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Zinc in PDB 8eik: Cryo-Em Structure of Human DNMT3B Homo-Hexamer

Enzymatic activity of Cryo-Em Structure of Human DNMT3B Homo-Hexamer

All present enzymatic activity of Cryo-Em Structure of Human DNMT3B Homo-Hexamer:
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-Hexamer (pdb code 8eik). 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-Hexamer, PDB code: 8eik:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 8eik

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Zinc binding site 1 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


Mono view


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:204.7
occ:1.00
 CB A:CYS438 1.8 180.9 1.0
SG A:CYS455 2.3 174.3 1.0
SG A:CYS458 2.3 175.6 1.0
SG A:CYS438 2.3 183.0 1.0
SG A:CYS435 2.4 179.2 1.0
CB A:CYS458 3.0 173.5 1.0
CB A:CYS455 3.1 173.7 1.0
CA A:CYS438 3.2 180.2 1.0
N A:CYS438 3.7 179.3 1.0
CB A:CYS435 3.8 178.0 1.0
N A:CYS455 3.9 173.7 1.0
N A:CYS458 4.0 173.2 1.0
CA A:CYS455 4.0 173.5 1.0
CA A:CYS458 4.1 172.8 1.0
OG1 A:THR457 4.2 167.8 1.0
C A:CYS438 4.2 180.9 1.0
C A:CYS455 4.7 172.6 1.0
O A:CYS438 4.9 180.9 1.0
N A:GLY439 4.9 184.7 1.0
C A:SER437 4.9 169.2 1.0
O A:CYS455 5.0 172.2 1.0

Zinc binding site 2 out of 12 in 8eik

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Zinc binding site 2 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


Mono view


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:224.3
occ:1.00
 CB A:CYS500 2.1 190.1 1.0
SG A:CYS503 2.3 193.1 1.0
SG A:CYS481 2.3 166.0 1.0
SG A:CYS478 2.3 168.8 1.0
SG A:CYS500 2.3 191.8 1.0
CB A:CYS478 3.1 165.8 1.0
CA A:CYS500 3.6 189.6 1.0
N A:CYS481 3.7 166.2 1.0
CB A:CYS503 3.7 191.4 1.0
CB A:CYS481 3.8 166.3 1.0
CB A:VAL480 4.1 165.9 1.0
N A:CYS500 4.2 188.4 1.0
O A:GLU483 4.3 168.6 1.0
CA A:CYS481 4.4 166.3 1.0
C A:CYS500 4.5 190.3 1.0
CA A:CYS478 4.6 165.6 1.0
N A:CYS503 4.7 192.0 1.0
C A:VAL480 4.7 165.0 1.0
CA A:CYS503 4.8 192.3 1.0
CA A:VAL480 4.8 165.5 1.0
CG1 A:VAL480 4.8 165.3 1.0
N A:VAL480 4.8 165.3 1.0
O A:CYS500 4.9 190.3 1.0
CG2 A:VAL480 4.9 165.9 1.0

Zinc binding site 3 out of 12 in 8eik

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Zinc binding site 3 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:211.9
occ:1.00
 SG A:CYS527 2.3 189.1 1.0
SG A:CYS524 2.3 185.8 1.0
SG A:CYS490 2.3 176.7 1.0
SG A:CYS495 2.3 172.0 1.0
CB A:CYS490 3.4 176.2 1.0
CB A:CYS495 3.5 172.8 1.0
CB A:CYS524 3.6 186.3 1.0
CB A:CYS527 3.6 187.5 1.0
N A:CYS524 3.9 186.6 1.0
CB A:ASN492 4.0 180.3 1.0
CA A:CYS524 4.3 186.7 1.0
N A:CYS527 4.4 187.0 1.0
CA A:CYS527 4.5 187.0 1.0
O A:CYS524 4.7 186.5 1.0
CB A:ARG497 4.8 159.6 1.0
CA A:CYS490 4.8 175.6 1.0
C A:CYS524 4.8 186.5 1.0
CA A:CYS495 4.9 172.2 1.0
CG A:ASN492 4.9 180.5 1.0
C A:SER523 5.0 185.1 1.0

