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Zinc in PDB 6p0r: Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor

Enzymatic activity of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor

All present enzymatic activity of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor:
2.1.1.43;

Protein crystallography data

The structure of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor, PDB code: 6p0r was solved by L.Halabelian, A.Dong, H.Zeng, P.Loppnau, C.Bountra, A.M.Edwards, C.H.Arrowsmith, P.J.Brown, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 146.701, 63.388, 65.616, 90.00, 113.17, 90.00
R / Rfree (%) 21.2 / 26.7

Other elements in 6p0r:

The structure of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor (pdb code 6p0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor, PDB code: 6p0r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6p0r

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Zinc binding site 1 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:54.2
occ:1.00
 SG A:CYS398 2.3 52.7 1.0
SG A:CYS333 2.3 47.6 1.0
SG A:CYS405 2.3 70.9 1.0
SG A:CYS400 2.3 60.7 1.0
CB A:CYS333 3.3 44.6 1.0
CB A:CYS405 3.3 69.1 1.0
CA A:CYS405 3.4 72.0 1.0
CB A:CYS398 3.4 54.7 1.0
CB A:CYS400 3.5 60.4 1.0
N A:ARG406 3.8 71.7 1.0
N A:CYS333 3.9 40.0 1.0
N A:CYS400 4.1 63.1 1.0
C A:CYS405 4.1 72.2 1.0
CA A:CYS400 4.2 61.5 1.0
CA A:CYS333 4.3 40.9 1.0
N A:CYS405 4.5 73.6 1.0
CA A:CYS398 4.6 57.2 1.0
C A:CYS398 4.7 59.1 1.0
N A:GLY407 4.8 65.6 1.0
CA A:ARG406 4.9 70.4 1.0
O A:CYS398 5.0 56.7 1.0
C A:SER332 5.0 38.9 1.0
NE2 A:HIS331 5.0 36.5 1.0

Zinc binding site 2 out of 7 in 6p0r

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Zinc binding site 2 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:38.6
occ:1.00
 SG A:CYS191 2.3 38.0 1.0
SG A:CYS193 2.3 35.6 1.0
SG A:CYS196 2.3 37.9 1.0
SG A:CYS201 2.3 36.3 1.0
CB A:CYS191 3.2 36.9 1.0
CB A:CYS196 3.3 39.1 1.0
CB A:CYS193 3.3 37.0 1.0
CB A:CYS201 3.4 33.8 1.0
ZN A:ZN505 3.6 32.4 1.0
ZN A:ZN504 3.6 37.9 1.0
CA A:CYS196 3.8 40.2 1.0
CA A:CYS201 3.9 33.0 1.0
SG A:CYS229 4.0 29.4 1.0
N A:CYS193 4.2 35.7 1.0
O A:HOH607 4.2 22.6 1.0
CA A:CYS193 4.4 36.3 1.0
N A:CYS202 4.4 32.0 1.0
CA A:CYS191 4.6 36.2 1.0
N A:CYS196 4.7 39.3 1.0
C A:CYS201 4.7 31.1 1.0
O A:CYS196 4.8 44.6 1.0
C A:CYS196 4.8 42.4 1.0
C A:CYS191 4.9 35.9 1.0

Zinc binding site 3 out of 7 in 6p0r

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Zinc binding site 3 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:37.9
occ:1.00
 SG A:CYS191 2.3 38.0 1.0
SG A:CYS202 2.3 33.1 1.0
SG A:CYS233 2.3 40.6 1.0
SG A:CYS229 2.4 29.4 1.0
CB A:CYS229 3.3 31.2 1.0
CB A:CYS191 3.3 36.9 1.0
CB A:CYS233 3.5 41.3 1.0
CA A:CYS229 3.5 31.7 1.0
CB A:CYS202 3.5 32.9 1.0
ZN A:ZN503 3.6 38.6 1.0
N A:CYS191 3.7 37.1 1.0
SG A:CYS201 3.8 36.3 1.0
ZN A:ZN505 3.9 32.4 1.0
CA A:CYS191 4.1 36.2 1.0
N A:CYS202 4.1 32.0 1.0
N A:CYS229 4.4 32.0 1.0
CA A:CYS202 4.4 32.2 1.0
SG A:CYS235 4.6 36.3 1.0
N A:ASN230 4.7 33.6 1.0
C A:CYS229 4.7 32.7 1.0
C A:GLY190 4.7 37.4 1.0
CA A:CYS233 4.7 41.5 1.0
SG A:CYS196 4.7 37.9 1.0
C A:CYS191 4.9 35.9 1.0
CA A:GLY190 4.9 38.9 1.0

