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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

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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

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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

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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

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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

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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

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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

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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

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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

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