Atomistry » Zinc » PDB 3phx-3ptm » 3pt6
Atomistry »
  Zinc »
    PDB 3phx-3ptm »
      3pt6 »

Zinc in PDB 3pt6: Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna

Enzymatic activity of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna

All present enzymatic activity of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna:
2.1.1.37;

Protein crystallography data

The structure of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna, PDB code: 3pt6 was solved by J.Song, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.192, 213.507, 86.274, 90.00, 99.64, 90.00
R / Rfree (%) 21.1 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna (pdb code 3pt6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna, PDB code: 3pt6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 1 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


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 Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:71.0
occ:1.00
 NE2 A:HIS1504 2.1 50.6 1.0
SG A:CYS1487 2.3 58.8 1.0
SG A:CYS1479 2.3 62.2 1.0
SG A:CYS1481 2.3 48.9 1.0
CB A:CYS1479 2.8 54.0 1.0
CD2 A:HIS1504 3.0 49.2 1.0
CB A:CYS1481 3.2 56.7 1.0
CE1 A:HIS1504 3.2 51.3 1.0
CB A:CYS1487 3.7 61.9 1.0
CA A:CYS1487 4.0 63.0 1.0
N A:CYS1481 4.1 57.0 1.0
CG A:HIS1504 4.2 48.5 1.0
CA A:CYS1481 4.3 58.8 1.0
ND1 A:HIS1504 4.3 49.5 1.0
CA A:CYS1479 4.3 51.5 1.0
C A:CYS1479 4.7 52.0 1.0
N A:SER1480 4.8 54.1 1.0
N A:CYS1487 4.8 66.3 1.0
CH2 A:TRP1500 5.0 49.4 1.0

Zinc binding site 2 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 2 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


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 Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:92.2
occ:1.00
 SG A:CYS662 2.3 91.7 1.0
SG A:CYS659 2.3 88.6 1.0
SG A:CYS694 2.3 82.8 1.0
SG A:CYS656 2.3 86.6 1.0
CB A:CYS694 3.0 82.1 1.0
CB A:CYS659 3.3 78.2 1.0
O A:CYS656 3.5 84.0 1.0
CB A:CYS662 3.7 86.8 1.0
CB A:CYS656 3.8 84.2 1.0
N A:CYS659 3.9 80.0 1.0
CB A:ASN696 4.0 73.0 1.0
C A:CYS656 4.1 84.5 1.0
N A:CYS656 4.1 85.1 1.0
CA A:CYS659 4.1 80.3 1.0
CA A:CYS694 4.1 82.8 1.0
N A:CYS662 4.2 83.7 1.0
CA A:CYS656 4.2 85.3 1.0
CG A:ARG655 4.4 79.7 1.0
CA A:CYS662 4.5 85.5 1.0
ND2 A:ASN696 4.6 72.2 1.0
N A:ASN696 4.6 77.9 1.0
C A:CYS659 4.7 84.1 1.0
O A:CYS659 4.7 84.5 1.0
C A:CYS694 4.7 82.2 1.0
CA A:ASN696 4.8 76.0 1.0
CG A:ASN696 4.8 71.2 1.0
CB A:VAL661 4.8 83.5 1.0
C A:ASN696 5.0 73.2 1.0
N A:VAL658 5.0 85.5 1.0

Zinc binding site 3 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 3 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