Zinc binding site 4 out of 7 in 6p0r

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Zinc binding site 4 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:32.4
occ:1.00
 SG A:CYS235 2.3 36.3 1.0
SG A:CYS196 2.3 37.9 1.0
SG A:CYS229 2.3 29.4 1.0
SG A:CYS239 2.4 33.3 1.0
CB A:CYS196 3.3 39.1 1.0
CB A:CYS235 3.3 37.7 1.0
CB A:CYS229 3.4 31.2 1.0
CB A:CYS239 3.5 35.6 1.0
ZN A:ZN503 3.6 38.6 1.0
ZN A:ZN504 3.9 37.9 1.0
SG A:CYS191 4.0 38.0 1.0
SG A:CYS201 4.3 36.3 1.0
CB A:ASN241 4.6 34.7 1.0
CA A:CYS196 4.7 40.2 1.0
CA A:CYS235 4.7 39.5 1.0
CA A:CYS229 4.8 31.7 1.0
O A:HOH607 4.8 22.6 1.0
CA A:CYS239 4.8 37.0 1.0
NE A:ARG242 4.8 33.4 1.0
CB A:CYS233 5.0 41.3 1.0

Zinc binding site 5 out of 7 in 6p0r

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Zinc binding site 5 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:33.9
occ:1.00
 SG B:CYS201 2.3 33.9 1.0
SG B:CYS196 2.3 32.4 1.0
SG B:CYS191 2.3 33.6 1.0
SG B:CYS193 2.4 30.5 1.0
CB B:CYS201 3.3 33.5 1.0
CB B:CYS191 3.3 34.3 1.0
CB B:CYS196 3.3 35.0 1.0
CB B:CYS193 3.3 33.4 1.0
ZN B:ZN503 3.6 33.3 1.0
ZN B:ZN504 3.6 35.0 1.0
SG B:CYS229 3.7 30.0 1.0
CA B:CYS201 3.8 33.9 1.0
CA B:CYS196 3.8 36.9 1.0
N B:CYS193 4.2 35.3 1.0
N B:CYS202 4.3 31.2 1.0
CA B:CYS193 4.3 34.9 1.0
C B:CYS201 4.6 31.8 1.0
CA B:CYS191 4.7 34.4 1.0
N B:CYS196 4.7 37.2 1.0
O B:CYS196 4.7 36.4 1.0
C B:CYS196 4.8 37.6 1.0
N B:CYS201 4.9 36.4 1.0
C B:CYS191 4.9 34.8 1.0
N B:SER192 5.0 35.6 1.0

Zinc binding site 6 out of 7 in 6p0r

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Zinc binding site 6 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:33.3
occ:1.00
 SG B:CYS229 2.3 30.0 1.0
SG B:CYS202 2.3 30.4 1.0
SG B:CYS191 2.3 33.6 1.0
SG B:CYS233 2.4 35.1 1.0
CB B:CYS229 3.2 30.6 1.0
CB B:CYS191 3.3 34.3 1.0
CA B:CYS229 3.4 30.3 1.0
CB B:CYS233 3.4 34.9 1.0
ZN B:ZN502 3.6 33.9 1.0
CB B:CYS202 3.6 30.7 1.0
N B:CYS191 3.7 34.4 1.0
SG B:CYS201 3.9 33.9 1.0
ZN B:ZN504 3.9 35.0 1.0
CA B:CYS191 4.1 34.4 1.0
N B:CYS202 4.2 31.2 1.0
N B:CYS229 4.3 29.7 1.0
N B:ASN230 4.4 32.2 1.0
CA B:CYS202 4.5 30.2 1.0
C B:CYS229 4.5 31.1 1.0
SG B:CYS235 4.6 36.8 1.0
CA B:CYS233 4.7 35.4 1.0
SG B:CYS196 4.7 32.4 1.0
C B:CYS191 4.8 34.8 1.0
O B:CYS191 4.9 33.3 1.0
C B:GLY190 4.9 36.5 1.0
O B:GLU228 5.0 28.2 1.0

Zinc binding site 7 out of 7 in 6p0r

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Zinc binding site 7 out of 7 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:35.0
occ:1.00
 SG B:CYS235 2.3 36.8 1.0
SG B:CYS239 2.3 35.6 1.0
SG B:CYS229 2.3 30.0 1.0
SG B:CYS196 2.3 32.4 1.0
CB B:CYS229 3.2 30.6 1.0
CB B:CYS196 3.3 35.0 1.0
CB B:CYS235 3.3 36.9 1.0
CB B:CYS239 3.4 36.1 1.0
ZN B:ZN502 3.6 33.9 1.0
ZN B:ZN503 3.9 33.3 1.0
SG B:CYS191 4.2 33.6 1.0
SG B:CYS201 4.4 33.9 1.0
CA B:CYS229 4.6 30.3 1.0
CB B:ASN241 4.6 34.5 1.0
CA B:CYS239 4.7 37.2 1.0
CA B:CYS235 4.7 37.2 1.0
CA B:CYS196 4.8 36.9 1.0
NE B:ARG242 4.8 35.0 1.0
CB B:CYS233 4.9 34.9 1.0
NH2 B:ARG242 4.9 33.1 1.0

Reference:

L.Halabelian, A.Dong, H.Zeng, P.Loppnau, C.Bountra, A.M.Edwards, C.H.Arrowsmith, P.J.Brown, Structural Genomics Consortium (Sgc). Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (SUV39H2) in Complex with OTS186935 Inhibitor To Be Published.
Page generated: Tue Oct 29 04:43:12 2024

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