Zinc in PDB 7o45: Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase

Enzymatic activity of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase

All present enzymatic activity of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase:
2.1.1.37;

Protein crystallography data

The structure of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase, PDB code: 7o45 was solved by K.M.Boyko, A.Y.Nikolaeva, A.N.Bonchuk, P.G.Georgiev, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.38 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.282, 89.943, 92.195, 90, 90, 90
R / Rfree (%) 20 / 22.8

Other elements in 7o45:

The structure of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase also contains other interesting chemical elements:

Bromine (Br) 3 atoms

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase (pdb code 7o45). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase, PDB code: 7o45:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 7o45

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Zinc binding site 1 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:43.4
occ:1.00
 SG A:CYS455 2.3 47.3 1.0
SG A:CYS458 2.3 46.6 1.0
SG A:CYS435 2.3 43.1 1.0
SG A:CYS438 2.3 51.4 1.0
CB A:CYS458 3.2 44.7 1.0
CB A:CYS435 3.2 44.2 1.0
CB A:CYS438 3.3 51.6 1.0
CB A:CYS455 3.4 46.1 1.0
N A:CYS438 3.8 48.3 1.0
N A:CYS455 4.0 42.4 1.0
CA A:CYS438 4.1 49.6 1.0
CA A:CYS455 4.2 44.6 1.0
N A:CYS458 4.3 46.0 1.0
CA A:CYS458 4.3 44.8 1.0
CB A:SER437 4.4 45.7 1.0
CA A:CYS435 4.6 41.9 1.0
OG A:SER437 4.7 49.9 1.0
C A:SER437 4.7 46.8 1.0
CB A:ARG440 4.8 59.7 1.0
C A:CYS438 4.8 51.4 1.0
C A:CYS455 4.9 45.9 1.0
O A:CYS455 4.9 41.2 1.0
OG1 A:THR457 4.9 54.7 1.0
CA A:SER437 5.0 44.3 1.0
N A:GLY439 5.0 52.7 1.0

Zinc binding site 2 out of 12 in 7o45

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Zinc binding site 2 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:42.8
occ:1.00
 SG A:CYS503 2.3 47.3 1.0
SG A:CYS481 2.3 47.6 1.0
SG A:CYS478 2.4 41.5 1.0
SG A:CYS500 2.4 46.2 1.0
CB A:CYS478 3.1 42.0 1.0
CB A:CYS503 3.3 48.1 1.0
CB A:CYS500 3.4 46.3 1.0
CB A:CYS481 3.4 45.7 1.0
N A:CYS481 3.8 41.9 1.0
N A:CYS500 3.9 44.9 1.0
CA A:CYS481 4.1 44.6 1.0
CA A:CYS500 4.2 46.3 1.0
N A:CYS503 4.3 50.8 1.0
CA A:CYS503 4.4 47.7 1.0
CB A:VAL480 4.5 40.4 1.0
CA A:CYS478 4.6 42.6 1.0
NH2 A:ARG417 4.7 53.9 1.0
O A:CYS500 4.8 44.6 1.0
C A:VAL480 4.8 40.8 1.0
C A:CYS500 4.8 47.4 1.0
CB A:GLU483 4.8 56.9 1.0
C A:CYS481 4.8 47.3 1.0
N A:CYS482 5.0 45.2 1.0
N A:VAL480 5.0 38.0 1.0
CA A:VAL480 5.0 40.0 1.0

Zinc binding site 3 out of 12 in 7o45

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Zinc binding site 3 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:36.9
occ:1.00
 SG A:CYS527 2.3 39.3 1.0
SG A:CYS490 2.3 42.2 1.0
SG A:CYS495 2.3 37.7 1.0
SG A:CYS524 2.3 38.2 1.0
CB A:CYS490 3.1 44.4 1.0
CB A:CYS495 3.2 39.0 1.0
CB A:CYS524 3.4 38.8 1.0
CB A:CYS527 3.4 41.3 1.0
N A:CYS524 3.8 41.5 1.0
CA A:CYS524 4.1 38.9 1.0
N A:CYS527 4.1 40.1 1.0
CA A:CYS527 4.3 39.6 1.0
O A:CYS524 4.5 38.7 1.0
C A:CYS524 4.5 37.5 1.0
CA A:CYS490 4.5 44.0 1.0
O A:HOH738 4.6 53.0 1.0
CB A:ASN492 4.6 45.0 1.0
CA A:CYS495 4.6 39.2 1.0
CB A:ARG497 4.8 41.9 1.0
CB A:MET526 4.8 40.2 1.0
C A:MET526 4.9 40.2 1.0
N A:CYS496 4.9 40.7 1.0
N A:ARG497 4.9 41.9 1.0
C A:SER523 5.0 40.9 1.0

