Zinc in PDB 3bo5: Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar

Enzymatic activity of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar

All present enzymatic activity of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar, PDB code: 3bo5 was solved by V.V.Lunin, H.Wu, H.Ren, E.Dobrovetsky, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, A.N.Plotnikov, Structural Genomicsconsortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.91 / 1.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.396, 67.827, 44.637, 90.00, 105.93, 90.00
R / Rfree (%) 15.5 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar (pdb code 3bo5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar, PDB code: 3bo5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3bo5

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Zinc binding site 1 out of 4 in the Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.7
occ:1.00
 SG A:CYS75 2.3 13.7 1.0
SG A:CYS104 2.4 12.7 1.0
SG A:CYS108 2.4 13.3 1.0
SG A:CYS61 2.4 14.0 1.0
CB A:CYS104 3.1 14.6 1.0
CB A:CYS61 3.2 15.4 1.0
CB A:CYS75 3.3 15.2 1.0
CB A:CYS108 3.3 14.5 1.0
CA A:CYS104 3.4 12.7 1.0
N A:CYS61 3.5 16.6 1.0
ZN A:ZN303 3.7 14.2 1.0
ZN A:ZN302 3.9 14.7 1.0
CA A:CYS61 4.0 16.7 1.0
SG A:CYS73 4.1 15.4 1.0
N A:CYS104 4.3 10.7 1.0
SG A:CYS110 4.5 15.8 1.0
C A:CYS104 4.6 13.3 1.0
N A:ASN105 4.6 13.6 1.0
CA A:CYS108 4.6 14.9 1.0
C A:GLY60 4.6 18.7 1.0
CA A:CYS75 4.6 14.2 1.0
SG A:CYS68 4.6 14.9 1.0
N A:CYS75 4.7 15.4 1.0
CA A:GLY60 4.8 16.6 1.0
C A:CYS61 4.9 16.5 1.0
O A:GLU103 5.0 13.9 1.0

Zinc binding site 2 out of 4 in 3bo5

Go back to Zinc Binding Sites List in 3bo5
Zinc binding site 2 out of 4 in the Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.7
occ:1.00
 SG A:CYS110 2.3 15.8 1.0
SG A:CYS114 2.3 14.5 1.0
SG A:CYS104 2.4 12.7 1.0
SG A:CYS68 2.4 14.9 1.0
CB A:CYS110 3.1 19.6 1.0
CB A:CYS104 3.1 14.6 1.0
CB A:CYS114 3.3 15.7 1.0
CB A:CYS68 3.3 13.9 1.0
ZN A:ZN301 3.9 13.7 1.0
ZN A:ZN303 4.0 14.2 1.0
O A:HOH443 4.1 18.0 1.0
SG A:CYS61 4.3 14.0 1.0
CA A:CYS110 4.5 19.1 1.0
CA A:CYS104 4.6 12.7 1.0
CA A:CYS68 4.7 15.0 1.0
CA A:CYS114 4.7 16.1 1.0
CB A:ASN116 4.7 12.9 1.0
NE A:ARG117 4.7 15.6 1.0
CB A:CYS108 4.8 14.5 1.0
O A:HOH499 4.9 26.7 1.0
N A:CYS68 4.9 16.0 1.0
SG A:CYS73 5.0 15.4 1.0

Zinc binding site 3 out of 4 in 3bo5

Go back to Zinc Binding Sites List in 3bo5
Zinc binding site 3 out of 4 in the Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:14.2
occ:1.00
 SG A:CYS73 2.3 15.4 1.0
SG A:CYS63 2.3 15.0 1.0
SG A:CYS61 2.4 14.0 1.0
SG A:CYS68 2.4 14.9 1.0
CB A:CYS61 3.1 15.4 1.0
CB A:CYS73 3.2 17.3 1.0
CB A:CYS68 3.2 13.9 1.0
CB A:CYS63 3.2 12.6 1.0
ZN A:ZN301 3.7 13.7 1.0
CA A:CYS73 3.8 16.9 1.0
CA A:CYS68 3.8 15.0 1.0
ZN A:ZN302 4.0 14.7 1.0
SG A:CYS104 4.2 12.7 1.0
N A:CYS63 4.3 17.4 1.0
CA A:CYS63 4.4 16.4 1.0
CA A:CYS61 4.5 16.7 1.0
C A:CYS73 4.5 16.4 1.0
O A:HOH562 4.6 17.6 1.0
O A:HOH465 4.7 20.4 1.0
N A:SER74 4.7 17.1 1.0
N A:CYS68 4.7 16.0 1.0
C A:CYS61 4.9 16.5 1.0
N A:ILE62 4.9 16.3 1.0
CB A:CYS75 4.9 15.2 1.0
SG A:CYS75 4.9 13.7 1.0
C A:CYS68 5.0 17.1 1.0
N A:CYS73 5.0 17.9 1.0

Zinc binding site 4 out of 4 in 3bo5

Go back to Zinc Binding Sites List in 3bo5
Zinc binding site 4 out of 4 in the Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:14.2
occ:1.00
 SG A:CYS275 2.3 14.1 1.0
SG A:CYS280 2.3 16.4 1.0
SG A:CYS273 2.4 13.8 1.0
SG A:CYS212 2.4 15.2 1.0
CB A:CYS275 3.3 16.7 1.0
CB A:CYS280 3.3 19.9 1.0
CB A:CYS212 3.3 15.1 1.0
CB A:CYS273 3.4 13.8 1.0
CA A:CYS280 3.7 19.9 1.0
N A:CYS212 3.8 13.0 1.0
N A:CYS275 3.9 14.9 1.0
CA A:CYS275 4.2 13.5 1.0
N A:THR281 4.2 19.8 1.0
CA A:CYS212 4.3 14.0 1.0
O A:HOH416 4.4 18.6 1.0
NE2 A:HIS210 4.5 12.1 1.0
CD2 A:HIS210 4.5 14.3 1.0
C A:CYS280 4.5 19.7 1.0
CA A:CYS273 4.6 13.3 1.0
C A:CYS273 4.6 14.0 1.0
O A:CYS273 4.7 15.9 1.0
N A:ALA282 4.7 17.8 1.0
N A:GLY276 4.8 14.8 1.0
C A:CYS275 4.8 15.2 1.0
C A:SER211 4.9 12.3 1.0
N A:CYS280 4.9 19.6 1.0
N A:TYR274 4.9 13.7 1.0
OG1 A:THR281 5.0 20.8 1.0

Reference:

H.Wu, V.V.Lunin, H.Ren, E.Dobrovetsky, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, A.N.Plotnikov. The Crystal Structure of Methyltransferase Domain of Human Histone-Lysine N-Methyltransferase Setmar in Complex with Adohcy. To Be Published.
Page generated: Thu Oct 24 11:35:34 2024

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