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Zinc in PDB 3ope: Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase

Enzymatic activity of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase

All present enzymatic activity of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase:
2.1.1.43;

Protein crystallography data

The structure of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase, PDB code: 3ope was solved by S.An, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 59.530, 59.530, 233.804, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 29.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase (pdb code 3ope). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase, PDB code: 3ope:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3ope

Go back to Zinc Binding Sites List in 3ope
Zinc binding site 1 out of 6 in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:74.6
occ:0.87
 CB A:CYS2270 2.3 52.5 1.0
SG A:CYS2220 2.4 60.0 1.0
SG A:CYS2268 2.5 58.2 1.0
SG A:CYS2275 2.6 61.6 1.0
SG A:CYS2270 2.7 53.8 1.0
CB A:CYS2275 3.4 63.9 1.0
CB A:CYS2220 3.6 58.1 1.0
CB A:CYS2268 3.6 59.0 1.0
CA A:CYS2270 3.7 53.2 1.0
N A:CYS2220 4.0 57.0 1.0
CA A:CYS2275 4.0 64.5 1.0
N A:CYS2270 4.1 53.0 1.0
N A:ARG2276 4.3 64.5 1.0
CA A:CYS2220 4.4 58.4 1.0
O A:CYS2268 4.5 61.6 1.0
C A:CYS2275 4.5 64.6 1.0
C A:CYS2270 4.6 54.9 1.0
CE1 A:HIS2218 4.6 59.8 1.0
C A:CYS2268 4.7 60.3 1.0
N A:GLY2277 4.7 63.7 1.0
CA A:CYS2268 4.8 60.8 1.0
ND1 A:HIS2218 4.8 57.8 1.0
N A:GLY2271 4.8 58.2 1.0
C A:SER2219 4.9 56.1 1.0
CB A:PHE2272 5.0 67.0 1.0

Zinc binding site 2 out of 6 in 3ope

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Zinc binding site 2 out of 6 in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:86.9
occ:0.71
 SG A:CYS2122 2.3 86.4 1.0
SG A:CYS2117 2.5 88.3 1.0
SG A:CYS2128 2.7 72.4 1.0
CB A:CYS2117 3.0 81.4 1.0
SG A:CYS2091 3.1 98.9 1.0
CB A:CYS2122 3.4 83.8 1.0
SG A:CYS2104 3.7 0.2 1.0
CB A:CYS2128 4.0 76.0 1.0
ZN A:ZN4 4.0 71.1 0.6
CB A:ASN2130 4.1 63.5 1.0
CB A:CYS2091 4.2 0.8 1.0
CA A:CYS2117 4.4 76.2 1.0
CB A:CYS2104 4.5 0.6 1.0
CA A:CYS2122 4.6 82.9 1.0
N A:ASN2130 4.7 67.1 1.0
NE2 A:GLN2131 4.7 68.6 1.0
N A:CYS2117 4.8 71.9 1.0
CA A:ASN2130 4.8 65.3 1.0
CG A:GLN2131 4.9 65.2 1.0
O A:ASN2130 4.9 65.7 1.0
OD1 A:ASN2130 5.0 63.9 1.0

Zinc binding site 3 out of 6 in 3ope

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Zinc binding site 3 out of 6 in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:71.1
occ:0.60
 SG A:CYS2104 2.3 0.2 1.0
SG A:CYS2093 2.5 0.0 1.0
CB A:CYS2108 2.5 0.8 1.0
CB A:CYS2091 2.7 0.8 1.0
SG A:CYS2091 2.8 98.9 1.0
SG A:CYS2108 2.8 0.1 1.0
CB A:CYS2093 3.0 0.9 1.0
O A:CYS2091 3.0 0.3 1.0
N A:CYS2093 3.4 0.3 1.0
C A:CYS2091 3.4 0.3 1.0
CA A:CYS2108 3.4 0.5 1.0
CA A:CYS2091 3.6 0.4 1.0
CA A:CYS2093 3.7 0.9 1.0
ZN A:ZN2 4.0 86.9 0.7
O A:CYS2093 4.1 0.8 1.0
CB A:CYS2104 4.1 0.6 1.0
C A:CYS2108 4.2 0.2 1.0
N A:ASN2092 4.2 0.1 1.0
SG A:CYS2117 4.3 88.3 1.0
C A:CYS2093 4.4 0.0 1.0
C A:ASN2092 4.4 0.3 1.0
N A:CYS2108 4.6 0.1 1.0
O A:CYS2108 4.7 0.8 1.0
N A:CYS2091 4.8 0.7 1.0
N A:LEU2109 4.8 0.4 1.0
CA A:ASN2092 4.9 0.6 1.0
SG A:CYS2122 4.9 86.4 1.0
CA A:CYS2104 5.0 0.6 1.0

