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Zinc in PDB 3gl6: Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide, PDB code: 3gl6 was solved by Z.Wang, J.Song, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.90
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 49.950, 49.950, 86.450, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide (pdb code 3gl6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide, PDB code: 3gl6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3gl6

Go back to Zinc Binding Sites List in 3gl6
Zinc binding site 1 out of 3 in the Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 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 JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:33.4
occ:1.00
O A:HOH23 2.1 31.6 1.0
O A:SER1608 2.1 35.4 1.0
N A:SER1608 2.1 37.5 1.0
SG A:CYS1619 2.3 34.2 1.0
C A:SER1608 2.7 38.2 1.0
CA A:SER1608 2.7 37.9 1.0
CB A:SER1608 3.2 36.8 1.0
CB A:CYS1619 3.2 31.4 1.0
O A:HOH32 3.9 42.6 1.0
OG A:SER1608 4.0 41.2 1.0
N A:VAL1609 4.0 36.7 1.0
CA A:CYS1619 4.6 30.9 1.0
CA A:VAL1609 4.7 36.5 1.0

Zinc binding site 2 out of 3 in 3gl6

Go back to Zinc Binding Sites List in 3gl6
Zinc binding site 2 out of 3 in the Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 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 JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:29.3
occ:1.00
SG A:CYS1610 2.4 29.7 1.0
SG A:CYS1615 2.4 31.9 1.0
CB A:CYS1610 3.2 27.6 1.0
CB A:CYS1615 3.2 35.5 1.0
CA A:CYS1615 3.6 36.9 1.0
N A:CYS1610 3.7 31.6 1.0
CA A:CYS1610 4.0 32.2 1.0
CD A:PRO1618 4.1 29.9 1.0
N A:GLN1616 4.1 37.1 1.0
C A:CYS1615 4.2 38.1 1.0
N A:ARG1617 4.3 36.4 1.0
CB A:ALA1612 4.7 41.5 1.0
C A:VAL1609 4.8 33.7 1.0
C A:CYS1610 4.8 33.5 1.0
CA A:ARG1617 4.9 35.6 1.0
N A:CYS1615 4.9 39.8 1.0
CG A:PRO1618 4.9 29.3 1.0

Zinc binding site 3 out of 3 in 3gl6

Go back to Zinc Binding Sites List in 3gl6
Zinc binding site 3 out of 3 in the Crystal Structure of JARID1A-PHD3 Complexed with H3(1-9) K4ME3 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 JARID1A-PHD3 Complexed with H3(1-9) K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:33.1
occ:1.00
SG A:CYS1655 2.2 32.3 1.0
SG A:CYS1632 2.3 34.4 1.0
SG A:CYS1628 2.3 30.4 1.0
SG A:CYS1658 2.4 34.4 1.0
CB A:CYS1628 3.2 29.8 1.0
CB A:CYS1658 3.2 35.3 1.0
CB A:CYS1632 3.4 37.2 1.0
CB A:CYS1655 3.4 29.5 1.0
N A:CYS1632 3.9 38.0 1.0
O A:HOH19 4.0 45.1 1.0
N A:CYS1655 4.1 28.2 1.0
N A:CYS1658 4.2 37.6 1.0
CA A:CYS1632 4.2 36.6 1.0
CA A:CYS1655 4.3 30.1 1.0
CA A:CYS1658 4.3 37.0 1.0
CA A:CYS1628 4.6 29.8 1.0
N A:GLY1631 4.7 38.4 1.0
CA A:GLY1630 4.7 36.1 1.0
N A:GLY1630 4.8 34.3 1.0
N A:ASP1633 4.8 35.9 1.0
CE1 A:PHE1636 4.8 26.9 1.0
C A:GLY1630 4.8 37.1 1.0
C A:CYS1655 4.9 32.1 1.0
CZ A:PHE1636 4.9 28.0 1.0
C A:CYS1632 4.9 36.8 1.0
O A:CYS1655 4.9 30.3 1.0

Reference:

G.G.Wang, J.Song, Z.Wang, H.L.Dormann, F.Casadio, H.Li, J.L.Luo, D.J.Patel, C.D.Allis. Haematopoietic Malignancies Caused By Dysregulation of A Chromatin-Binding Phd Finger. Nature V. 459 847 2009.
ISSN: ISSN 0028-0836
PubMed: 19430464
DOI: 10.1038/NATURE08036
Page generated: Wed Dec 16 04:20:57 2020

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