Atomistry » Zinc » PDB 4gy1-4h84 » 4h12
Atomistry »
  Zinc »
    PDB 4gy1-4h84 »
      4h12 »

Zinc in PDB 4h12: The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine

Enzymatic activity of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine

All present enzymatic activity of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine:
2.1.1.43;

Protein crystallography data

The structure of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine, PDB code: 4h12 was solved by M.F.Amaya, A.Dong, H.Zeng, F.Mackenzie, M.Bunnage, J.Weigelt, C.Bountra, C.H.Arrowsmith, A.M.Edwards, J.Min, H.Wu, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.36 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.293, 76.663, 78.093, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.9

Other elements in 4h12:

The structure of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine (pdb code 4h12). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine, PDB code: 4h12:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4h12

Go back to Zinc Binding Sites List in 4h12
Zinc binding site 1 out of 3 in the The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:38.9
occ:1.00
 SG A:CYS1499 2.2 39.2 1.0
SG A:CYS1501 2.3 37.7 1.0
SG A:CYS1516 2.4 31.9 1.0
SG A:CYS1520 2.4 35.5 1.0
CB A:CYS1516 3.2 32.5 1.0
CB A:CYS1499 3.2 40.1 1.0
CB A:CYS1520 3.2 35.3 1.0
CB A:CYS1501 3.3 42.2 1.0
CA A:CYS1516 3.7 36.0 1.0
ZN A:ZN1802 3.8 34.6 1.0
CA A:CYS1520 3.9 37.9 1.0
O A:HOH1929 4.0 41.0 1.0
SG A:CYS1529 4.1 31.3 1.0
N A:CYS1501 4.3 45.2 1.0
CA A:CYS1501 4.4 45.4 1.0
N A:CYS1516 4.6 37.3 1.0
CA A:CYS1499 4.6 42.3 1.0
SG A:CYS1533 4.7 36.7 1.0
C A:CYS1520 4.7 37.0 1.0
N A:LEU1521 4.7 38.1 1.0
C A:CYS1516 4.8 36.5 1.0

Zinc binding site 2 out of 3 in 4h12

Go back to Zinc Binding Sites List in 4h12
Zinc binding site 2 out of 3 in the The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:34.6
occ:1.00
 SG A:CYS1533 2.2 36.7 1.0
SG A:CYS1539 2.3 32.8 1.0
SG A:CYS1516 2.3 31.9 1.0
SG A:CYS1529 2.3 31.3 1.0
CB A:CYS1529 3.1 31.6 1.0
CB A:CYS1516 3.3 32.5 1.0
CB A:CYS1539 3.3 32.8 1.0
CB A:CYS1533 3.4 35.8 1.0
ZN A:ZN1801 3.8 38.9 1.0
SG A:CYS1499 4.3 39.2 1.0
CA A:CYS1539 4.3 34.2 1.0
CB A:ASN1541 4.4 30.6 1.0
O A:HOH1911 4.4 39.4 1.0
CA A:CYS1529 4.6 32.5 1.0
CA A:CYS1533 4.7 38.3 1.0
CA A:CYS1516 4.7 36.0 1.0
SG A:CYS1520 4.8 35.5 1.0
N A:ASN1541 5.0 32.5 1.0

Zinc binding site 3 out of 3 in 4h12

Go back to Zinc Binding Sites List in 4h12
Zinc binding site 3 out of 3 in the The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Methyltransferase Domain of Human Set Domain- Containing Protein 2 in Complex with S-Adenosyl-L-Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1803

b:36.4
occ:1.00
 SG A:CYS1678 2.2 34.2 1.0
SG A:CYS1680 2.4 37.3 1.0
SG A:CYS1631 2.4 39.2 1.0
SG A:CYS1685 2.4 41.1 1.0
CB A:CYS1680 3.2 37.1 1.0
CB A:CYS1678 3.3 35.1 1.0
CB A:CYS1685 3.4 42.5 1.0
CB A:CYS1631 3.4 36.9 1.0
CA A:CYS1685 3.7 44.4 1.0
N A:CYS1680 4.0 35.6 1.0
N A:CYS1631 4.0 35.4 1.0
O A:HOH1923 4.0 43.2 1.0
CA A:CYS1680 4.1 37.6 1.0
N A:ARG1686 4.1 44.1 1.0
NE2 A:HIS1629 4.3 32.0 1.0
CA A:CYS1631 4.3 38.2 1.0
CD2 A:HIS1629 4.4 31.7 1.0
C A:CYS1685 4.4 45.5 1.0
CA A:CYS1678 4.6 34.3 1.0
N A:GLY1687 4.6 42.2 1.0
C A:CYS1678 4.6 34.7 1.0
N A:GLY1681 4.7 42.1 1.0
O A:CYS1678 4.8 38.7 1.0
OG A:SER1682 4.8 46.1 1.0
C A:CYS1680 4.8 39.3 1.0
N A:CYS1685 5.0 46.9 1.0
C A:SER1630 5.0 33.7 1.0

Reference:

W.Zheng, G.Ibanez, H.Wu, G.Blum, H.Zeng, A.Dong, F.Li, T.Hajian, A.Allali-Hassani, M.F.Amaya, A.Siarheyeva, W.Yu, P.J.Brown, M.Schapira, M.Vedadi, J.Min, M.Luo. Sinefungin Derivatives As Inhibitors and Structure Probes of Protein Lysine Methyltransferase SETD2. J.Am.Chem.Soc. V. 134 18004 2012.
ISSN: ISSN 0002-7863
PubMed: 23043551
DOI: 10.1021/JA307060P
Page generated: Sat Oct 26 23:47:16 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy