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Zinc in PDB 4wxx: The Crystal Structure of Human DNMT1(351-1600)

Enzymatic activity of The Crystal Structure of Human DNMT1(351-1600)

All present enzymatic activity of The Crystal Structure of Human DNMT1(351-1600):
2.1.1.37;

Protein crystallography data

The structure of The Crystal Structure of Human DNMT1(351-1600), PDB code: 4wxx was solved by Z.M.Zhang, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 2.62
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 138.568, 138.568, 221.536, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Human DNMT1(351-1600) (pdb code 4wxx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the The Crystal Structure of Human DNMT1(351-1600), PDB code: 4wxx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4wxx

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Zinc binding site 1 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


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 Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:42.5
occ:1.00
 NE2 A:HIS1502 2.1 38.6 1.0
SG A:CYS1478 2.3 40.0 1.0
SG A:CYS1476 2.4 37.2 1.0
SG A:CYS1485 2.4 44.9 1.0
CD2 A:HIS1502 3.0 34.2 1.0
CB A:CYS1478 3.0 46.4 1.0
CB A:CYS1476 3.1 42.7 1.0
CE1 A:HIS1502 3.2 28.9 1.0
CB A:CYS1485 3.2 31.5 1.0
CA A:CYS1485 3.7 40.9 1.0
N A:CYS1478 4.0 47.9 1.0
CA A:CYS1478 4.1 49.0 1.0
O A:HOH2041 4.2 52.0 1.0
CG A:HIS1502 4.2 38.8 1.0
ND1 A:HIS1502 4.2 33.5 1.0
CA A:CYS1476 4.5 35.3 1.0
N A:CYS1485 4.6 42.4 1.0
N A:SER1477 4.7 45.6 1.0
O A:HOH1898 4.7 31.0 1.0
O A:HOH2025 4.7 29.1 1.0
C A:CYS1485 4.8 41.1 1.0
C A:CYS1476 4.8 42.4 1.0
N A:ASP1486 4.8 46.1 1.0
C A:CYS1478 5.0 47.1 1.0

Zinc binding site 2 out of 10 in 4wxx

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Zinc binding site 2 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


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 Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:42.8
occ:1.00
 NE2 A:HIS793 2.2 37.8 1.0
SG A:CYS893 2.4 37.6 1.0
SG A:CYS820 2.4 41.7 1.0
SG A:CYS896 2.4 45.1 1.0
CB A:CYS820 2.8 26.1 1.0
CD2 A:HIS793 3.0 35.6 1.0
CE1 A:HIS793 3.2 39.0 1.0
CB A:CYS893 3.4 25.8 1.0
N A:CYS896 3.4 47.0 1.0
CB A:CYS896 3.4 32.9 1.0
CA A:CYS896 3.8 53.8 1.0
CB A:SER895 4.0 38.8 1.0
CG A:HIS793 4.2 34.4 1.0
CA A:CYS820 4.2 37.0 1.0
ND1 A:HIS793 4.3 34.1 1.0
C A:SER895 4.3 44.0 1.0
OG A:SER895 4.5 44.3 1.0
CA A:SER895 4.6 44.7 1.0
C A:CYS820 4.7 34.5 1.0
CA A:CYS893 4.8 36.7 1.0
N A:GLU821 4.8 34.3 1.0
N A:SER895 4.9 40.1 1.0
O A:CYS893 5.0 41.3 1.0