Zinc binding site 4 out of 12 in 8eik

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Zinc binding site 4 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:162.9
occ:1.00
 CB B:CYS438 1.9 113.8 1.0
SG B:CYS455 2.3 105.2 1.0
SG B:CYS458 2.3 108.4 1.0
SG B:CYS438 2.3 118.1 1.0
SG B:CYS435 2.3 103.3 1.0
CB B:CYS458 3.1 105.9 1.0
CA B:CYS438 3.3 111.8 1.0
CB B:CYS455 3.4 101.0 1.0
OG1 B:THR457 3.6 105.5 1.0
CB B:CYS435 3.8 101.0 1.0
N B:CYS438 3.8 110.5 1.0
N B:CYS458 4.0 106.3 1.0
CA B:CYS458 4.1 106.7 1.0
N B:CYS455 4.3 99.2 1.0
C B:CYS438 4.3 111.8 1.0
CA B:CYS455 4.3 99.8 1.0
N B:GLY439 4.8 111.7 1.0
C B:THR457 4.8 103.6 1.0
C B:CYS455 4.8 101.0 1.0
O B:CYS455 4.9 103.7 1.0
NH1 B:ARG440 4.9 118.0 1.0
CB B:THR457 4.9 106.4 1.0

Zinc binding site 5 out of 12 in 8eik

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Zinc binding site 5 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn903

b:175.2
occ:1.00
 CB B:CYS500 2.0 115.0 1.0
SG B:CYS503 2.3 115.0 1.0
SG B:CYS481 2.3 112.2 1.0
SG B:CYS478 2.3 119.0 1.0
SG B:CYS500 2.3 116.8 1.0
CB B:CYS478 3.1 111.5 1.0
CA B:CYS500 3.5 115.3 1.0
CB B:CYS481 3.6 109.1 1.0
CB B:CYS503 3.7 118.2 1.0
N B:CYS481 3.7 107.3 1.0
O B:GLU483 3.9 117.4 1.0
N B:CYS500 4.1 114.3 1.0
CB B:VAL480 4.2 110.8 1.0
CA B:CYS481 4.3 108.5 1.0
C B:CYS500 4.4 117.7 1.0
N B:CYS503 4.5 118.0 1.0
CA B:CYS478 4.6 110.1 1.0
CA B:CYS503 4.7 118.2 1.0
C B:VAL480 4.7 109.5 1.0
O B:CYS500 4.7 117.9 1.0
CG B:GLU502 4.7 119.1 1.0
CA B:VAL480 4.8 112.1 1.0
N B:VAL480 4.8 113.3 1.0
CG1 B:VAL480 4.9 109.8 1.0
N B:GLU483 5.0 116.0 1.0

Zinc binding site 6 out of 12 in 8eik

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Zinc binding site 6 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn904

b:157.3
occ:1.00
 SG B:CYS524 2.3 120.3 1.0
SG B:CYS490 2.3 113.0 1.0
SG B:CYS527 2.3 120.3 1.0
SG B:CYS495 2.3 121.6 1.0
CB B:CYS490 3.1 108.1 1.0
CB B:CYS495 3.3 118.5 1.0
CB B:CYS527 3.5 118.3 1.0
CB B:CYS524 3.6 118.4 1.0
N B:CYS524 4.2 117.4 1.0
N B:CYS527 4.3 118.0 1.0
CA B:CYS524 4.4 118.2 1.0
CA B:CYS527 4.4 118.6 1.0
CA B:CYS490 4.5 109.3 1.0
CA B:CYS495 4.6 117.9 1.0
O B:CYS495 4.6 118.7 1.0
O B:CYS524 4.7 119.1 1.0
C B:CYS495 4.8 117.3 1.0
C B:CYS524 4.8 118.5 1.0
CB B:MET526 4.9 113.0 1.0
CB B:ASN492 5.0 109.2 1.0

Zinc binding site 7 out of 12 in 8eik

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Zinc binding site 7 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:241.3
occ:1.00
 CB C:CYS438 1.9 202.4 1.0
SG C:CYS455 2.3 182.1 1.0
SG C:CYS458 2.3 179.6 1.0
SG C:CYS438 2.3 204.3 1.0
SG C:CYS435 2.3 180.0 1.0
CB C:CYS458 2.9 179.6 1.0
CB C:CYS455 3.3 181.4 1.0
CA C:CYS438 3.4 202.0 1.0
CB C:CYS435 3.7 177.9 1.0
OG1 C:THR457 3.9 175.1 1.0
N C:CYS438 3.9 201.1 1.0
N C:CYS458 3.9 179.7 1.0
CA C:CYS458 4.0 179.9 1.0
N C:CYS455 4.2 181.5 1.0
CA C:CYS455 4.3 181.5 1.0
C C:CYS438 4.4 202.4 1.0
O C:CYS455 4.8 180.5 1.0
C C:CYS455 4.8 181.2 1.0

