Zinc in PDB 8eih: Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)

Enzymatic activity of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)

All present enzymatic activity of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I):
2.1.1.37;

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) (pdb code 8eih). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I), PDB code: 8eih:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 8eih

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Zinc binding site 1 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:189.5
occ:1.00
 SG A:CYS455 2.3 127.1 1.0
SG A:CYS435 2.3 126.7 1.0
SG A:CYS438 2.3 137.3 1.0
SG A:CYS458 2.3 133.7 1.0
OG A:SER437 3.0 134.8 1.0
CB A:CYS458 3.1 128.5 1.0
CB A:CYS455 3.4 125.0 1.0
CB A:CYS435 3.4 125.6 1.0
CB A:CYS438 3.9 137.4 1.0
N A:CYS438 4.1 137.9 1.0
N A:CYS455 4.1 124.7 1.0
CA A:CYS455 4.2 125.1 1.0
CA A:CYS458 4.3 125.9 1.0
N A:CYS458 4.3 125.3 1.0
CB A:SER437 4.3 132.7 1.0
CA A:CYS438 4.6 138.5 1.0
CG2 A:THR457 4.7 128.6 1.0
C A:SER437 4.7 133.3 1.0
CA A:CYS435 4.8 125.2 1.0
C A:CYS455 4.8 125.9 1.0
CA A:SER437 4.9 132.7 1.0
N A:SER437 4.9 130.7 1.0

Zinc binding site 2 out of 12 in 8eih

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Zinc binding site 2 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:187.7
occ:1.00
 CB A:CYS500 2.1 141.4 1.0
SG A:CYS481 2.3 128.1 1.0
SG A:CYS503 2.3 142.6 1.0
SG A:CYS478 2.3 130.8 1.0
SG A:CYS500 2.3 142.4 1.0
CB A:CYS478 3.3 124.8 1.0
CA A:CYS500 3.6 140.5 1.0
CB A:CYS503 3.7 145.1 1.0
CB A:CYS481 3.7 125.6 1.0
O A:GLU483 3.8 134.7 1.0
N A:CYS481 4.0 123.3 1.0
N A:CYS500 4.2 140.9 1.0
CA A:CYS481 4.4 125.3 1.0
C A:CYS500 4.5 142.4 1.0
C A:GLU483 4.6 133.9 1.0
N A:CYS503 4.6 145.5 1.0
CA A:CYS503 4.7 145.8 1.0
CA A:CYS478 4.7 123.1 1.0
N A:CYS482 4.8 121.7 1.0
N A:GLU483 4.8 133.2 1.0
CB A:VAL480 4.9 122.5 1.0
O A:CYS500 4.9 142.7 1.0
C A:CYS481 4.9 125.5 1.0

Zinc binding site 3 out of 12 in 8eih

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Zinc binding site 3 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:221.2
occ:1.00
 SG A:CYS527 2.3 153.3 1.0
SG A:CYS524 2.3 149.1 1.0
SG A:CYS495 2.3 138.5 1.0
SG A:CYS490 2.3 133.2 1.0
CB A:CYS495 3.1 135.2 1.0
CB A:CYS490 3.5 134.6 1.0
CB A:CYS524 3.7 149.1 1.0
CB A:CYS527 3.8 152.4 1.0
N A:CYS524 4.0 149.6 1.0
CB A:ASN492 4.4 134.3 1.0
CA A:CYS524 4.4 149.9 1.0
N A:CYS527 4.4 151.4 1.0
CA A:CYS495 4.5 134.4 1.0
CA A:CYS527 4.6 152.1 1.0
C A:MET526 4.8 141.0 1.0
C A:CYS524 4.9 149.9 1.0
O A:CYS495 4.9 133.8 1.0
CA A:CYS490 4.9 132.8 1.0
O A:CYS524 4.9 149.7 1.0
C A:CYS495 4.9 134.1 1.0
CB A:MET526 5.0 140.4 1.0