Zinc binding site 3 out of 10 in 4wxx

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Zinc binding site 3 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:93.3
occ:1.00
 SG A:CYS664 2.4 94.7 1.0
SG A:CYS667 2.4 88.4 1.0
SG A:CYS670 2.4 90.6 1.0
SG A:CYS686 2.6 81.7 1.0
CB A:CYS670 3.0 83.9 1.0
N A:GLY665 3.3 98.0 1.0
CB A:CYS686 3.5 71.1 1.0
N A:CYS664 3.7 78.9 1.0
N A:GLN687 3.7 84.2 1.0
CA A:CYS686 3.8 70.0 1.0
CB A:CYS664 3.8 91.5 1.0
CB A:CYS667 3.9 97.0 1.0
CA A:CYS664 4.1 87.9 1.0
N A:CYS670 4.1 84.3 1.0
CA A:CYS670 4.1 85.9 1.0
N A:CYS667 4.2 0.8 1.0
CA A:GLY665 4.2 90.7 1.0
C A:CYS686 4.2 78.3 1.0
C A:CYS664 4.2 93.4 1.0
N A:LYS666 4.4 92.1 1.0
C A:GLU663 4.6 79.3 1.0
N A:GLU688 4.6 86.1 1.0
CA A:CYS667 4.6 0.9 1.0
C A:GLY665 4.7 95.8 1.0
CA A:GLN687 4.7 82.1 1.0
CA A:GLU663 4.9 78.5 1.0
O A:CYS667 5.0 98.9 1.0
CB A:GLU663 5.0 76.9 1.0

Zinc binding site 4 out of 10 in 4wxx

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Zinc binding site 4 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1704

b:50.3
occ:1.00
 SG A:CYS653 2.3 46.3 1.0
SG A:CYS656 2.3 45.2 1.0
SG A:CYS691 2.4 52.8 1.0
SG A:CYS659 2.4 54.5 1.0
CB A:CYS691 3.3 36.7 1.0
CB A:CYS653 3.5 54.3 1.0
CB A:CYS656 3.5 48.3 1.0
CB A:CYS659 3.5 53.0 1.0
N A:CYS653 3.6 54.0 1.0
N A:GLY654 3.7 65.4 1.0
CA A:CYS653 3.9 46.9 1.0
N A:CYS656 3.9 55.9 1.0
ND2 A:ASN693 4.0 41.1 1.0
CA A:CYS691 4.0 44.5 1.0
CA A:CYS656 4.2 58.2 1.0
C A:CYS653 4.2 64.3 1.0
N A:CYS659 4.3 51.0 1.0
N A:VAL655 4.4 66.0 1.0
CA A:CYS659 4.5 59.3 1.0
CD A:PRO692 4.6 36.4 1.0
C A:ARG652 4.6 59.1 1.0
CA A:GLY654 4.6 63.1 1.0
O A:CYS656 4.6 59.7 1.0
CB A:ASN693 4.7 39.0 1.0
CB A:ARG652 4.7 61.9 1.0
C A:CYS656 4.8 53.8 1.0
C A:CYS691 4.8 48.6 1.0
CG A:ASN693 4.8 50.2 1.0
CA A:ARG652 4.9 71.2 1.0
C A:GLY654 4.9 68.1 1.0
N A:PRO692 5.0 45.8 1.0

Zinc binding site 5 out of 10 in 4wxx

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Zinc binding site 5 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1705

b:71.4
occ:1.00
 ND1 A:HIS418 2.2 65.4 1.0
SG A:CYS356 2.4 67.0 1.0
SG A:CYS414 2.4 70.9 1.0
SG A:CYS353 2.5 77.5 1.0
CE1 A:HIS418 3.0 69.2 1.0
CB A:CYS353 3.1 67.7 1.0
CG A:HIS418 3.3 72.0 1.0
CB A:CYS356 3.6 68.8 1.0
CB A:HIS418 3.7 74.5 1.0
N A:CYS356 3.7 70.0 1.0
CB A:CYS414 3.7 74.2 1.0
CA A:CYS356 4.1 76.3 1.0
NE2 A:HIS418 4.2 67.9 1.0
CB A:HIS416 4.3 77.1 1.0
O A:CYS356 4.3 81.3 1.0
CD2 A:HIS418 4.3 68.6 1.0
CB A:GLN355 4.4 86.3 1.0
CA A:CYS353 4.6 70.7 1.0
N A:HIS418 4.6 74.4 1.0
C A:CYS356 4.6 77.5 1.0
CA A:HIS418 4.8 72.6 1.0
C A:GLN355 4.8 69.5 1.0
SG A:CYS420 4.8 83.3 1.0
ND1 A:HIS416 4.9 86.6 1.0
CG A:HIS416 4.9 79.3 1.0
CA A:GLN355 5.0 78.1 1.0
N A:GLN355 5.0 68.2 1.0
N A:HIS416 5.0 76.3 1.0