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 Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:65.3
occ:1.00
 NE2 A:HIS796 2.0 54.1 1.0
SG A:CYS900 2.3 55.3 1.0
SG A:CYS823 2.3 43.1 1.0
SG A:CYS897 2.3 48.3 1.0
CE1 A:HIS796 2.9 54.4 1.0
CB A:CYS823 2.9 47.6 1.0
CD2 A:HIS796 3.1 54.5 1.0
CB A:CYS900 3.4 50.0 1.0
CB A:CYS897 3.4 49.0 1.0
N A:CYS900 3.5 46.5 1.0
CA A:CYS900 3.9 49.0 1.0
ND1 A:HIS796 4.0 55.4 1.0
CG A:HIS796 4.1 54.7 1.0
CB A:SER899 4.2 45.8 1.0
CA A:CYS823 4.4 49.8 1.0
C A:SER899 4.4 46.3 1.0
OG A:SER899 4.7 45.3 1.0
C A:CYS823 4.7 54.4 1.0
CA A:SER899 4.7 45.5 1.0
CA A:CYS897 4.8 50.7 1.0
O A:ALA797 4.9 50.7 1.0
O A:CYS823 4.9 55.1 1.0
O A:CYS897 4.9 48.3 1.0
N A:SER899 4.9 46.2 1.0
C A:CYS897 4.9 49.5 1.0

Zinc binding site 4 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 4 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


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 Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:0.5
occ:1.00
 SG A:CYS670 2.3 0.8 1.0
SG A:CYS673 2.3 92.7 1.0
SG A:CYS667 2.4 0.5 1.0
SG A:CYS689 2.4 0.0 1.0
CB A:CYS673 3.2 1.0 1.0
CB A:CYS689 3.2 93.2 1.0
CB A:CYS670 3.5 0.9 1.0
CA A:CYS689 3.7 87.8 1.0
CB A:CYS667 3.8 0.5 1.0
N A:CYS667 3.9 97.8 1.0
N A:LEU690 3.9 92.1 1.0
N A:GLY668 3.9 0.2 1.0
N A:CYS670 4.0 0.7 1.0
C A:CYS689 4.2 89.3 1.0
CA A:CYS667 4.3 0.8 1.0
CA A:CYS670 4.4 0.7 1.0
CA A:CYS673 4.5 0.8 1.0
N A:LYS669 4.5 0.7 1.0
C A:CYS667 4.6 0.1 1.0
N A:LYS691 4.8 92.7 1.0
N A:CYS673 4.8 0.4 1.0
CA A:GLY668 4.9 0.7 1.0
N A:CYS689 5.0 85.5 1.0
CA A:LEU690 5.0 88.7 1.0
C A:GLU666 5.0 95.6 1.0

Zinc binding site 5 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 5 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:91.1
occ:1.00
 NE2 B:HIS796 2.0 78.8 1.0
SG B:CYS823 2.3 65.8 1.0
SG B:CYS900 2.3 65.2 1.0
SG B:CYS897 2.3 61.8 1.0
CE1 B:HIS796 3.0 75.9 1.0
CD2 B:HIS796 3.0 74.6 1.0
CB B:CYS823 3.2 69.7 1.0
CB B:CYS897 3.3 68.1 1.0
CB B:CYS900 3.4 70.6 1.0
N B:CYS900 3.6 65.9 1.0
CA B:CYS900 3.9 67.6 1.0
ND1 B:HIS796 4.1 77.0 1.0
CG B:HIS796 4.2 77.5 1.0
C B:SER899 4.4 63.9 1.0
CB B:SER899 4.4 63.1 1.0
CA B:CYS823 4.5 72.4 1.0
O B:CYS823 4.7 75.7 1.0
C B:CYS823 4.7 75.6 1.0
CA B:CYS897 4.7 71.4 1.0
CA B:SER899 4.8 63.8 1.0
N B:SER899 4.9 63.0 1.0
C B:CYS897 5.0 68.2 1.0

