Zinc in PDB 6u9n: MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139)

Enzymatic activity of MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139)

All present enzymatic activity of MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139):
2.1.1.43;

Protein crystallography data

The structure of MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139), PDB code: 6u9n was solved by E.M.Petrunak, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.60 / 1.95
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 54.629, 54.629, 105.832, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 24.8

Other elements in 6u9n:

The structure of MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139) (pdb code 6u9n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139), PDB code: 6u9n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6u9n

Go back to Zinc Binding Sites List in 6u9n
Zinc binding site 1 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4002

b:36.5
occ:1.00
SG A:CYS3909 2.2 48.1 1.0
SG A:CYS3959 2.3 37.0 1.0
SG A:CYS3957 2.3 40.8 1.0
SG A:CYS3964 2.5 40.6 1.0
CB A:CYS3909 3.2 44.4 1.0
CB A:CYS3959 3.5 33.2 1.0
CB A:CYS3957 3.5 36.9 1.0
CB A:CYS3964 3.6 37.2 1.0
N A:CYS3909 3.7 42.5 1.0
CA A:CYS3964 3.9 37.4 1.0
N A:CYS3959 4.0 32.6 1.0
CA A:CYS3909 4.1 43.9 1.0
N A:ARG3965 4.2 35.9 1.0
CA A:CYS3959 4.3 33.1 1.0
O A:HOH4155 4.3 32.0 1.0
NE2 A:HIS3907 4.4 33.8 1.0
H5 A:Q344001 4.5 19.4 0.0
C A:CYS3964 4.5 40.2 1.0
CD2 A:HIS3907 4.6 33.5 1.0
N A:LYS3966 4.6 32.7 1.0
C A:SER3908 4.7 40.8 1.0
C A:CYS3957 4.7 35.9 1.0
CA A:CYS3957 4.7 35.5 1.0
N A:GLY3960 4.7 35.8 1.0
CA A:SER3908 4.8 33.8 1.0
O A:CYS3957 4.9 37.0 1.0
C A:CYS3959 4.9 38.3 1.0
N A:ASN3958 5.0 28.2 1.0

Zinc binding site 2 out of 2 in 6u9n

Go back to Zinc Binding Sites List in 6u9n
Zinc binding site 2 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MLL1 Set N3861I/Q3867L Bound to Inhibitor 14 (Tc-5139) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4002

b:37.8
occ:1.00
SG B:CYS3909 2.2 52.7 1.0
SG B:CYS3959 2.3 36.4 1.0
SG B:CYS3957 2.3 38.4 1.0
SG B:CYS3964 2.5 40.4 1.0
CB B:CYS3909 3.3 48.1 1.0
CB B:CYS3959 3.4 32.8 1.0
CB B:CYS3957 3.5 34.5 1.0
CB B:CYS3964 3.6 36.6 1.0
N B:CYS3909 3.7 44.9 1.0
CA B:CYS3964 4.0 36.4 1.0
N B:CYS3959 4.0 32.7 1.0
CA B:CYS3909 4.1 46.9 1.0
CA B:CYS3959 4.2 33.0 1.0
N B:ARG3965 4.3 35.3 1.0
O B:HOH4177 4.3 28.4 1.0
H5 B:Q344001 4.4 19.4 0.0
NE2 B:HIS3907 4.5 34.2 1.0
C B:CYS3964 4.6 39.1 1.0
C B:SER3908 4.6 43.5 1.0
C B:CYS3957 4.6 34.2 1.0
N B:LYS3966 4.6 33.8 1.0
CD2 B:HIS3907 4.6 34.2 1.0
N B:GLY3960 4.6 34.1 1.0
CA B:CYS3957 4.7 33.2 1.0
CA B:SER3908 4.8 35.2 1.0
O B:CYS3957 4.8 35.4 1.0
C B:CYS3959 4.9 37.5 1.0
N B:ASN3958 4.9 27.5 1.0

Reference:

T.R.Chern, L.Liu, E.Petrunak, J.A.Stuckey, M.Wang, D.Bernard, H.Zhou, S.Lee, Y.Dou, S.Wang. Discovery of Potent Small-Molecule Inhibitors of Mll Methyltransferase. Acs Med.Chem.Lett. V. 11 1348 2020.
ISSN: ISSN 1948-5875
PubMed: 32551023
DOI: 10.1021/ACSMEDCHEMLETT.0C00229
Page generated: Wed Dec 16 12:58:00 2020

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