Zinc binding site 6 out of 10 in 4wxx

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Zinc binding site 6 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1701

b:42.2
occ:1.00
 NE2 B:HIS1502 2.2 37.3 1.0
SG B:CYS1485 2.4 46.7 1.0
SG B:CYS1476 2.4 38.3 1.0
SG B:CYS1478 2.4 40.1 1.0
CD2 B:HIS1502 3.0 38.5 1.0
CB B:CYS1476 3.1 41.2 1.0
CE1 B:HIS1502 3.2 32.0 1.0
CB B:CYS1478 3.3 42.0 1.0
CB B:CYS1485 3.3 29.1 1.0
CA B:CYS1485 3.8 42.3 1.0
N B:CYS1478 4.1 44.8 1.0
O B:HOH2118 4.2 44.7 1.0
O B:HOH1930 4.2 53.7 1.0
CG B:HIS1502 4.2 37.5 1.0
ND1 B:HIS1502 4.3 35.1 1.0
CA B:CYS1478 4.3 45.2 1.0
CA B:CYS1476 4.5 32.4 1.0
N B:SER1477 4.7 43.8 1.0
N B:CYS1485 4.7 41.3 1.0
C B:CYS1476 4.8 39.4 1.0
N B:ASP1486 4.8 44.4 1.0
C B:CYS1485 4.9 42.0 1.0

Zinc binding site 7 out of 10 in 4wxx

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Zinc binding site 7 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1702

b:56.8
occ:1.00
 NE2 B:HIS793 2.2 41.2 1.0
SG B:CYS893 2.3 41.9 1.0
SG B:CYS820 2.4 46.1 1.0
SG B:CYS896 2.4 42.9 1.0
CB B:CYS820 2.7 28.2 1.0
CD2 B:HIS793 3.1 37.6 1.0
CE1 B:HIS793 3.2 37.5 1.0
CB B:CYS893 3.2 30.8 1.0
N B:CYS896 3.3 47.9 1.0
CB B:CYS896 3.4 29.4 1.0
CA B:CYS896 3.7 46.3 1.0
CB B:SER895 4.0 39.5 1.0
CA B:CYS820 4.2 40.8 1.0
C B:SER895 4.2 50.9 1.0
CG B:HIS793 4.3 34.3 1.0
ND1 B:HIS793 4.3 33.5 1.0
OG B:SER895 4.5 47.2 1.0
CA B:SER895 4.6 43.5 1.0
C B:CYS820 4.6 37.2 1.0
CA B:CYS893 4.6 44.6 1.0
N B:SER895 4.8 43.0 1.0
N B:GLU821 4.8 34.9 1.0
C B:CYS893 5.0 48.6 1.0

Zinc binding site 8 out of 10 in 4wxx

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Zinc binding site 8 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1703

b:0.1
occ:1.00
 SG B:CYS664 2.4 87.8 1.0
SG B:CYS667 2.4 93.8 1.0
SG B:CYS670 2.4 87.0 1.0
SG B:CYS686 2.4 89.3 1.0
CB B:CYS670 3.1 82.3 1.0
CB B:CYS686 3.4 69.6 1.0
N B:GLN687 3.6 87.0 1.0
N B:GLY665 3.7 0.5 1.0
N B:CYS664 3.7 78.9 1.0
CA B:CYS686 3.7 70.2 1.0
CB B:CYS664 3.8 78.5 1.0
CB B:CYS667 3.9 93.2 1.0
N B:CYS670 4.1 86.2 1.0
C B:CYS686 4.1 79.9 1.0
CA B:CYS670 4.1 87.8 1.0
CA B:CYS664 4.2 83.9 1.0
N B:CYS667 4.3 92.3 1.0
N B:GLU688 4.3 92.5 1.0
C B:CYS664 4.4 94.5 1.0
C B:GLU663 4.6 80.5 1.0
CA B:GLY665 4.6 89.5 1.0
N B:LYS666 4.6 86.4 1.0
CA B:GLN687 4.6 80.0 1.0
CA B:CYS667 4.6 94.2 1.0
CA B:GLU663 4.8 78.8 1.0
CB B:GLU688 4.9 85.4 1.0
CB B:GLU663 5.0 77.7 1.0

