Chlorine in PDB 5y2f: Human SIRT6 in Complex with Allosteric Activator Mdl-801

Protein crystallography data

The structure of Human SIRT6 in Complex with Allosteric Activator Mdl-801, PDB code: 5y2f was solved by J.Zhang, Z.Huang, K.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 114.85 / 2.53
Space group P 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 162.422, 162.422, 162.422, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.7

Other elements in 5y2f:

The structure of Human SIRT6 in Complex with Allosteric Activator Mdl-801 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Zinc (Zn) 1 atom
Bromine (Br) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human SIRT6 in Complex with Allosteric Activator Mdl-801 (pdb code 5y2f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human SIRT6 in Complex with Allosteric Activator Mdl-801, PDB code: 5y2f:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5y2f

Go back to Chlorine Binding Sites List in 5y2f
Chlorine binding site 1 out of 2 in the Human SIRT6 in Complex with Allosteric Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human SIRT6 in Complex with Allosteric Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:1.0
occ:1.00
CL1 A:8L9402 0.0 1.0 1.0
C09 A:8L9402 1.7 0.4 1.0
C01 A:8L9402 2.7 0.5 1.0
C07 A:8L9402 2.7 0.9 1.0
CD1 A:PHE80 3.2 0.7 1.0
C12 C:HDR101 3.4 99.3 1.0
C13 C:HDR101 3.4 92.5 1.0
CE1 A:PHE80 3.9 0.3 1.0
CG A:PHE80 3.9 0.5 1.0
C03 A:8L9402 4.0 0.4 1.0
C06 A:8L9402 4.0 0.9 1.0
C14 C:HDR101 4.1 87.2 1.0
CB A:PHE80 4.1 0.2 1.0
CB A:PRO78 4.3 95.1 1.0
C11 C:HDR101 4.3 0.0 1.0
C04 A:8L9402 4.5 0.6 1.0
CG2 A:VAL68 4.7 53.0 1.0
CG A:PRO60 4.7 50.3 1.0
C10 C:HDR101 4.7 85.1 1.0
CZ A:PHE80 4.9 0.0 1.0
CD2 A:PHE80 4.9 0.5 1.0
CG A:PRO78 5.0 0.0 1.0

Chlorine binding site 2 out of 2 in 5y2f

Go back to Chlorine Binding Sites List in 5y2f
Chlorine binding site 2 out of 2 in the Human SIRT6 in Complex with Allosteric Activator Mdl-801


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human SIRT6 in Complex with Allosteric Activator Mdl-801 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:0.4
occ:1.00
CL2 A:8L9402 0.0 0.4 1.0
C03 A:8L9402 1.7 0.4 1.0
C01 A:8L9402 2.7 0.5 1.0
C04 A:8L9402 2.7 0.6 1.0
OD1 A:ASN2 2.9 0.1 1.0
OE2 A:GLU72 3.2 91.6 1.0
O A:HOH562 3.2 85.1 1.0
CG A:ASN2 3.6 0.7 1.0
C09 A:8L9402 4.0 0.4 1.0
C06 A:8L9402 4.0 0.9 1.0
CG A:PRO78 4.0 0.0 1.0
ND2 A:ASN2 4.2 0.7 1.0
CD A:PRO78 4.2 98.8 1.0
CD A:GLU72 4.4 98.5 1.0
CB A:ASN2 4.4 0.2 1.0
CG1 A:VAL68 4.5 52.1 1.0
C07 A:8L9402 4.5 0.9 1.0
CA A:ASN2 4.7 0.5 1.0
O A:VAL1 4.9 0.1 1.0
CG A:GLU72 4.9 84.5 1.0

Reference:

Z.Huang, J.Zhao, W.Deng, Y.Chen, J.Shang, K.Song, L.Zhang, C.Wang, S.Lu, X.Yang, B.He, J.Min, H.Hu, M.Tan, J.Xu, Q.Zhang, J.Zhong, X.Sun, Z.Mao, H.Lin, M.Xiao, Y.E.Chin, H.Jiang, Y.Xu, G.Chen, J.Zhang. Identification of A Cellularly Active SIRT6 Allosteric Activator. Nat. Chem. Biol. V. 14 1118 2018.
ISSN: ESSN 1552-4469
PubMed: 30374165
DOI: 10.1038/S41589-018-0150-0
Page generated: Sat Dec 12 12:40:04 2020

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