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Zinc in PDB 3lqj: Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide

Protein crystallography data

The structure of Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide, PDB code: 3lqj was solved by Z.Wang, 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 P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.190, 113.337, 46.673, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide (pdb code 3lqj). 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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide, PDB code: 3lqj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3lqj

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Zinc binding site 1 out of 4 in the Crystal Structure of MLL1 PHD3-Bromo 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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:19.6
occ:1.00
ND1 A:HIS1596 2.2 13.1 1.0
SG A:CYS1599 2.3 18.4 1.0
SG A:CYS1569 2.4 14.5 1.0
SG A:CYS1572 2.5 16.6 1.0
CB A:CYS1569 3.0 14.4 1.0
CG A:HIS1596 3.1 14.8 1.0
CB A:CYS1572 3.1 18.4 1.0
CB A:HIS1596 3.2 12.0 1.0
CE1 A:HIS1596 3.3 14.6 1.0
CB A:CYS1599 3.4 13.1 1.0
N A:CYS1572 3.7 22.3 1.0
CA A:CYS1572 4.0 21.6 1.0
N A:HIS1596 4.1 14.1 1.0
O A:HOH106 4.2 25.3 1.0
CD2 A:HIS1596 4.3 15.7 1.0
CA A:HIS1596 4.3 13.5 1.0
NE2 A:HIS1596 4.3 12.5 1.0
CA A:CYS1569 4.4 15.2 1.0
CA A:CYS1599 4.7 12.8 1.0
C A:LEU1571 4.7 20.0 1.0
CB A:LEU1571 4.7 17.1 1.0
C A:CYS1569 4.9 13.1 1.0
C A:CYS1572 4.9 22.5 1.0
N A:CYS1599 5.0 11.8 1.0

Zinc binding site 2 out of 4 in 3lqj

Go back to Zinc Binding Sites List in 3lqj
Zinc binding site 2 out of 4 in the Crystal Structure of MLL1 PHD3-Bromo 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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:30.0
occ:1.00
SG A:CYS1621 2.3 24.7 1.0
SG A:CYS1591 2.4 30.9 1.0
SG A:CYS1588 2.4 23.0 1.0
SG A:CYS1624 2.5 26.9 1.0
CB A:CYS1624 3.0 30.0 1.0
CB A:CYS1588 3.2 20.9 1.0
CB A:CYS1591 3.4 32.8 1.0
CB A:CYS1621 3.6 23.4 1.0
N A:CYS1591 3.7 33.5 1.0
N A:CYS1621 4.1 26.0 1.0
CA A:CYS1591 4.2 32.3 1.0
CA A:CYS1624 4.3 25.2 1.0
CB A:LYS1590 4.4 50.7 1.0
CA A:CYS1621 4.4 24.9 1.0
N A:CYS1624 4.5 26.5 1.0
CG A:ARG1593 4.5 22.4 1.0
CA A:CYS1588 4.7 18.6 1.0
CD A:ARG1593 4.7 21.0 1.0
C A:LYS1590 4.8 44.5 1.0
O A:CYS1621 4.8 27.0 1.0
C A:CYS1621 4.9 25.9 1.0
C A:CYS1591 4.9 32.6 1.0
CA A:LYS1590 4.9 44.3 1.0
N A:LYS1590 5.0 42.6 1.0

Zinc binding site 3 out of 4 in 3lqj

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Zinc binding site 3 out of 4 in the Crystal Structure of MLL1 PHD3-Bromo 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 MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:22.4
occ:1.00
ND1 B:HIS1596 2.2 28.9 1.0
SG B:CYS1599 2.3 20.7 1.0
SG B:CYS1572 2.4 18.1 1.0
SG B:CYS1569 2.4 18.3 1.0
CB B:CYS1569 3.0 17.7 1.0
CG B:HIS1596 3.1 26.7 1.0
CE1 B:HIS1596 3.2 28.0 1.0
CB B:CYS1572 3.2 20.9 1.0
CB B:HIS1596 3.3 26.7 1.0
CB B:CYS1599 3.3 16.9 1.0
N B:CYS1572 3.7 23.3 1.0
CA B:CYS1572 4.1 25.7 1.0
N B:HIS1596 4.1 15.4 1.0
CD2 B:HIS1596 4.3 27.1 1.0
NZ B:LYS1598 4.3 23.5 1.0
NE2 B:HIS1596 4.3 26.8 1.0
CA B:HIS1596 4.3 16.9 1.0
O B:HOH263 4.4 33.4 1.0
CB B:LEU1571 4.5 18.0 1.0
CA B:CYS1569 4.5 20.9 1.0
C B:LEU1571 4.6 28.9 1.0
CA B:CYS1599 4.6 16.1 1.0
O B:CYS1569 4.8 22.8 1.0
C B:CYS1569 4.8 22.6 1.0
N B:LEU1571 4.8 27.9 1.0
CA B:LEU1571 4.9 27.9 1.0
N B:CYS1599 5.0 11.6 1.0
C B:CYS1572 5.0 28.1 1.0

Zinc binding site 4 out of 4 in 3lqj

Go back to Zinc Binding Sites List in 3lqj
Zinc binding site 4 out of 4 in the Crystal Structure of MLL1 PHD3-Bromo 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 4 of Crystal Structure of MLL1 PHD3-Bromo Complexed with H3(1-9)K4ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:25.9
occ:1.00
SG B:CYS1591 2.4 25.3 1.0
SG B:CYS1588 2.4 18.8 1.0
SG B:CYS1624 2.4 28.5 1.0
SG B:CYS1621 2.5 25.1 1.0
CB B:CYS1588 3.2 18.9 1.0
CB B:CYS1624 3.2 30.3 1.0
CB B:CYS1591 3.3 28.4 1.0
CB B:CYS1621 3.6 23.4 1.0
N B:CYS1591 3.7 31.8 1.0
N B:CYS1621 4.0 21.0 1.0
CA B:CYS1591 4.1 30.2 1.0
N B:CYS1624 4.3 35.9 1.0
CA B:CYS1621 4.3 21.6 1.0
CA B:CYS1624 4.3 36.5 1.0
CA B:CYS1588 4.6 17.8 1.0
CB B:LYS1590 4.7 28.7 1.0
C B:LYS1590 4.8 32.4 1.0
O B:CYS1621 4.8 20.7 1.0
C B:CYS1621 4.8 21.7 1.0
C B:CYS1591 4.9 30.8 1.0
N B:LYS1590 4.9 31.3 1.0

Reference:

Z.Wang, J.Song, T.A.Milne, G.G.Wang, H.Li, C.D.Allis, D.J.Patel. Pro Isomerization in MLL1 PHD3-Bromo Cassette Connects H3K4ME Readout to CYP33 and Hdac-Mediated Repression. Cell(Cambridge,Mass.) V. 141 1183 2010.
ISSN: ISSN 0092-8674
PubMed: 20541251
DOI: 10.1016/J.CELL.2010.05.016
Page generated: Wed Dec 16 04:32:48 2020

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