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Zinc in PDB 4w5a: Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide

Enzymatic activity of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide

All present enzymatic activity of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide:
3.6.4.12;

Protein crystallography data

The structure of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide, PDB code: 4w5a was solved by D.Zhao, B.Xiang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.50 / 2.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.522, 75.522, 137.599, 90.00, 90.00, 120.00
R / Rfree (%) 22.1 / 26

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide (pdb code 4w5a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide, PDB code: 4w5a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4w5a

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Zinc binding site 1 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:53.4
occ:1.00
 SG A:CYS11 2.2 49.8 1.0
SG A:CYS14 2.3 53.4 1.0
SG A:CYS40 2.3 54.9 1.0
SG A:CYS37 2.4 53.3 1.0
CB A:CYS11 3.0 53.8 1.0
CB A:CYS40 3.4 49.1 1.0
CB A:CYS14 3.4 44.2 1.0
CB A:CYS37 3.5 52.1 1.0
N A:CYS14 3.7 54.0 1.0
N A:CYS37 3.9 53.6 1.0
CA A:CYS14 4.2 49.0 1.0
N A:CYS40 4.2 60.8 1.0
CA A:CYS37 4.2 51.8 1.0
CB A:ALA13 4.4 46.2 1.0
CA A:CYS40 4.4 52.3 1.0
CA A:CYS11 4.5 52.1 1.0
C A:ALA13 4.7 49.4 1.0
N A:GLY15 4.8 55.6 1.0
C A:CYS37 4.8 59.8 1.0
C A:CYS11 4.9 47.9 1.0
O A:CYS37 4.9 59.5 1.0
O A:CYS11 4.9 53.9 1.0
CA A:ALA13 4.9 49.7 1.0
CB A:GLN16 4.9 62.1 1.0
N A:ALA13 5.0 47.0 1.0
C A:CYS14 5.0 54.5 1.0

Zinc binding site 2 out of 9 in 4w5a

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Zinc binding site 2 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:48.0
occ:1.00
 SG A:CYS83 2.3 52.8 1.0
SG A:CYS80 2.3 45.8 1.0
SG A:CYS60 2.4 46.2 1.0
SG A:CYS63 2.5 45.9 1.0
CB A:CYS60 3.0 43.0 1.0
CB A:CYS83 3.3 45.0 1.0
CB A:CYS63 3.3 39.8 1.0
CB A:CYS80 3.5 37.6 1.0
N A:CYS63 3.7 42.2 1.0
O A:HOH606 3.9 45.4 1.0
N A:CYS80 4.0 47.2 1.0
CA A:CYS63 4.1 40.2 1.0
CA A:CYS80 4.3 43.1 1.0
N A:CYS83 4.3 45.9 1.0
CB A:TRP62 4.3 41.1 1.0
O A:HOH608 4.4 43.0 1.0
CA A:CYS83 4.4 45.8 1.0
CA A:CYS60 4.5 42.7 1.0
O A:CYS80 4.5 44.7 1.0
C A:TRP62 4.7 45.3 1.0
C A:CYS80 4.7 45.1 1.0
CA A:TRP62 4.9 43.4 1.0
N A:TRP62 5.0 44.7 1.0
C A:CYS63 5.0 47.7 1.0

Zinc binding site 3 out of 9 in 4w5a

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Zinc binding site 3 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:43.9
occ:1.00
 SG A:CYS75 2.3 52.5 1.0
SG A:CYS108 2.3 50.2 1.0
SG A:CYS72 2.3 48.2 1.0
SG A:CYS105 2.4 50.4 1.0
CB A:CYS75 3.2 39.9 1.0
CB A:CYS72 3.2 44.7 1.0
CB A:CYS105 3.5 45.6 1.0
CB A:CYS108 3.6 52.5 1.0
N A:CYS75 3.8 44.6 1.0
N A:CYS105 3.8 47.4 1.0
CA A:CYS75 4.0 41.5 1.0
N A:CYS108 4.2 52.9 1.0
CA A:CYS105 4.2 49.1 1.0
C A:PHE74 4.3 46.5 1.0
CA A:CYS108 4.5 54.9 1.0
ND2 A:ASN77 4.6 49.1 1.0
C A:CYS75 4.6 41.4 1.0
CA A:CYS72 4.7 43.7 1.0
CB A:PHE74 4.8 48.8 1.0
C A:CYS105 4.8 50.0 1.0
O A:PHE74 4.8 48.6 1.0
N A:PHE74 4.8 45.7 1.0
CA A:PHE74 4.8 46.0 1.0
CB A:ILE107 4.9 50.5 1.0
O A:CYS105 4.9 49.2 1.0
CB A:ASN77 4.9 43.9 1.0
C A:TYR104 4.9 49.2 1.0
O A:CYS75 5.0 47.0 1.0

