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

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

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 9 in 8eii

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Zinc binding site 1 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:180.4
occ:1.00
 CB A:CYS438 1.8 139.3 1.0
SG A:CYS455 2.3 124.6 1.0
SG A:CYS458 2.3 127.3 1.0
SG A:CYS435 2.3 133.8 1.0
SG A:CYS438 2.3 140.1 1.0
CA A:CYS438 3.3 137.9 1.0
CB A:CYS458 3.3 123.0 1.0
CB A:CYS455 3.6 124.0 1.0
CB A:CYS435 3.7 132.2 1.0
N A:CYS438 3.8 136.8 1.0
N A:CYS455 4.2 124.4 1.0
OG1 A:THR457 4.2 119.2 1.0
C A:CYS438 4.2 138.8 1.0
N A:CYS458 4.2 120.8 1.0
CA A:CYS458 4.4 119.5 1.0
CA A:CYS455 4.4 124.6 1.0
OG A:SER437 4.5 134.5 1.0
C A:SER437 4.5 134.5 1.0
N A:GLY439 4.7 141.2 1.0
O A:SER437 4.9 134.8 1.0
O A:CYS438 5.0 140.2 1.0
C A:CYS455 5.0 124.8 1.0

Zinc binding site 2 out of 9 in 8eii

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Zinc binding site 2 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:200.9
occ:1.00
 CB A:CYS500 2.2 134.9 1.0
SG A:CYS481 2.3 138.6 1.0
SG A:CYS478 2.3 129.0 1.0
SG A:CYS503 2.3 143.3 1.0
SG A:CYS500 2.3 137.7 1.0
CB A:CYS478 3.1 127.9 1.0
CB A:CYS481 3.2 137.3 1.0
CB A:CYS503 3.7 144.1 1.0
CA A:CYS500 3.7 134.1 1.0
N A:CYS481 3.9 136.2 1.0
O A:GLU483 4.0 138.7 1.0
CA A:CYS481 4.1 137.4 1.0
N A:CYS500 4.3 133.2 1.0
CA A:CYS478 4.5 126.5 1.0
C A:CYS500 4.7 135.6 1.0
N A:CYS482 4.7 132.1 1.0
C A:CYS481 4.7 137.2 1.0
N A:CYS503 4.7 143.8 1.0
CA A:CYS503 4.8 144.1 1.0
N A:GLU483 4.9 142.4 1.0

Zinc binding site 3 out of 9 in 8eii

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Zinc binding site 3 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:220.7
occ:1.00
 SG A:CYS527 2.3 152.3 1.0
SG A:CYS495 2.3 138.9 1.0
SG A:CYS524 2.3 142.9 1.0
SG A:CYS490 2.3 144.2 1.0
CB A:CYS495 3.3 138.1 1.0
CB A:CYS524 3.4 146.3 1.0
CB A:CYS490 3.6 144.7 1.0
CB A:CYS527 3.6 146.8 1.0
N A:CYS524 3.9 148.3 1.0
CA A:CYS524 4.2 149.2 1.0
CB A:ASN492 4.4 140.0 1.0
N A:CYS527 4.4 146.5 1.0
CA A:CYS527 4.5 146.6 1.0
O A:ARG497 4.6 131.8 1.0
CA A:CYS495 4.7 139.8 1.0
C A:CYS524 4.8 148.3 1.0
O A:CYS524 4.8 147.8 1.0
C A:CYS495 4.9 137.1 1.0
CA A:CYS490 5.0 142.8 1.0

