Zinc in PDB 6u9k: MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153)

Enzymatic activity of MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153)

All present enzymatic activity of MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153):
2.1.1.43;

Protein crystallography data

The structure of MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153), PDB code: 6u9k 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) 43.34 / 2.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 54.949, 54.949, 104.895, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 24.4

Zinc Binding Sites:

The binding sites of Zinc atom in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153) (pdb code 6u9k). 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 18 (Tc-5153), PDB code: 6u9k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6u9k

Go back to Zinc Binding Sites List in 6u9k
Zinc binding site 1 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153)


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 18 (Tc-5153) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4001

b:37.1
occ:1.00
SG A:CYS3909 2.3 41.4 1.0
SG A:CYS3959 2.3 37.0 1.0
SG A:CYS3957 2.4 40.3 1.0
SG A:CYS3964 2.4 40.0 1.0
CB A:CYS3957 3.3 36.6 1.0
CB A:CYS3909 3.3 38.0 1.0
CB A:CYS3959 3.4 33.2 1.0
CB A:CYS3964 3.5 36.9 1.0
N A:CYS3909 3.8 36.7 1.0
CA A:CYS3964 3.8 37.1 1.0
N A:CYS3959 4.1 33.1 1.0
N A:ARG3965 4.1 35.8 1.0
CA A:CYS3909 4.2 37.9 1.0
CA A:CYS3959 4.3 33.4 1.0
NE2 A:HIS3907 4.4 32.8 1.0
C A:CYS3964 4.4 39.2 1.0
O A:HOH4149 4.4 32.6 1.0
H5 A:Q2V4002 4.5 23.7 1.0
N A:LYS3966 4.5 37.2 1.0
CD2 A:HIS3907 4.6 33.0 1.0
CA A:CYS3957 4.6 36.0 1.0
C A:CYS3957 4.7 36.6 1.0
C A:SER3908 4.8 37.5 1.0
N A:GLY3960 4.8 34.8 1.0
O A:CYS3957 4.9 37.2 1.0
C A:CYS3959 4.9 38.4 1.0
CA A:SER3908 5.0 29.7 1.0
N A:ASN3958 5.0 29.5 1.0

Zinc binding site 2 out of 2 in 6u9k

Go back to Zinc Binding Sites List in 6u9k
Zinc binding site 2 out of 2 in the MLL1 Set N3861I/Q3867L Bound to Inhibitor 18 (Tc-5153)


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 18 (Tc-5153) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4001

b:38.0
occ:1.00
SG B:CYS3909 2.3 44.6 1.0
SG B:CYS3959 2.3 37.3 1.0
SG B:CYS3957 2.4 43.1 1.0
SG B:CYS3964 2.4 41.1 1.0
CB B:CYS3957 3.3 39.4 1.0
CB B:CYS3909 3.4 41.0 1.0
CB B:CYS3964 3.4 37.8 1.0
CB B:CYS3959 3.4 33.8 1.0
N B:CYS3909 3.8 39.4 1.0
CA B:CYS3964 3.9 38.0 1.0
N B:CYS3959 4.0 34.1 1.0
N B:ARG3965 4.2 36.9 1.0
CA B:CYS3909 4.2 40.7 1.0
CA B:CYS3959 4.3 34.1 1.0
O B:HOH4162 4.3 30.6 1.0
H5 B:Q2V4003 4.5 22.4 1.0
NE2 B:HIS3907 4.5 34.9 1.0
C B:CYS3964 4.5 40.6 1.0
CD2 B:HIS3907 4.6 34.8 1.0
CA B:CYS3957 4.6 38.6 1.0
N B:LYS3966 4.6 35.3 1.0
C B:CYS3957 4.6 39.1 1.0
N B:GLY3960 4.7 35.8 1.0
C B:SER3908 4.8 40.4 1.0
O B:CYS3957 4.8 39.7 1.0
C B:CYS3959 4.9 39.3 1.0
CA B:SER3908 5.0 31.3 1.0
N B:ASN3958 5.0 32.5 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 12:57:49 2020

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