Zinc binding site 4 out of 9 in 4w5a

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Zinc binding site 4 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:57.2
occ:1.00
 SG B:CYS14 2.3 59.4 1.0
SG B:CYS11 2.3 55.1 1.0
SG B:CYS37 2.4 59.0 1.0
SG B:CYS40 2.4 57.1 1.0
CB B:CYS11 3.2 56.7 1.0
CB B:CYS37 3.3 56.0 1.0
CB B:CYS14 3.4 56.1 1.0
CB B:CYS40 3.4 59.1 1.0
N B:CYS14 3.7 56.1 1.0
N B:CYS37 3.8 58.9 1.0
CA B:CYS14 4.1 60.6 1.0
CA B:CYS37 4.2 64.2 1.0
CB B:ALA13 4.2 52.2 1.0
N B:CYS40 4.3 72.3 1.0
CA B:CYS40 4.4 62.2 1.0
C B:ALA13 4.5 56.3 1.0
CA B:CYS11 4.6 60.0 1.0
CA B:ALA13 4.7 56.3 1.0
N B:ALA13 4.8 58.1 1.0
C B:CYS37 4.8 65.7 1.0
C B:CYS14 4.9 59.7 1.0

Zinc binding site 5 out of 9 in 4w5a

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Zinc binding site 5 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:48.8
occ:1.00
 SG B:CYS83 2.3 50.0 1.0
SG B:CYS80 2.3 44.9 1.0
SG B:CYS63 2.3 50.5 1.0
SG B:CYS60 2.4 48.6 1.0
CB B:CYS60 3.1 46.5 1.0
CB B:CYS83 3.3 48.0 1.0
CB B:CYS63 3.4 43.9 1.0
CB B:CYS80 3.6 45.1 1.0
N B:CYS63 3.7 46.8 1.0
CA B:CYS63 4.1 48.1 1.0
N B:CYS80 4.1 53.3 1.0
CB B:TRP62 4.2 48.6 1.0
N B:CYS83 4.3 43.2 1.0
CA B:CYS80 4.4 51.6 1.0
CA B:CYS83 4.4 52.5 1.0
CA B:CYS60 4.5 48.5 1.0
O B:CYS80 4.6 44.3 1.0
C B:TRP62 4.6 48.2 1.0
CA B:TRP62 4.8 48.0 1.0
C B:CYS80 4.8 45.9 1.0
N B:TRP62 4.9 52.3 1.0
C B:CYS63 5.0 54.2 1.0
C B:CYS60 5.0 49.1 1.0

Zinc binding site 6 out of 9 in 4w5a

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Zinc binding site 6 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:46.9
occ:1.00
 SG B:CYS72 2.3 47.4 1.0
SG B:CYS108 2.3 48.6 1.0
SG B:CYS75 2.3 45.4 1.0
SG B:CYS105 2.4 52.3 1.0
CB B:CYS72 3.2 43.8 1.0
CB B:CYS75 3.3 40.0 1.0
CB B:CYS105 3.4 46.4 1.0
CB B:CYS108 3.5 51.4 1.0
N B:CYS105 3.7 49.7 1.0
N B:CYS75 3.8 43.3 1.0
CA B:CYS75 4.1 39.9 1.0
N B:CYS108 4.1 48.8 1.0
CA B:CYS105 4.1 48.8 1.0
C B:PHE74 4.4 46.8 1.0
CA B:CYS108 4.4 54.3 1.0
ND2 B:ASN77 4.5 48.7 1.0
CA B:CYS72 4.6 45.5 1.0
C B:CYS75 4.7 40.0 1.0
CB B:PHE74 4.7 47.0 1.0
C B:CYS105 4.7 51.7 1.0
N B:PHE74 4.7 47.6 1.0
CA B:PHE74 4.8 46.5 1.0
O B:CYS105 4.8 51.1 1.0
C B:TYR104 4.9 48.1 1.0
CB B:ILE107 4.9 50.9 1.0
CB B:ASN77 4.9 41.1 1.0
O B:PHE74 5.0 47.4 1.0