Zinc binding site 6 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 6 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:99.5
occ:1.00
 SG B:CYS656 2.3 75.3 1.0
SG B:CYS662 2.3 86.1 1.0
SG B:CYS659 2.3 89.9 1.0
SG B:CYS694 2.3 85.3 1.0
CB B:CYS659 3.0 82.3 1.0
CB B:CYS694 3.3 85.5 1.0
O B:CYS656 3.4 84.7 1.0
CB B:CYS662 3.5 88.5 1.0
CB B:CYS656 3.7 80.0 1.0
N B:CYS656 3.7 84.3 1.0
C B:CYS656 3.9 83.3 1.0
CA B:CYS659 4.0 81.6 1.0
CA B:CYS656 4.0 83.1 1.0
N B:CYS659 4.0 81.8 1.0
CB B:ASN696 4.0 78.7 1.0
CA B:CYS694 4.3 86.4 1.0
N B:CYS662 4.3 92.0 1.0
CA B:CYS662 4.4 90.7 1.0
CG1 B:VAL661 4.5 89.1 1.0
C B:CYS659 4.6 85.9 1.0
C B:ARG655 4.7 85.3 1.0
ND2 B:ASN696 4.7 71.2 1.0
N B:GLY657 4.8 79.9 1.0
CB B:ARG655 4.8 83.2 1.0
O B:CYS659 4.8 84.5 1.0
CG B:ASN696 4.9 73.7 1.0
N B:ASN696 4.9 80.5 1.0
CA B:ASN696 4.9 80.4 1.0
C B:CYS694 5.0 87.3 1.0

Zinc binding site 7 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 7 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:91.2
occ:1.00
 NE2 B:HIS1504 2.2 68.7 1.0
SG B:CYS1487 2.3 63.0 1.0
SG B:CYS1479 2.4 72.8 1.0
SG B:CYS1481 2.4 66.3 1.0
CD2 B:HIS1504 3.0 66.3 1.0
CB B:CYS1479 3.0 73.5 1.0
CE1 B:HIS1504 3.3 67.0 1.0
CB B:CYS1481 3.3 70.2 1.0
CB B:CYS1487 3.7 73.7 1.0
N B:CYS1481 4.1 71.5 1.0
CA B:CYS1487 4.2 75.2 1.0
CG B:HIS1504 4.2 64.7 1.0
ND1 B:HIS1504 4.3 63.2 1.0
CA B:CYS1481 4.3 69.2 1.0
CA B:CYS1479 4.4 74.6 1.0
C B:CYS1479 4.7 71.0 1.0
N B:SER1480 4.8 71.3 1.0
N B:CYS1487 5.0 73.4 1.0

Zinc binding site 8 out of 8 in 3pt6

Go back to Zinc Binding Sites List in 3pt6
Zinc binding site 8 out of 8 in the Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Mouse DNMT1(650-1602) in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:0.2
occ:1.00
 SG B:CYS673 2.3 0.0 1.0
SG B:CYS689 2.3 0.2 1.0
SG B:CYS670 2.3 0.3 1.0
SG B:CYS667 2.4 0.6 1.0
CB B:CYS670 2.8 0.5 1.0
CB B:CYS689 3.5 0.2 1.0
CB B:CYS673 3.6 0.5 1.0
N B:CYS670 3.7 0.8 1.0
N B:CYS667 3.8 0.5 1.0
CA B:CYS670 3.8 0.5 1.0
CA B:CYS689 3.9 96.6 1.0
CB B:CYS667 4.0 0.3 1.0
N B:GLY668 4.0 0.7 1.0
CB B:GLU666 4.2 0.1 1.0
N B:LEU690 4.2 95.9 1.0
CA B:CYS667 4.4 0.3 1.0
C B:CYS689 4.5 95.1 1.0
C B:GLU666 4.5 0.7 1.0
CA B:GLU666 4.5 1.0 1.0
N B:LYS669 4.6 0.4 1.0
N B:CYS673 4.6 0.5 1.0
CA B:CYS673 4.7 0.1 1.0
C B:CYS667 4.7 0.1 1.0
C B:LYS669 4.9 0.3 1.0
N B:LYS691 4.9 96.9 1.0
CA B:GLY668 5.0 0.2 1.0

Reference:

J.Song, O.Rechkoblit, T.H.Bestor, D.J.Patel. Structure of DNMT1-Dna Complex Reveals A Role For Autoinhibition in Maintenance Dna Methylation. Science V. 331 1036 2011.
ISSN: ISSN 0036-8075
PubMed: 21163962
DOI: 10.1126/SCIENCE.1195380
Page generated: Sat Oct 26 11:42:18 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy