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Zinc in PDB 5wvo: Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3

Enzymatic activity of Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3

All present enzymatic activity of Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3:
2.1.1.37;

Protein crystallography data

The structure of Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3, PDB code: 5wvo was solved by S.Ishiyama, A.Nishiyama, M.Nakanishi, K.Arita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.18 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.362, 198.779, 76.904, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3 (pdb code 5wvo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3, PDB code: 5wvo:

Zinc binding site 1 out of 1 in 5wvo

Go back to Zinc Binding Sites List in 5wvo
Zinc binding site 1 out of 1 in the Crystal Structure of DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3


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 DNMT1 Rfts Domain in Complex with K18/K23 Mono- Ubiquitylated Histone H3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:65.7
occ:1.00
CB C:CYS356 2.3 51.7 1.0
ND1 C:HIS418 2.4 54.1 1.0
SG C:CYS353 2.6 73.4 1.0
SG C:CYS414 2.7 59.2 1.0
CE1 C:HIS418 3.0 65.4 1.0
N C:CYS356 3.0 61.1 1.0
CB C:CYS353 3.1 65.4 1.0
SG C:CYS356 3.1 65.6 1.0
CA C:CYS356 3.2 49.8 1.0
CB C:CYS414 3.5 52.6 1.0
CG C:HIS418 3.5 64.3 1.0
NE2 C:HIS416 4.0 78.1 1.0
CD2 C:HIS416 4.1 72.7 1.0
CB C:HIS418 4.1 55.1 1.0
NE2 C:HIS418 4.2 63.4 1.0
C C:GLN355 4.3 51.3 1.0
CD2 C:HIS418 4.5 58.5 1.0
CB C:GLN355 4.5 53.0 1.0
C C:CYS356 4.5 66.0 1.0
CA C:CYS353 4.6 43.2 1.0
N C:GLY357 4.7 66.1 1.0
CA C:GLN355 4.8 62.6 1.0
SG C:CYS420 4.8 47.0 0.6
N C:HIS418 4.8 46.5 1.0
N C:GLN355 4.9 65.5 1.0
CA C:CYS414 4.9 36.2 1.0

Reference:

S.Ishiyama, A.Nishiyama, Y.Saeki, K.Moritsugu, D.Morimoto, L.Yamaguchi, N.Arai, R.Matsumura, T.Kawakami, Y.Mishima, H.Hojo, S.Shimamura, F.Ishikawa, S.Tajima, K.Tanaka, M.Ariyoshi, M.Shirakawa, M.Ikeguchi, A.Kidera, I.Suetake, K.Arita, M.Nakanishi. Structure of the DNMT1 Reader Module Complexed with A Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis For Dna Methylation Maintenance Mol. Cell V. 68 350 2017.
ISSN: ISSN 1097-4164
PubMed: 29053958
DOI: 10.1016/J.MOLCEL.2017.09.037
Page generated: Wed Dec 16 11:18:33 2020

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