Zinc binding site 4 out of 12 in 7o45

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Zinc binding site 4 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:47.7
occ:1.00
 SG B:CYS455 2.3 56.5 1.0
SG B:CYS458 2.3 56.1 1.0
SG B:CYS438 2.3 56.4 1.0
SG B:CYS435 2.4 47.1 1.0
CB B:CYS458 3.2 56.5 1.0
CB B:CYS435 3.2 51.5 1.0
CB B:CYS438 3.2 58.1 1.0
CB B:CYS455 3.4 56.1 1.0
N B:CYS438 3.7 53.6 1.0
CA B:CYS438 4.0 55.3 1.0
N B:CYS455 4.0 50.2 1.0
CA B:CYS455 4.2 53.4 1.0
N B:CYS458 4.3 59.4 1.0
CA B:CYS458 4.3 57.1 1.0
CB B:SER437 4.4 53.2 1.0
C B:SER437 4.6 53.7 1.0
CA B:CYS435 4.6 47.9 1.0
OG B:SER437 4.6 55.3 1.0
C B:CYS438 4.8 55.2 1.0
CB B:ARG440 4.8 68.6 1.0
C B:CYS455 4.9 55.0 1.0
O B:CYS455 4.9 51.2 1.0
CA B:SER437 4.9 51.8 1.0
N B:GLY439 4.9 53.7 1.0

Zinc binding site 5 out of 12 in 7o45

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Zinc binding site 5 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:45.9
occ:1.00
 SG B:CYS503 2.3 51.8 1.0
SG B:CYS481 2.3 53.6 1.0
SG B:CYS500 2.3 57.3 1.0
SG B:CYS478 2.3 48.0 1.0
CB B:CYS478 3.1 49.9 1.0
CB B:CYS503 3.3 50.6 1.0
CB B:CYS500 3.3 56.0 1.0
CB B:CYS481 3.4 51.0 1.0
N B:CYS481 3.8 45.3 1.0
N B:CYS500 3.9 50.6 1.0
CA B:CYS500 4.1 54.2 1.0
CA B:CYS481 4.2 49.6 1.0
N B:CYS503 4.2 53.2 1.0
CA B:CYS503 4.3 50.5 1.0
CA B:CYS478 4.6 46.2 1.0
CB B:VAL480 4.6 43.8 1.0
NH2 B:ARG417 4.7 50.8 1.0
O B:CYS500 4.7 50.3 1.0
C B:CYS500 4.8 53.3 1.0
CA B:GLY484 4.8 79.0 1.0
C B:CYS481 4.9 50.5 1.0
C B:VAL480 4.9 43.8 1.0
N B:CYS482 5.0 52.0 1.0
N B:GLY484 5.0 76.2 1.0

Zinc binding site 6 out of 12 in 7o45

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Zinc binding site 6 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:43.1
occ:1.00
 SG B:CYS524 2.3 44.1 1.0
SG B:CYS527 2.3 45.9 1.0
SG B:CYS490 2.3 49.0 1.0
SG B:CYS495 2.3 45.0 1.0
CB B:CYS490 3.2 48.4 1.0
CB B:CYS495 3.2 45.7 1.0
CB B:CYS524 3.4 45.6 1.0
CB B:CYS527 3.4 46.9 1.0
N B:CYS524 3.8 46.0 1.0
N B:CYS527 4.0 45.0 1.0
CA B:CYS524 4.1 45.4 1.0
ND2 B:ASN492 4.2 44.1 0.5
CA B:CYS527 4.3 45.3 1.0
O B:CYS524 4.5 42.3 1.0
C B:CYS524 4.5 42.9 1.0
CA B:CYS490 4.6 49.6 1.0
CA B:CYS495 4.6 44.7 1.0
CB B:ASN492 4.7 45.7 0.5
CB B:ASN492 4.7 46.4 0.5
CB B:ARG497 4.8 44.9 1.0
CB B:MET526 4.8 39.6 1.0
C B:MET526 4.8 42.7 1.0
N B:ARG497 4.9 46.5 1.0
C B:SER523 5.0 47.8 1.0
N B:CYS496 5.0 45.4 1.0
CG B:ASN492 5.0 47.0 0.5

Zinc binding site 7 out of 12 in 7o45

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Zinc binding site 7 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:40.8
occ:1.00
 SG C:CYS458 2.3 42.5 1.0
SG C:CYS455 2.3 45.2 1.0
SG C:CYS435 2.3 43.3 1.0
SG C:CYS438 2.3 45.0 1.0
CB C:CYS458 3.2 40.5 1.0
CB C:CYS435 3.2 43.5 1.0
CB C:CYS438 3.2 44.5 1.0
CB C:CYS455 3.4 44.2 1.0
N C:CYS438 3.7 42.9 1.0
N C:CYS455 4.0 42.0 1.0
CA C:CYS438 4.0 44.0 1.0
CA C:CYS455 4.2 42.3 1.0
N C:CYS458 4.3 42.1 1.0
CA C:CYS458 4.3 40.0 1.0
NH1 C:ARG440 4.4 84.9 1.0
CB C:SER437 4.4 41.6 1.0
CG C:ARG440 4.5 69.2 1.0
OG C:SER437 4.6 43.0 1.0
CA C:CYS435 4.6 41.7 1.0
C C:SER437 4.6 42.2 1.0
C C:CYS438 4.8 45.4 1.0
C C:CYS455 4.9 42.9 1.0
CA C:SER437 4.9 40.6 1.0
O C:CYS455 4.9 38.8 1.0
N C:GLY439 4.9 46.8 1.0