Zinc binding site 4 out of 6 in 3ope

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Zinc binding site 4 out of 6 in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:72.8
occ:0.64
 CB B:CYS2268 2.2 97.3 1.0
SG B:CYS2220 2.2 93.5 1.0
CB B:CYS2220 2.4 85.5 1.0
SG B:CYS2268 2.9 97.3 1.0
CA B:CYS2220 3.3 80.8 1.0
CB B:CYS2275 3.4 0.9 1.0
SG B:CYS2275 3.5 100.0 1.0
CA B:CYS2268 3.6 97.2 1.0
N B:GLY2277 3.6 95.9 1.0
CE1 B:HIS2218 3.8 63.3 1.0
C B:CYS2275 3.9 99.7 1.0
N B:CYS2220 3.9 78.2 1.0
CA B:CYS2275 3.9 0.4 1.0
SG B:CYS2270 3.9 96.6 1.0
N B:ARG2276 4.1 98.2 1.0
CA B:GLY2277 4.1 95.4 1.0
N B:CYS2268 4.2 98.9 1.0
O B:CYS2275 4.2 0.8 1.0
O B:GLY2277 4.3 94.6 1.0
ND1 B:HIS2218 4.4 62.6 1.0
C B:GLY2277 4.6 94.9 1.0
C B:CYS2220 4.6 79.3 1.0
C B:ARG2276 4.6 96.3 1.0
C B:CYS2268 4.7 96.5 1.0
CA B:ARG2276 4.8 96.9 1.0
NE2 B:HIS2218 4.9 64.0 1.0
C B:SER2219 4.9 74.9 1.0
CB B:ARG2276 4.9 96.6 1.0
O B:CYS2268 5.0 96.8 1.0

Zinc binding site 5 out of 6 in 3ope

Go back to Zinc Binding Sites List in 3ope
Zinc binding site 5 out of 6 in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:81.1
occ:0.51
 SG B:CYS2122 2.1 99.0 1.0
SG B:CYS2128 2.4 96.4 1.0
SG B:CYS2117 2.7 81.3 1.0
ZN B:ZN6 3.0 83.7 0.5
CB B:CYS2122 3.6 98.9 1.0
CB B:CYS2117 3.7 78.6 1.0
CB B:CYS2128 3.9 96.2 1.0
SG B:CYS2104 4.1 0.7 1.0
CB B:CYS2124 4.1 0.9 1.0
CA B:CYS2122 4.4 99.8 1.0
CA B:CYS2128 4.4 96.5 1.0
SG B:CYS2124 4.7 97.8 1.0
SG B:CYS2108 4.9 96.3 1.0
NE2 B:GLN2131 5.0 68.5 1.0

Zinc binding site 6 out of 6 in 3ope

Go back to Zinc Binding Sites List in 3ope
Zinc binding site 6 out of 6 in the Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis of Auto-Inhibitory Mechanism of Histone Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:83.7
occ:0.50
 SG B:CYS2108 2.6 96.3 1.0
SG B:CYS2104 2.8 0.7 1.0
CB B:CYS2104 2.9 0.1 1.0
ZN B:ZN5 3.0 81.1 0.5
CB B:CYS2108 3.4 99.0 1.0
SG B:CYS2117 3.8 81.3 1.0
CA B:CYS2104 4.4 0.2 1.0
CA B:CYS2108 4.5 99.7 1.0
O B:CYS2104 4.7 0.7 1.0
O B:ASP2107 4.9 0.1 1.0

Reference:

S.An, K.J.Yeo, Y.H.Jeon, J.Song. Crystal Structure of the Human Histone Methyltransferase ASH1L Catalytic Domain and Its Implications For the Regulatory Mechanism J.Biol.Chem. V. 286 8369 2011.
ISSN: ISSN 0021-9258
PubMed: 21239497
DOI: 10.1074/JBC.M110.203380
Page generated: Wed Dec 16 04:41:03 2020

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