Zinc binding site 4 out of 12 in 8eih

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Zinc binding site 4 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:132.1
occ:1.00
 SG B:CYS458 2.3 82.5 1.0
SG B:CYS435 2.3 107.1 1.0
SG B:CYS455 2.3 89.9 1.0
SG B:CYS438 2.3 105.4 1.0
OG B:SER437 3.1 102.9 1.0
CB B:CYS458 3.2 75.1 1.0
CB B:CYS435 3.4 102.1 1.0
CB B:CYS455 3.6 87.9 1.0
CB B:CYS438 3.9 105.9 1.0
N B:CYS455 4.0 84.8 1.0
N B:CYS438 4.1 105.1 1.0
CA B:CYS455 4.4 87.0 1.0
CA B:CYS458 4.4 71.0 1.0
CB B:SER437 4.4 101.9 1.0
N B:CYS458 4.4 71.6 1.0
CA B:CYS438 4.6 105.5 1.0
C B:SER437 4.8 101.7 1.0
CA B:CYS435 4.8 101.7 1.0
CG2 B:THR457 4.9 74.0 1.0
NH2 B:ARG461 4.9 68.7 1.0
N B:SER437 4.9 100.7 1.0
CA B:SER437 4.9 101.2 1.0
C B:CYS455 5.0 88.2 1.0

Zinc binding site 5 out of 12 in 8eih

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Zinc binding site 5 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn903

b:161.9
occ:1.00
 CB B:CYS500 2.1 116.7 1.0
SG B:CYS503 2.3 114.5 1.0
SG B:CYS481 2.3 99.1 1.0
SG B:CYS478 2.3 103.6 1.0
SG B:CYS500 2.3 119.1 1.0
CB B:CYS478 3.0 98.9 1.0
CB B:CYS503 3.5 118.0 1.0
CA B:CYS500 3.6 116.4 1.0
CB B:CYS481 3.8 96.2 1.0
O B:GLU483 4.1 105.1 1.0
N B:CYS481 4.1 96.9 1.0
N B:CYS500 4.1 116.9 1.0
CA B:CYS481 4.5 96.4 1.0
CA B:CYS478 4.5 95.3 1.0
C B:CYS500 4.5 117.5 1.0
N B:CYS503 4.6 118.3 1.0
CA B:CYS503 4.6 117.9 1.0
CB B:VAL480 4.8 94.0 1.0
C B:GLU483 4.8 104.7 1.0

Zinc binding site 6 out of 12 in 8eih

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Zinc binding site 6 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn904

b:149.5
occ:1.00
 SG B:CYS527 2.3 118.6 1.0
SG B:CYS524 2.3 115.6 1.0
SG B:CYS495 2.3 117.4 1.0
SG B:CYS490 2.3 114.8 1.0
CB B:CYS495 3.2 114.1 1.0
CB B:CYS490 3.4 114.9 1.0
CB B:CYS524 3.6 115.8 1.0
CB B:CYS527 3.7 118.1 1.0
N B:CYS524 4.1 117.9 1.0
CA B:CYS524 4.4 115.6 1.0
N B:CYS527 4.4 119.5 1.0
O B:CYS495 4.4 112.2 1.0
CA B:CYS495 4.5 114.2 1.0
CA B:CYS527 4.6 118.6 1.0
C B:CYS495 4.7 112.1 1.0
CA B:CYS490 4.8 115.1 1.0
C B:CYS524 4.9 116.1 1.0
C B:MET526 5.0 110.0 1.0

Zinc binding site 7 out of 12 in 8eih

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Zinc binding site 7 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:159.7
occ:1.00
 SG C:CYS455 2.3 120.7 1.0
SG C:CYS435 2.3 137.7 1.0
SG C:CYS458 2.3 118.2 1.0
CB C:CYS438 2.7 135.0 1.0
CB C:CYS435 3.0 134.6 1.0
CB C:CYS458 3.3 115.1 1.0
CB C:CYS455 3.4 117.8 1.0
CA C:CYS438 3.8 134.3 1.0
N C:CYS438 3.9 134.3 1.0
CB C:ARG440 4.2 140.3 1.0
CA C:CYS435 4.4 134.1 1.0
C C:CYS438 4.5 135.5 1.0
CA C:CYS458 4.6 113.8 1.0
N C:ARG440 4.6 141.8 1.0
CA C:CYS455 4.6 117.9 1.0
N C:CYS458 4.6 112.1 1.0
N C:CYS455 4.6 116.2 1.0
N C:GLY439 4.8 139.9 1.0
CG2 C:THR457 4.8 113.2 1.0
C C:SER437 4.9 131.3 1.0

