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Zinc in PDB 2r3a: Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2

Enzymatic activity of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2

All present enzymatic activity of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2:
2.1.1.43;

Protein crystallography data

The structure of Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2, PDB code: 2r3a was solved by V.V.Lunin, H.Wu, H.Zeng, H.Ren, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.38 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.748, 63.925, 64.529, 90.00, 109.33, 90.00
R / Rfree (%) 17.7 / 21.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2 (pdb code 2r3a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2, PDB code: 2r3a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2r3a

Go back to Zinc Binding Sites List in 2r3a
Zinc binding site 1 out of 4 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:27.2
occ:1.00
SG A:CYS289 2.3 23.9 1.0
SG A:CYS287 2.3 24.6 1.0
SG A:CYS294 2.4 26.4 1.0
SG A:CYS222 2.4 24.1 1.0
CB A:CYS289 3.3 25.8 1.0
CB A:CYS294 3.3 28.1 1.0
CB A:CYS287 3.3 25.0 1.0
CB A:CYS222 3.4 23.5 1.0
CA A:CYS294 3.6 27.9 1.0
N A:ARG295 3.9 27.9 1.0
N A:CYS289 3.9 24.9 1.0
N A:CYS222 4.0 23.6 1.0
CA A:CYS289 4.1 25.6 1.0
C A:CYS294 4.2 28.4 1.0
O A:HOH308 4.3 22.6 1.0
CA A:CYS222 4.3 23.8 1.0
NE2 A:HIS220 4.4 22.2 1.0
C A:CYS287 4.5 24.5 1.0
CA A:CYS287 4.5 24.8 1.0
CD2 A:HIS220 4.5 22.8 1.0
N A:GLY296 4.6 28.8 1.0
O A:CYS287 4.6 23.3 1.0
N A:GLY290 4.8 28.1 1.0
C A:CYS289 4.9 26.5 1.0
N A:CYS294 4.9 28.0 1.0
C A:SER221 4.9 22.6 1.0
N A:LYS288 4.9 24.6 1.0

Zinc binding site 2 out of 4 in 2r3a

Go back to Zinc Binding Sites List in 2r3a
Zinc binding site 2 out of 4 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:33.6
occ:1.00
SG A:CYS85 2.2 28.9 1.0
SG A:CYS80 2.4 26.3 1.0
SG A:CYS82 2.4 31.5 1.0
SG A:CYS90 2.4 31.7 1.0
CB A:CYS85 3.1 30.5 1.0
CB A:CYS82 3.2 32.3 1.0
CB A:CYS90 3.2 30.2 1.0
CB A:CYS80 3.2 31.4 1.0
CA A:CYS85 3.6 31.0 1.0
ZN A:ZN303 3.7 30.0 1.0
CA A:CYS90 3.7 29.6 1.0
ZN A:ZN302 3.7 29.2 1.0
SG A:CYS118 3.9 25.2 1.0
N A:CYS82 4.3 32.7 1.0
O A:HOH362 4.3 32.1 1.0
CA A:CYS82 4.3 32.6 1.0
N A:CYS91 4.4 27.6 1.0
N A:CYS85 4.5 31.9 1.0
C A:CYS90 4.6 29.1 1.0
CA A:CYS80 4.7 32.8 1.0
C A:CYS85 4.7 31.5 1.0
O A:CYS85 4.7 30.7 1.0
N A:CYS90 4.9 31.8 1.0
O A:LYS89 4.9 33.4 1.0
C A:CYS80 4.9 31.9 1.0
N A:SER81 5.0 32.1 1.0

Zinc binding site 3 out of 4 in 2r3a

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Zinc binding site 3 out of 4 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:29.2
occ:1.00
SG A:CYS91 2.3 26.6 1.0
SG A:CYS122 2.3 25.7 1.0
SG A:CYS80 2.4 26.3 1.0
SG A:CYS118 2.4 25.2 1.0
CB A:CYS118 3.1 23.1 1.0
CB A:CYS80 3.3 31.4 1.0
CB A:CYS122 3.3 27.4 1.0
CA A:CYS118 3.4 24.9 1.0
CB A:CYS91 3.6 27.1 1.0
N A:CYS80 3.7 34.9 1.0
ZN A:ZN301 3.7 33.6 1.0
SG A:CYS90 3.9 31.7 1.0
ZN A:ZN303 4.0 30.0 1.0
CA A:CYS80 4.1 32.8 1.0
N A:CYS91 4.1 27.6 1.0
N A:CYS118 4.4 23.3 1.0
CA A:CYS91 4.5 27.6 1.0
N A:ASN119 4.5 27.4 1.0
C A:CYS118 4.5 25.9 1.0
CA A:CYS122 4.6 29.2 1.0
SG A:CYS124 4.6 27.6 1.0
SG A:CYS85 4.7 28.9 1.0
C A:GLY79 4.8 36.9 1.0
CA A:GLY79 4.9 38.1 1.0
C A:CYS80 4.9 31.9 1.0
O A:CYS80 5.0 31.7 1.0

Zinc binding site 4 out of 4 in 2r3a

Go back to Zinc Binding Sites List in 2r3a
Zinc binding site 4 out of 4 in the Methyltransferase Domain of Human Suppressor of Variegation 3-9 Homolog 2


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:30.0
occ:1.00
SG A:CYS124 2.3 27.6 1.0
SG A:CYS118 2.4 25.2 1.0
SG A:CYS85 2.4 28.9 1.0
SG A:CYS128 2.4 29.2 1.0
CB A:CYS124 3.2 31.0 1.0
CB A:CYS118 3.2 23.1 1.0
CB A:CYS85 3.2 30.5 1.0
CB A:CYS128 3.4 30.4 1.0
ZN A:ZN301 3.7 33.6 1.0
ZN A:ZN302 4.0 29.2 1.0
SG A:CYS80 4.0 26.3 1.0
SG A:CYS90 4.5 31.7 1.0
NE A:ARG131 4.6 23.3 1.0
CA A:CYS124 4.6 31.8 1.0
CB A:ASN130 4.6 25.1 1.0
CA A:CYS85 4.7 31.0 1.0
CA A:CYS118 4.7 24.9 1.0
O A:HOH362 4.7 32.1 1.0
CA A:CYS128 4.8 31.1 1.0
CB A:CYS122 4.8 27.4 1.0
OG A:SER305 4.8 49.8 1.0

Reference:

H.Wu, J.Min, V.V.Lunin, T.Antoshenko, L.Dombrovski, H.Zeng, A.Allali-Hassani, V.Campagna-Slater, M.Vedadi, C.H.Arrowsmith, A.N.Plotnikov, M.Schapira. Structural Biology of Human H3K9 Methyltransferases Plos One V. 5 E8570 2010.
ISSN: ESSN 1932-6203
PubMed: 20084102
DOI: 10.1371/JOURNAL.PONE.0008570
Page generated: Wed Dec 16 03:51:32 2020

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