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Zinc in PDB 4qeo: Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah

Enzymatic activity of Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah

All present enzymatic activity of Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah, PDB code: 4qeo was solved by J.Du, S.Li, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.10 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.460, 96.765, 122.411, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah (pdb code 4qeo). 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 Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah, PDB code: 4qeo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4qeo

Go back to Zinc Binding Sites List in 4qeo
Zinc binding site 1 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah


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 Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:38.8
occ:1.00
SG A:CYS397 2.1 36.4 1.0
SG A:CYS383 2.3 41.4 1.0
SG A:CYS429 2.4 36.0 1.0
SG A:CYS425 2.5 35.1 1.0
CB A:CYS383 3.2 39.9 1.0
CB A:CYS425 3.2 32.3 1.0
CB A:CYS429 3.3 33.7 1.0
CB A:CYS397 3.4 36.7 1.0
CA A:CYS425 3.5 37.1 1.0
N A:CYS383 3.6 51.0 1.0
ZN A:ZN804 3.8 42.4 1.0
ZN A:ZN803 3.9 36.2 1.0
CA A:CYS383 4.0 52.3 1.0
SG A:CYS389 4.3 39.8 1.0
SG A:CYS395 4.3 49.9 1.0
N A:CYS425 4.4 41.0 1.0
CA A:CYS429 4.5 35.4 1.0
SG A:CYS431 4.5 38.1 1.0
C A:GLY382 4.6 56.1 1.0
N A:GLY426 4.6 34.2 1.0
C A:CYS425 4.6 35.4 1.0
CA A:CYS397 4.7 44.1 1.0
CA A:GLY382 4.7 54.1 1.0
N A:CYS397 4.8 43.8 1.0
C A:CYS383 4.8 41.0 1.0
O A:CYS383 4.9 42.4 1.0

Zinc binding site 2 out of 4 in 4qeo

Go back to Zinc Binding Sites List in 4qeo
Zinc binding site 2 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah


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 Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:36.2
occ:1.00
SG A:CYS389 2.2 39.8 1.0
SG A:CYS425 2.2 35.1 1.0
SG A:CYS435 2.4 34.5 1.0
SG A:CYS431 2.4 38.1 1.0
CB A:CYS431 3.1 41.0 1.0
CB A:CYS425 3.2 32.3 1.0
CB A:CYS435 3.3 40.4 1.0
CB A:CYS389 3.4 37.3 1.0
ZN A:ZN802 3.9 38.8 1.0
ZN A:ZN804 4.1 42.4 1.0
N A:CYS389 4.1 50.1 1.0
SG A:CYS383 4.1 41.4 1.0
CA A:CYS389 4.3 46.1 1.0
CB A:ASN437 4.5 39.2 1.0
CA A:CYS431 4.6 42.7 1.0
CA A:CYS425 4.7 37.1 1.0
NE A:ARG438 4.7 34.1 1.0
CA A:CYS435 4.7 38.8 1.0
CG A:ARG438 4.9 30.6 1.0
CB A:CYS429 4.9 33.7 1.0
N A:CYS431 5.0 40.2 1.0

Zinc binding site 3 out of 4 in 4qeo

Go back to Zinc Binding Sites List in 4qeo
Zinc binding site 3 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah


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 Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn804

b:42.4
occ:1.00
SG A:CYS395 2.3 49.9 1.0
SG A:CYS383 2.3 41.4 1.0
SG A:CYS389 2.4 39.8 1.0
SG A:CYS385 2.4 46.6 1.0
CB A:CYS383 3.1 39.9 1.0
CB A:CYS395 3.1 46.6 1.0
CB A:CYS389 3.2 37.3 1.0
CB A:CYS385 3.3 48.1 1.0
ZN A:ZN802 3.8 38.8 1.0
CA A:CYS395 3.8 56.8 1.0
ZN A:ZN803 4.1 36.2 1.0
CA A:CYS389 4.2 46.1 1.0
N A:CYS385 4.3 50.2 1.0
SG A:CYS425 4.3 35.1 1.0
O A:HOH1000 4.4 48.8 1.0
CA A:CYS385 4.4 52.5 1.0
CA A:CYS383 4.5 52.3 1.0
C A:CYS395 4.7 53.3 1.0
SG A:CYS397 4.8 36.4 1.0
C A:CYS383 4.8 41.0 1.0
N A:ALA396 4.8 47.3 1.0
N A:CYS395 4.9 64.8 1.0
N A:ASN384 4.9 46.0 1.0

Zinc binding site 4 out of 4 in 4qeo

Go back to Zinc Binding Sites List in 4qeo
Zinc binding site 4 out of 4 in the Crystal Structure of Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah


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 Kryptonite in Complex with Mchh Dna, H3(1-15) Peptide and Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:62.2
occ:1.00
SG A:CYS612 2.4 79.7 1.0
SG A:CYS619 2.4 88.4 1.0
SG A:CYS614 2.5 76.4 1.0
SG A:CYS554 2.5 63.3 1.0
O A:CYS619 3.2 88.9 1.0
CB A:CYS619 3.5 90.5 1.0
CB A:CYS612 3.5 84.5 1.0
CB A:CYS614 3.6 72.9 1.0
CA A:CYS619 3.7 89.5 1.0
CB A:CYS554 3.7 60.9 1.0
N A:CYS614 3.8 82.1 1.0
C A:CYS619 3.8 90.9 1.0
N A:CYS554 4.2 56.7 1.0
CA A:CYS614 4.3 78.4 1.0
C A:CYS612 4.5 94.4 1.0
NE2 A:HIS552 4.5 51.8 1.0
CA A:CYS554 4.5 58.6 1.0
N A:TYR613 4.6 0.7 1.0
CA A:CYS612 4.6 85.5 1.0
CD2 A:HIS552 4.7 54.3 1.0
O A:CYS612 4.7 89.4 1.0
N A:LYS621 4.8 0.6 1.0
N A:GLY615 4.8 80.8 1.0
C A:TYR613 4.9 82.8 1.0
CB A:ALA616 4.9 98.3 1.0
C A:CYS614 5.0 77.9 1.0

Reference:

J.Du, L.M.Johnson, M.Groth, S.Feng, C.J.Hale, S.Li, A.A.Vashisht, J.Gallego-Bartolome, J.A.Wohlschlegel, D.J.Patel, S.E.Jacobsen. Mechanism of Dna Methylation-Directed Histone Methylation By Kryptonite. Mol.Cell V. 55 495 2014.
ISSN: ISSN 1097-2765
PubMed: 25018018
DOI: 10.1016/J.MOLCEL.2014.06.009
Page generated: Wed Dec 16 05:43:19 2020

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