Zinc binding site 4 out of 9 in 8eii

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Zinc binding site 4 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:110.2
occ:1.00
 SG B:CYS435 2.3 77.4 1.0
SG B:CYS455 2.3 64.7 1.0
SG B:CYS438 2.3 74.6 1.0
SG B:CYS458 2.3 52.3 1.0
CB B:CYS458 3.3 50.7 1.0
CB B:CYS435 3.5 66.9 1.0
CB B:CYS455 3.6 57.3 1.0
CB B:CYS438 4.0 72.6 1.0
N B:CYS455 4.1 57.8 1.0
N B:CYS438 4.1 67.3 1.0
N B:CYS458 4.3 53.7 1.0
CA B:CYS455 4.4 58.2 1.0
CA B:CYS458 4.4 54.8 1.0
CB B:SER437 4.5 71.3 1.0
O B:CYS455 4.7 59.1 1.0
CA B:CYS438 4.7 67.7 1.0
C B:SER437 4.7 71.2 1.0
N B:SER437 4.8 67.0 1.0
C B:CYS455 4.8 59.5 1.0
CA B:CYS435 4.9 69.5 1.0
CA B:SER437 4.9 69.8 1.0
NH2 B:ARG461 4.9 56.0 1.0

Zinc binding site 5 out of 9 in 8eii

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Zinc binding site 5 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:100.6
occ:1.00
 SG B:CYS500 2.3 79.4 1.0
SG B:CYS481 2.3 73.9 1.0
SG B:CYS503 2.3 83.0 1.0
SG B:CYS478 2.3 74.9 1.0
CB B:CYS478 2.9 64.9 1.0
CB B:CYS503 3.2 77.8 1.0
CB B:CYS500 3.4 72.6 1.0
CB B:CYS481 3.5 66.5 1.0
N B:CYS481 3.9 65.5 1.0
N B:CYS503 4.2 76.2 1.0
N B:CYS500 4.3 72.6 1.0
CA B:CYS503 4.3 77.5 1.0
CA B:CYS481 4.3 66.6 1.0
CA B:CYS500 4.3 71.8 1.0
O B:GLU483 4.4 80.9 1.0
CA B:CYS478 4.4 64.0 1.0
CB B:VAL480 4.4 60.4 1.0
O B:CYS500 4.7 79.3 1.0
C B:CYS500 4.8 76.1 1.0
N B:VAL480 4.9 65.0 1.0
OE1 B:GLU502 4.9 81.3 1.0
C B:VAL480 4.9 59.5 1.0
CG2 B:VAL480 5.0 60.9 1.0
CA B:VAL480 5.0 60.8 1.0

Zinc binding site 6 out of 9 in 8eii

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Zinc binding site 6 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:146.4
occ:1.00
 SG B:CYS527 2.3 89.8 1.0
SG B:CYS524 2.3 83.5 1.0
SG B:CYS495 2.3 92.7 1.0
SG B:CYS490 2.3 88.2 1.0
CB B:CYS495 3.0 93.4 1.0
CB B:CYS524 3.5 85.8 1.0
CB B:CYS490 3.6 86.2 1.0
CB B:CYS527 3.7 85.0 1.0
N B:CYS524 3.8 89.9 1.0
CA B:CYS524 4.2 86.2 1.0
N B:CYS527 4.4 85.1 1.0
CA B:CYS495 4.5 95.3 1.0
CA B:CYS527 4.5 85.5 1.0
C B:CYS524 4.7 86.3 1.0
O B:CYS524 4.7 88.8 1.0
C B:SER523 4.9 91.8 1.0
CA B:CYS490 4.9 85.1 1.0
C B:MET526 5.0 77.7 1.0
CB B:ASN492 5.0 91.7 1.0

