Zinc in PDB 7lmk: Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3

Enzymatic activity of Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3

All present enzymatic activity of Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3:
2.1.1.37;

Protein crystallography data

The structure of Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3, PDB code: 7lmk was solved by W.Ren, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.06 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.06, 81.372, 129.653, 90, 90, 90
R / Rfree (%) 20.6 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3 (pdb code 7lmk). 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 Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3, PDB code: 7lmk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7lmk

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Zinc binding site 1 out of 4 in the Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3


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 Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:54.6
occ:1.00
NE2 A:HIS790 2.0 64.4 1.0
SG A:CYS817 2.4 64.2 1.0
CB A:CYS817 2.8 59.7 1.0
CE1 A:HIS790 2.9 63.3 1.0
CD2 A:HIS790 3.1 60.4 1.0
ND1 A:HIS790 4.0 61.4 1.0
CG A:HIS790 4.1 57.0 1.0
CA A:CYS817 4.1 57.0 1.0

Zinc binding site 2 out of 4 in 7lmk

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Zinc binding site 2 out of 4 in the Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3


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 Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:63.4
occ:1.00
NE2 B:HIS790 2.0 77.2 1.0
SG B:CYS817 2.3 74.7 1.0
CB B:CYS817 2.9 67.3 1.0
CE1 B:HIS790 3.0 74.1 1.0
CD2 B:HIS790 3.0 70.6 1.0
ND1 B:HIS790 4.0 73.3 1.0
CG B:HIS790 4.1 68.1 1.0
CA B:CYS817 4.1 66.5 1.0

Zinc binding site 3 out of 4 in 7lmk

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Zinc binding site 3 out of 4 in the Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3


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 Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:70.2
occ:1.00
NE2 C:HIS790 2.0 77.3 1.0
SG C:CYS817 2.3 74.1 1.0
CB C:CYS817 2.8 74.5 1.0
CE1 C:HIS790 2.9 68.5 1.0
CD2 C:HIS790 3.1 67.7 1.0
ND1 C:HIS790 4.0 71.3 1.0
CA C:CYS817 4.1 74.5 1.0
CG C:HIS790 4.1 68.0 1.0
N C:CYS817 5.0 76.7 1.0
N C:GLU818 5.0 76.3 1.0

Zinc binding site 4 out of 4 in 7lmk

Go back to Zinc Binding Sites List in 7lmk
Zinc binding site 4 out of 4 in the Crystal Structure of Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3


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 Bovine DNMT1 BAH1 Domain in Complex with H4K20ME3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:87.0
occ:1.00
NE2 D:HIS790 2.0 112.3 1.0
SG D:CYS817 2.1 97.8 1.0
CD2 D:HIS790 3.0 104.9 1.0
CB D:CYS817 3.0 94.0 1.0
CE1 D:HIS790 3.0 111.1 1.0
ND1 D:HIS790 4.1 110.9 1.0
CG D:HIS790 4.1 103.7 1.0
CA D:CYS817 4.2 88.8 1.0

Reference:

W.Ren, J.Song. DNMT1 Reads Heterochromatic H4K20ME3 to Reinforce Line-1 Dna Methylation To Be Published.
Page generated: Wed Mar 3 16:22:20 2021

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