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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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

Go back to Zinc Binding Sites List in 8eik
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: Wed Oct 30 19:49:05 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