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Zinc in PDB 5gut: The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A

Enzymatic activity of The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A

All present enzymatic activity of The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A:
2.1.1.37;

Protein crystallography data

The structure of The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A, PDB code: 5gut was solved by S.J.Chen, F.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.36 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.424, 78.554, 164.544, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A (pdb code 5gut). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A, PDB code: 5gut:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5gut

Go back to Zinc Binding Sites List in 5gut
Zinc binding site 1 out of 2 in the The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:50.4
occ:1.00
NE2 A:HIS796 2.2 58.9 1.0
SG A:CYS900 2.2 49.0 1.0
SG A:CYS823 2.3 44.2 1.0
SG A:CYS897 2.3 51.6 1.0
CB A:CYS823 2.9 43.5 1.0
CD2 A:HIS796 3.1 52.6 1.0
CE1 A:HIS796 3.2 57.1 1.0
CB A:CYS897 3.3 63.1 1.0
CB A:CYS900 3.4 41.5 1.0
N A:CYS900 3.4 53.4 1.0
CA A:CYS900 3.8 55.5 1.0
CB A:SER899 4.1 51.4 1.0
CG A:HIS796 4.3 62.2 1.0
ND1 A:HIS796 4.3 57.1 1.0
C A:SER899 4.4 47.0 1.0
CA A:CYS823 4.4 51.3 1.0
OG A:SER899 4.5 45.9 1.0
O A:CYS897 4.6 44.1 1.0
CA A:CYS897 4.6 58.9 1.0
CA A:SER899 4.7 46.1 1.0
C A:CYS823 4.8 59.6 1.0
C A:CYS897 4.8 57.1 1.0
N A:SER899 4.9 43.4 1.0
N A:GLU824 5.0 52.5 1.0

Zinc binding site 2 out of 2 in 5gut

Go back to Zinc Binding Sites List in 5gut
Zinc binding site 2 out of 2 in the The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Mouse DNMT1 (731-1602) Mutant - N1248A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:25.2
occ:1.00
NE2 A:HIS1504 2.1 22.2 1.0
SG A:CYS1481 2.3 27.9 1.0
SG A:CYS1487 2.4 28.8 1.0
SG A:CYS1479 2.4 26.3 1.0
CD2 A:HIS1504 3.0 16.8 1.0
CB A:CYS1479 3.2 25.0 1.0
CE1 A:HIS1504 3.2 28.7 1.0
CB A:CYS1481 3.2 31.5 1.0
CB A:CYS1487 3.3 26.0 1.0
CA A:CYS1487 3.9 30.7 1.0
N A:CYS1481 4.0 25.5 1.0
CG A:HIS1504 4.2 29.5 1.0
ND1 A:HIS1504 4.2 26.5 1.0
CA A:CYS1481 4.3 28.5 1.0
O A:HOH2253 4.3 44.5 1.0
CA A:CYS1479 4.6 24.8 1.0
OG A:SER1491 4.7 30.6 1.0
N A:CYS1487 4.8 33.5 1.0
C A:CYS1479 4.8 29.2 1.0
O A:HOH2110 4.9 34.7 1.0
N A:SER1480 4.9 28.4 1.0
C A:CYS1487 5.0 35.0 1.0
O A:HOH1934 5.0 24.9 1.0

Reference:

F.Ye, X.Kong, H.Zhang, Y.Liu, Z.Shao, J.Jin, Y.Cai, R.Zhang, L.Li, Y.W.Zhang, Y.C.Liu, C.Zhang, W.Xie, K.Yu, H.Ding, K.Zhao, S.Chen, H.Jiang, S.B.Baylin, C.Luo. Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in Dna Methyltransferase-1. Acs Chem. Biol. V. 13 772 2018.
ISSN: ESSN 1554-8937
PubMed: 29381856
DOI: 10.1021/ACSCHEMBIO.7B00890
Page generated: Wed Dec 16 06:19:47 2020

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