Zinc binding site 7 out of 9 in 4w5a

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Zinc binding site 7 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:73.2
occ:1.00
 SG E:CYS37 2.4 69.8 1.0
SG E:CYS11 2.5 74.2 1.0
SG E:CYS40 2.5 63.4 1.0
SG E:CYS14 2.5 80.1 1.0
CB E:CYS14 3.3 74.1 1.0
CB E:CYS11 3.4 78.2 1.0
CB E:CYS40 3.4 80.8 1.0
CB E:CYS37 3.6 72.5 1.0
N E:CYS14 3.8 80.6 1.0
N E:CYS37 4.0 85.0 1.0
CA E:CYS14 4.2 80.8 1.0
N E:CYS40 4.2 73.3 1.0
CA E:CYS37 4.3 74.7 1.0
CB E:ALA13 4.4 73.1 1.0
CA E:CYS40 4.4 77.9 1.0
C E:ALA13 4.8 81.2 1.0
C E:CYS37 4.8 81.5 1.0
CA E:CYS11 4.9 79.9 1.0
CB E:GLN16 4.9 77.8 1.0
N E:GLY15 4.9 79.1 1.0
C E:CYS14 4.9 81.7 1.0
O E:CYS37 5.0 80.3 1.0

Zinc binding site 8 out of 9 in 4w5a

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Zinc binding site 8 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:67.3
occ:1.00
 SG E:CYS63 2.4 65.5 1.0
SG E:CYS83 2.5 69.0 1.0
SG E:CYS80 2.6 56.8 1.0
SG E:CYS60 2.7 72.2 1.0
CB E:CYS60 3.2 70.9 1.0
CB E:CYS63 3.2 68.6 1.0
CB E:CYS83 3.4 73.6 1.0
N E:CYS63 3.6 62.7 1.0
CB E:CYS80 3.7 68.0 1.0
CA E:CYS63 4.0 71.4 1.0
CB E:TRP62 4.2 67.7 1.0
N E:CYS80 4.4 75.7 1.0
N E:CYS83 4.4 71.4 1.0
CA E:CYS83 4.5 74.0 1.0
CA E:CYS80 4.6 78.0 1.0
C E:TRP62 4.6 70.1 1.0
CA E:CYS60 4.7 69.9 1.0
CA E:TRP62 4.8 71.8 1.0
C E:CYS63 4.8 70.9 1.0
N E:TRP62 4.9 72.7 1.0
O E:CYS80 4.9 78.0 1.0

Zinc binding site 9 out of 9 in 4w5a

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Zinc binding site 9 out of 9 in the Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Complex Structure of Atrx Add Bound to H3K9ME3S10PH Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:93.5
occ:1.00
 SG E:CYS75 2.4 87.2 1.0
SG E:CYS105 2.4 83.3 1.0
SG E:CYS108 2.5 94.2 1.0
SG E:CYS72 2.7 85.9 1.0
CB E:CYS72 3.3 84.9 1.0
CB E:CYS75 3.5 88.3 1.0
CB E:CYS105 3.6 82.6 1.0
CB E:CYS108 3.7 92.1 1.0
N E:CYS105 3.8 92.3 1.0
N E:CYS75 4.0 94.0 1.0
CA E:CYS105 4.2 90.4 1.0
N E:CYS108 4.2 88.2 1.0
CA E:CYS75 4.3 85.1 1.0
CA E:CYS108 4.6 92.7 1.0
ND2 E:ASN77 4.7 76.1 1.0
C E:CYS105 4.8 91.1 1.0
CA E:CYS72 4.8 90.2 1.0
C E:CYS75 4.8 83.3 1.0
C E:TYR104 4.9 93.7 1.0
CB E:ASN77 4.9 79.4 1.0
O E:CYS105 4.9 89.7 1.0
CB E:ILE107 5.0 82.3 1.0

Reference:

K.M.Noh, I.Maze, D.Zhao, B.Xiang, W.Wenderski, P.W.Lewis, L.Shen, H.Li, C.D.Allis. Atrx Tolerates Activity-Dependent Histone H3 Methyl/Phos Switching to Maintain Repetitive Element Silencing in Neurons. Proc.Natl.Acad.Sci.Usa 2014.
ISSN: ESSN 1091-6490
PubMed: 25538301
DOI: 10.1073/PNAS.1411258112
Page generated: Sun Oct 27 09:38:23 2024

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