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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

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