Zinc binding site 8 out of 12 in 8eih

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Zinc binding site 8 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:160.8
occ:1.00
 CB C:CYS500 2.1 130.5 1.0
SG C:CYS481 2.3 122.8 1.0
SG C:CYS503 2.3 134.4 1.0
SG C:CYS500 2.3 131.7 1.0
SG C:CYS478 2.3 120.8 1.0
CB C:CYS478 3.2 109.9 1.0
CA C:CYS500 3.5 129.2 1.0
CB C:CYS481 3.8 117.2 1.0
CB C:CYS503 3.8 138.3 1.0
N C:CYS500 3.9 126.6 1.0
N C:CYS481 4.0 113.6 1.0
O C:GLU483 4.1 125.0 1.0
CA C:CYS481 4.5 115.4 1.0
NH2 C:ARG485 4.5 133.9 1.0
C C:CYS500 4.6 132.5 1.0
CB C:VAL480 4.6 110.3 1.0
CA C:CYS478 4.7 110.0 1.0
NH1 C:ARG485 4.7 135.1 1.0
N C:CYS503 4.8 138.0 1.0
N C:VAL501 4.9 137.3 1.0
CA C:CYS503 4.9 139.0 1.0

Zinc binding site 9 out of 12 in 8eih

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Zinc binding site 9 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn903

b:166.2
occ:1.00
 SG C:CYS524 2.3 146.4 1.0
SG C:CYS495 2.3 138.4 1.0
SG C:CYS527 2.3 141.7 1.0
SG C:CYS490 2.3 131.1 1.0
CB C:CYS495 3.3 136.4 1.0
CB C:CYS524 3.4 143.9 1.0
CB C:CYS490 3.7 132.0 1.0
CB C:CYS527 3.7 140.2 1.0
N C:CYS524 3.9 145.5 1.0
O C:CYS495 4.1 137.1 1.0
CA C:CYS524 4.2 144.8 1.0
N C:CYS527 4.2 140.5 1.0
CB C:ASN492 4.5 139.1 1.0
CA C:CYS527 4.5 140.6 1.0
CA C:CYS495 4.6 135.8 1.0
C C:CYS495 4.6 136.0 1.0
ND2 C:ASN492 4.6 139.1 1.0
C C:CYS524 4.7 143.5 1.0
C C:MET526 4.7 136.1 1.0
CB C:MET526 4.8 135.2 1.0
O C:CYS524 4.9 143.2 1.0
N C:MET526 4.9 135.2 1.0

Zinc binding site 10 out of 12 in 8eih

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Zinc binding site 10 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:247.0
occ:1.00
 O D:GLY453 2.3 235.3 1.0
CA D:LEU454 2.5 233.7 1.0
C D:GLY453 3.1 235.2 1.0
N D:LEU436 3.1 227.0 1.0
N D:LEU454 3.2 234.3 1.0
N D:CYS455 3.2 222.0 1.0
CB D:CYS435 3.2 230.1 1.0
C D:LEU454 3.3 234.0 1.0
N D:SER437 3.3 223.6 1.0
CA D:CYS435 3.5 229.9 1.0
CB D:LEU454 3.5 232.9 1.0
CB D:CYS458 3.7 202.2 1.0
C D:CYS435 3.7 229.8 1.0
CB D:SER437 4.0 223.2 1.0
N D:CYS438 4.0 221.1 1.0
CA D:LEU436 4.0 225.9 1.0
C D:LEU436 4.1 225.9 1.0
CA D:SER437 4.2 223.2 1.0
O D:LEU454 4.5 234.2 1.0
CA D:CYS455 4.5 220.6 1.0
CA D:GLY453 4.5 234.4 1.0
CB D:LEU436 4.5 225.3 1.0
C D:SER437 4.6 222.9 1.0
CB D:CYS455 4.8 219.8 1.0
N D:CYS435 4.9 229.0 1.0
O D:CYS435 4.9 229.2 1.0
N D:GLY439 5.0 227.0 1.0

Reference:

J.W.Lu, J.K.Song. Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form I) To Be Published.
Page generated: Wed Oct 30 19:47:56 2024

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