Zinc binding site 9 out of 10 in 4wxx

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Zinc binding site 9 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1704

b:51.4
occ:1.00
 SG B:CYS653 2.3 50.2 1.0
SG B:CYS656 2.3 43.6 1.0
SG B:CYS659 2.4 62.5 1.0
SG B:CYS691 2.5 46.8 1.0
CB B:CYS659 3.3 61.4 1.0
CB B:CYS656 3.4 48.5 1.0
CB B:CYS691 3.4 35.0 1.0
CB B:CYS653 3.5 55.4 1.0
N B:GLY654 3.7 64.8 1.0
N B:CYS653 3.7 54.0 1.0
N B:CYS656 3.9 58.0 1.0
CA B:CYS653 4.0 47.1 1.0
ND2 B:ASN693 4.2 38.6 1.0
CA B:CYS656 4.2 53.2 1.0
CA B:CYS691 4.2 42.9 1.0
N B:CYS659 4.2 55.8 1.0
C B:CYS653 4.3 62.8 1.0
CA B:CYS659 4.3 62.6 1.0
N B:VAL655 4.4 63.9 1.0
CD B:PRO692 4.5 35.7 1.0
O B:CYS656 4.6 56.3 1.0
CA B:GLY654 4.6 63.6 1.0
CB B:ASN693 4.7 31.8 1.0
C B:ARG652 4.7 59.0 1.0
C B:CYS656 4.7 55.7 1.0
C B:CYS691 4.9 49.1 1.0
CG B:ASN693 4.9 46.5 1.0
C B:GLY654 5.0 69.9 1.0
CB B:ARG652 5.0 64.8 1.0
N B:PRO692 5.0 42.0 1.0

Zinc binding site 10 out of 10 in 4wxx

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Zinc binding site 10 out of 10 in the The Crystal Structure of Human DNMT1(351-1600)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of Human DNMT1(351-1600) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1705

b:74.6
occ:1.00
 ND1 B:HIS418 2.2 56.5 1.0
SG B:CYS356 2.4 69.4 1.0
SG B:CYS353 2.5 75.4 1.0
SG B:CYS414 2.6 99.9 1.0
CB B:CYS414 3.0 71.0 1.0
CE1 B:HIS418 3.1 74.4 1.0
CG B:HIS418 3.2 76.0 1.0
CB B:CYS353 3.2 73.9 1.0
CB B:CYS356 3.4 64.0 1.0
CB B:HIS418 3.6 77.2 1.0
N B:CYS356 3.8 67.1 1.0
CA B:CYS356 4.1 78.1 1.0
CB B:HIS416 4.2 75.5 1.0
NE2 B:HIS418 4.2 75.8 1.0
CD2 B:HIS418 4.3 76.0 1.0
N B:HIS418 4.5 81.4 1.0
CA B:CYS414 4.5 75.0 1.0
O B:CYS356 4.6 82.3 1.0
CA B:HIS418 4.6 77.4 1.0
C B:CYS356 4.7 80.5 1.0
CA B:CYS353 4.7 72.7 1.0
N B:HIS416 4.7 83.8 1.0
CB B:GLN355 4.8 76.9 1.0
CA B:HIS416 4.8 80.0 1.0
SG B:CYS420 4.8 75.3 1.0
C B:HIS416 4.9 79.2 1.0
C B:GLN355 4.9 77.7 1.0
CG B:HIS416 4.9 82.2 1.0

Reference:

Z.M.Zhang, S.Liu, K.Lin, Y.Luo, J.J.Perry, Y.Wang, J.Song. Crystal Structure of Human Dna Methyltransferase 1. J.Mol.Biol. V. 427 2520 2015.
ISSN: ESSN 1089-8638
PubMed: 26070743
DOI: 10.1016/J.JMB.2015.06.001
Page generated: Sun Oct 27 10:09:25 2024

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