Zinc binding site 8 out of 12 in 8eik

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Zinc binding site 8 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn903

b:251.7
occ:1.00
 CB C:CYS500 2.2 192.8 1.0
SG C:CYS478 2.3 189.8 1.0
SG C:CYS503 2.3 184.9 1.0
SG C:CYS481 2.3 202.6 1.0
SG C:CYS500 2.3 193.9 1.0
CB C:CYS478 3.2 189.1 1.0
N C:CYS481 3.7 199.6 1.0
CA C:CYS500 3.7 192.6 1.0
CB C:CYS503 3.8 184.2 1.0
CB C:CYS481 3.8 201.0 1.0
O C:GLU483 4.1 199.6 1.0
OE2 C:GLU502 4.1 186.5 1.0
CB C:VAL480 4.2 194.5 1.0
N C:CYS500 4.3 191.8 1.0
CA C:CYS481 4.3 200.1 1.0
CG2 C:VAL480 4.6 193.9 1.0
CD C:GLU502 4.6 187.1 1.0
CA C:CYS478 4.6 189.5 1.0
C C:CYS500 4.6 193.2 1.0
N C:GLU483 4.7 200.2 1.0
C C:VAL480 4.7 193.3 1.0
N C:VAL480 4.8 195.2 1.0
CA C:VAL480 4.8 194.4 1.0
N C:CYS482 4.8 194.8 1.0
N C:CYS503 4.8 184.3 1.0
CA C:CYS503 4.8 184.3 1.0
OE1 C:GLU502 4.9 187.6 1.0
O C:CYS500 5.0 192.7 1.0

Zinc binding site 9 out of 12 in 8eik

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Zinc binding site 9 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn904

b:246.4
occ:1.00
 SG C:CYS524 2.3 197.7 1.0
SG C:CYS495 2.3 186.8 1.0
SG C:CYS490 2.3 186.6 1.0
SG C:CYS527 2.3 202.5 1.0
CB C:CYS495 3.4 186.8 1.0
CB C:CYS490 3.4 185.7 1.0
CB C:CYS527 3.6 200.5 1.0
CB C:CYS524 3.7 197.0 1.0
N C:CYS524 4.0 197.2 1.0
N C:CYS527 4.2 199.9 1.0
CB C:ASN492 4.3 184.1 1.0
CA C:CYS524 4.4 197.7 1.0
CA C:CYS527 4.4 200.5 1.0
O C:CYS495 4.7 188.2 1.0
CA C:CYS495 4.7 187.3 1.0
CA C:CYS490 4.8 185.4 1.0
O C:CYS524 4.9 197.7 1.0
C C:CYS524 4.9 197.8 1.0
C C:CYS495 5.0 187.8 1.0
O C:ASN492 5.0 186.1 1.0

Zinc binding site 10 out of 12 in 8eik

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Zinc binding site 10 out of 12 in the Cryo-Em Structure of Human DNMT3B Homo-Hexamer


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-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn901

b:170.6
occ:1.00
 O E:CYS455 2.1 165.4 1.0
N E:CYS455 2.2 167.1 1.0
CB E:CYS458 2.5 172.7 1.0
C E:CYS455 2.8 166.1 1.0
C E:LEU454 2.8 169.5 1.0
CA E:CYS455 2.9 166.8 1.0
N E:ARG459 3.1 178.6 1.0
SG E:CYS455 3.1 165.9 1.0
CA E:LEU454 3.1 169.1 1.0
CA E:CYS458 3.2 173.7 1.0
CB E:LEU454 3.2 169.2 1.0
N E:CYS458 3.2 174.8 1.0
SG E:CYS435 3.4 139.2 1.0
C E:CYS458 3.4 172.6 1.0
CB E:CYS455 3.5 166.3 1.0
CD2 E:LEU454 3.7 168.4 1.0
O E:LEU454 3.7 169.8 1.0
SG E:CYS458 3.9 170.3 1.0
CG E:LEU454 4.1 168.6 1.0
N E:GLN456 4.1 169.1 1.0
CA E:ARG459 4.2 178.6 1.0
CB E:ARG459 4.4 178.4 1.0
O E:CYS458 4.4 173.0 1.0
C E:THR457 4.5 173.6 1.0
CB E:CYS435 4.5 141.6 1.0
N E:LEU454 4.6 169.2 1.0
N E:THR457 4.7 170.6 1.0
CA E:GLN456 4.8 169.3 1.0
C E:GLN456 4.8 168.6 1.0
OG1 E:THR457 5.0 171.7 1.0

Reference:

J.W.Lu, J.K.Song. Cryo-Em Structure of Human DNMT3B Homo-Hexamer To Be Published.
Page generated: Thu Dec 28 12:58:22 2023

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