS742 3.4 33.7 1.0
N A:CYS742 3.6 39.6 1.0
OG1 A:THR719 3.6 42.9 1.0
CB A:CYS745 3.7 44.1 1.0
N A:CYS720 3.8 30.1 1.0
CA A:CYS720 4.0 30.6 1.0
CA A:CYS742 4.0 31.4 1.0
N A:CYS745 4.2 49.4 1.0
C A:THR719 4.4 40.7 1.0
O A:CYS720 4.5 24.3 1.0
C A:CYS720 4.5 27.8 1.0
CA A:CYS745 4.6 47.1 1.0
C A:CYS742 4.6 30.9 1.0
O A:CYS742 4.7 32.9 1.0
C A:SER741 4.7 45.0 1.0
CA A:CYS717 4.8 42.5 1.0
CB A:THR719 4.9 43.1 1.0
N A:THR719 4.9 41.8 1.0
NH1 A:ARG722 4.9 37.9 1.0
CA A:SER741 5.0 43.8 1.0
CA A:THR719 5.0 42.9 1.0

Zinc binding site 3 out of 4 in 5fb0

Go back to Zinc Binding Sites List in 5fb0
Zinc binding site 3 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:36.8
occ:1.00
ND1 C:HIS725 2.3 48.8 1.0
SG C:CYS708 2.3 50.9 1.0
SG C:CYS705 2.5 33.8 1.0
SG C:CYS728 2.5 38.5 1.0
CB C:CYS705 3.0 28.9 1.0
CB C:CYS728 3.0 39.0 1.0
CE1 C:HIS725 3.1 51.6 1.0
CG C:HIS725 3.2 44.2 1.0
CB C:HIS725 3.5 36.7 1.0
CB C:CYS708 3.7 40.4 1.0
N C:CYS708 3.9 32.5 1.0
NE2 C:HIS725 4.1 54.2 1.0
N C:HIS725 4.1 33.9 1.0
CD2 C:HIS725 4.2 53.0 1.0
CA C:CYS708 4.4 33.8 1.0
CA C:CYS705 4.5 25.2 1.0
CA C:HIS725 4.5 40.1 1.0
CB C:VAL707 4.5 40.6 1.0
CA C:CYS728 4.5 49.1 1.0
N C:VAL707 4.9 35.8 1.0
C C:VAL707 4.9 40.3 1.0

Zinc binding site 4 out of 4 in 5fb0

Go back to Zinc Binding Sites List in 5fb0
Zinc binding site 4 out of 4 in the Crystal Structure of A Phd Finger Bound to Histone H3 T3PH 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 A Phd Finger Bound to Histone H3 T3PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:41.0
occ:1.00
SG C:CYS742 2.3 38.0 1.0
SG C:CYS717 2.4 40.0 1.0
SG C:CYS720 2.4 37.7 1.0
SG C:CYS745 2.5 41.1 1.0
CB C:CYS720 3.2 34.7 1.0
CB C:CYS742 3.3 37.3 1.0
CB C:CYS717 3.4 38.8 1.0
N C:CYS742 3.6 41.8 1.0
OG1 C:THR719 3.6 47.0 1.0
CB C:CYS745 3.7 49.4 1.0
N C:CYS720 3.8 32.8 1.0
CA C:CYS742 4.0 38.8 1.0
CA C:CYS720 4.0 33.1 1.0
N C:CYS745 4.2 50.3 1.0
C C:THR719 4.4 40.8 1.0
O C:CYS720 4.4 29.9 1.0
C C:CYS720 4.5 28.9 1.0
C C:CYS742 4.5 37.2 1.0
O C:CYS742 4.6 36.6 1.0
CA C:CYS745 4.6 52.2 1.0
C C:SER741 4.7 44.7 1.0
N C:THR719 4.8 50.2 1.0
CA C:CYS717 4.8 45.2 1.0
CB C:THR719 4.8 49.0 1.0
CA C:SER741 4.9 45.8 1.0
O C:HOH1009 4.9 51.6 1.0
CA C:THR719 4.9 49.3 1.0
NH1 C:ARG722 5.0 40.5 1.0

Reference:

X.Zhang, D.Zhao, X.Xiong, Z.He, H.Li. Multifaceted Histone H3 Methylation and Phosphorylation Readout By the Plant Homeodomain Finger of Human Nuclear Antigen SP100C J.Biol.Chem. V. 291 12786 2016.
ISSN: ESSN 1083-351X
PubMed: 27129259
DOI: 10.1074/JBC.M116.721159
Page generated: Wed Dec 16 06:13:27 2020

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