Zinc binding site 8 out of 12 in 7o45

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Zinc binding site 8 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:40.2
occ:1.00
 SG C:CYS481 2.3 44.9 1.0
SG C:CYS500 2.3 44.0 1.0
SG C:CYS503 2.3 43.9 1.0
SG C:CYS478 2.4 38.3 1.0
CB C:CYS478 3.1 38.7 1.0
CB C:CYS503 3.3 44.3 1.0
CB C:CYS500 3.4 44.2 1.0
CB C:CYS481 3.4 43.4 1.0
N C:CYS481 3.8 40.0 1.0
N C:CYS500 3.9 42.0 1.0
CA C:CYS500 4.1 44.0 1.0
CA C:CYS481 4.2 41.5 1.0
N C:CYS503 4.2 46.0 1.0
CA C:CYS503 4.3 45.6 1.0
CB C:VAL480 4.5 40.1 1.0
CB C:GLU483 4.6 53.6 1.0
CA C:CYS478 4.6 37.1 1.0
O C:CYS500 4.7 43.2 1.0
NH2 C:ARG417 4.7 50.2 1.0
C C:CYS500 4.7 46.7 1.0
C C:VAL480 4.8 39.5 1.0
C C:CYS481 4.8 42.1 1.0
N C:CYS482 5.0 42.7 1.0
N C:VAL480 5.0 36.9 1.0
CA C:VAL480 5.0 39.8 1.0

Zinc binding site 9 out of 12 in 7o45

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Zinc binding site 9 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn603

b:38.1
occ:1.00
 SG C:CYS495 2.3 37.7 1.0
SG C:CYS490 2.3 41.3 1.0
SG C:CYS524 2.3 41.8 1.0
SG C:CYS527 2.3 41.0 1.0
CB C:CYS490 3.2 42.9 1.0
CB C:CYS495 3.2 39.8 1.0
CB C:CYS524 3.4 42.2 1.0
CB C:CYS527 3.4 42.7 1.0
N C:CYS524 3.8 43.1 1.0
N C:CYS527 4.1 40.9 1.0
CA C:CYS524 4.1 43.3 1.0
O C:HOH729 4.3 45.3 1.0
CA C:CYS527 4.4 42.0 1.0
O C:CYS524 4.5 41.2 1.0
C C:CYS524 4.6 42.3 1.0
CB C:ASN492 4.6 40.0 0.5
CA C:CYS490 4.6 42.1 1.0
ND2 C:ASN492 4.6 47.3 0.5
CA C:CYS495 4.6 38.8 1.0
CB C:ASN492 4.7 43.4 0.5
CB C:MET526 4.7 38.4 1.0
CB C:ARG497 4.8 39.6 1.0
C C:MET526 4.8 40.4 1.0
N C:ARG497 5.0 41.3 1.0
N C:CYS496 5.0 39.6 1.0
C C:SER523 5.0 45.7 1.0

Zinc binding site 10 out of 12 in 7o45

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Zinc binding site 10 out of 12 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:89.3
occ:0.50
 OG D:SER437 2.2 118.1 1.0
SG D:CYS455 2.3 119.8 1.0
SG D:CYS438 2.3 118.5 1.0
SG D:CYS435 2.3 114.3 1.0
N D:CYS438 3.0 110.6 1.0
CB D:CYS435 3.4 115.5 1.0
CB D:CYS438 3.4 118.9 1.0
CB D:CYS455 3.4 121.6 1.0
CB D:SER437 3.5 111.3 1.0
CA D:CYS438 3.7 112.8 1.0
N D:GLY439 3.7 109.3 1.0
C D:SER437 3.7 110.2 1.0
CA D:SER437 4.0 109.6 1.0
N D:CYS455 4.1 116.3 1.0
C D:CYS438 4.2 111.3 1.0
N D:SER437 4.3 108.2 1.0
CA D:CYS455 4.4 119.9 1.0
O D:SER437 4.6 107.8 1.0
CA D:CYS435 4.7 111.2 1.0
CA D:GLY439 4.8 107.9 1.0
C D:GLY439 4.8 107.8 1.0
C D:CYS435 4.8 109.7 1.0
O D:CYS435 4.8 109.8 1.0

Reference:

K.Boyko, O.Arkova, A.Nikolaeva, V.O.Popov, P.Georgiev, A.Bonchuk. Structure of the DNMT3B Add Domain Suggests the Absence of A DNMT3A-Like Autoinhibitory Mechanism. Biochem.Biophys.Res.Commun. V. 619 124 2022.
ISSN: ESSN 1090-2104
PubMed: 35760008
DOI: 10.1016/J.BBRC.2022.06.036
Page generated: Wed Oct 30 08:11:01 2024

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