Zinc binding site 7 out of 9 in 8eii

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Zinc binding site 7 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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 II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:178.8
occ:1.00
 SG C:CYS455 2.3 120.4 1.0
SG C:CYS438 2.3 123.0 1.0
SG C:CYS435 2.3 112.1 1.0
SG C:CYS458 2.3 120.8 1.0
CB C:CYS458 2.6 119.1 1.0
CB C:CYS438 2.9 121.4 1.0
CB C:CYS435 3.1 111.8 1.0
CB C:CYS455 3.6 117.7 1.0
N C:CYS438 3.7 120.9 1.0
OG C:SER437 3.8 121.8 1.0
CA C:CYS438 3.9 120.5 1.0
CA C:CYS458 3.9 118.1 1.0
N C:CYS458 4.1 116.8 1.0
N C:CYS455 4.1 116.7 1.0
OG1 C:THR457 4.4 119.0 1.0
CA C:CYS455 4.4 117.7 1.0
CA C:CYS435 4.6 113.6 1.0
O C:CYS455 4.6 115.6 1.0
C C:CYS438 4.7 121.6 1.0
C C:CYS455 4.8 117.7 1.0
C C:SER437 4.9 121.5 1.0
C C:CYS458 5.0 119.5 1.0
N C:GLY439 5.0 114.9 1.0

Zinc binding site 8 out of 9 in 8eii

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Zinc binding site 8 out of 9 in the Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II)


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

b:157.0
occ:1.00
 SG C:CYS503 2.3 118.3 1.0
SG C:CYS500 2.3 124.5 1.0
SG C:CYS481 2.3 122.5 1.0
SG C:CYS478 2.3 117.6 1.0
CB C:CYS481 2.8 122.2 1.0
CB C:CYS478 3.0 115.2 1.0
CB C:CYS503 3.1 116.3 1.0
N C:CYS481 3.2 121.5 1.0
CB C:CYS500 3.2 120.1 1.0
CA C:CYS481 3.6 122.0 1.0
N C:CYS500 4.1 120.5 1.0
CA C:CYS500 4.2 120.0 1.0
OE2 C:GLU502 4.2 114.0 1.0
CA C:CYS503 4.3 117.1 1.0
N C:CYS503 4.3 117.2 1.0
C C:VAL480 4.4 113.1 1.0
CB C:VAL480 4.4 113.2 1.0
N C:CYS482 4.4 126.0 1.0
C C:CYS481 4.5 122.0 1.0
CA C:CYS478 4.5 114.3 1.0
CD C:GLU502 4.5 114.4 1.0
N C:VAL480 4.7 112.0 1.0
CA C:VAL480 4.7 113.4 1.0
OE1 C:GLU502 4.9 114.4 1.0
C C:CYS478 4.9 114.2 1.0
C C:CYS500 5.0 120.2 1.0

Zinc binding site 9 out of 9 in 8eii

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


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

b:156.3
occ:1.00
 SG C:CYS495 2.3 119.5 1.0
SG C:CYS490 2.3 126.6 1.0
SG C:CYS524 2.3 115.2 1.0
SG C:CYS527 2.3 119.3 1.0
CB C:CYS490 3.2 124.7 1.0
CB C:CYS527 3.4 113.8 1.0
CB C:CYS524 3.4 112.4 1.0
CB C:CYS495 3.5 116.6 1.0
N C:CYS524 3.8 112.1 1.0
OD1 C:ASN492 3.9 117.6 1.0
CA C:CYS524 4.1 111.6 1.0
N C:CYS527 4.2 112.3 1.0
NH2 C:ARG497 4.2 118.6 1.0
NE C:ARG497 4.3 120.2 1.0
CA C:CYS527 4.3 113.4 1.0
CB C:ASN492 4.5 118.5 1.0
CB C:ARG497 4.5 119.2 1.0
CG C:ASN492 4.6 118.8 1.0
CA C:CYS490 4.7 125.0 1.0
CZ C:ARG497 4.7 120.3 1.0
O C:CYS524 4.7 108.1 1.0
C C:CYS524 4.8 109.3 1.0
CA C:CYS495 4.8 117.5 1.0
C C:SER523 4.9 112.0 1.0

Reference:

J.W.Lu, J.K.Song. Cryo-Em Structure of Human DNMT3B Homo-Tetramer (Form II) To Be Published.
Page generated: Wed Oct 30 19:48:01 2024

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