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Zinc in PDB 1peg: Structural Basis For the Product Specificity of Histone Lysine Methyltransferases

Enzymatic activity of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases

All present enzymatic activity of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases:
2.1.1.43;

Protein crystallography data

The structure of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases, PDB code: 1peg was solved by X.Zhang, Z.Yang, S.I.Khan, J.R.Horton, H.Tamaru, E.U.Selker, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.90 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.260, 94.170, 114.690, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 32

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases (pdb code 1peg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases, PDB code: 1peg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1peg

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Zinc binding site 1 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:44.9
occ:1.00
 SG A:CYS81 2.3 40.4 1.0
SG A:CYS66 2.3 46.9 1.0
SG A:CYS132 2.3 45.9 1.0
SG A:CYS128 2.4 42.5 1.0
CB A:CYS132 3.0 48.4 1.0
CB A:CYS66 3.2 52.9 1.0
CB A:CYS128 3.4 36.3 1.0
N A:CYS66 3.5 51.7 1.0
CB A:CYS81 3.7 41.4 1.0
CA A:CYS128 3.8 33.5 1.0
ZN A:ZN2 3.8 44.9 1.0
ZN A:ZN3 3.9 44.9 1.0
CA A:CYS66 4.0 54.7 1.0
SG A:CYS79 4.1 41.6 1.0
CA A:CYS132 4.4 49.8 1.0
C A:GLY65 4.4 46.3 1.0
SG A:CYS134 4.5 48.6 1.0
N A:HIS129 4.6 45.0 1.0
SG A:CYS74 4.7 37.5 1.0
CA A:GLY65 4.7 44.1 1.0
C A:CYS128 4.8 37.4 1.0
N A:CYS128 4.8 25.7 1.0
O A:CYS66 4.9 57.6 1.0
C A:CYS66 4.9 59.9 1.0
N A:CYS132 4.9 46.0 1.0
CA A:CYS81 5.0 43.1 1.0

Zinc binding site 2 out of 8 in 1peg

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Zinc binding site 2 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:44.9
occ:1.00
 SG A:CYS74 2.2 37.5 1.0
SG A:CYS134 2.3 48.6 1.0
SG A:CYS128 2.3 42.5 1.0
SG A:CYS138 2.3 58.8 1.0
CB A:CYS74 3.1 43.1 1.0
CB A:CYS128 3.2 36.3 1.0
CB A:CYS134 3.2 57.0 1.0
CB A:CYS138 3.4 45.5 1.0
ZN A:ZN3 3.7 44.9 1.0
SG A:CYS66 3.8 46.9 1.0
ZN A:ZN1 3.8 44.9 1.0
CA A:CYS74 4.6 44.8 1.0
CB A:CYS132 4.6 48.4 1.0
CA A:CYS138 4.7 42.2 1.0
CA A:CYS128 4.7 33.5 1.0
CA A:CYS134 4.7 62.0 1.0

Zinc binding site 3 out of 8 in 1peg

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Zinc binding site 3 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:44.9
occ:1.00
 SG A:CYS66 2.3 46.9 1.0
SG A:CYS74 2.3 37.5 1.0
SG A:CYS79 2.3 41.6 1.0
SG A:CYS68 2.3 56.6 1.0
CB A:CYS74 3.2 43.1 1.0
CB A:CYS66 3.2 52.9 1.0
CB A:CYS68 3.2 54.6 1.0
CB A:CYS79 3.3 55.9 1.0
CA A:CYS74 3.7 44.8 1.0
ZN A:ZN2 3.7 44.9 1.0
ZN A:ZN1 3.9 44.9 1.0
SG A:CYS128 4.1 42.5 1.0
CA A:CYS79 4.3 66.8 1.0
N A:CYS74 4.4 55.5 1.0
CA A:CYS68 4.5 58.5 1.0
CA A:CYS66 4.6 54.7 1.0
N A:CYS68 4.7 60.4 1.0
O A:GLU73 4.8 48.6 1.0
SG A:CYS81 4.8 40.4 1.0
C A:GLU73 4.8 57.1 1.0
C A:CYS66 4.9 59.9 1.0
C A:CYS74 4.9 42.4 1.0

Zinc binding site 4 out of 8 in 1peg

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Zinc binding site 4 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:71.5
occ:1.00
 SG A:CYS313 2.3 93.8 1.0
SG A:CYS308 2.3 60.1 1.0
SG A:CYS306 2.3 72.7 1.0
SG A:CYS244 2.3 72.6 1.0
CB A:CYS313 3.3 84.2 1.0
CB A:CYS306 3.3 68.0 1.0
CB A:CYS244 3.3 66.8 1.0
CB A:CYS308 3.3 69.7 1.0
CA A:CYS313 3.6 82.6 1.0
N A:CYS244 4.1 56.1 1.0
N A:ARG314 4.2 90.3 1.0
NE2 A:HIS242 4.2 62.9 1.0
C A:CYS313 4.3 81.9 1.0
N A:CYS308 4.3 73.5 1.0
CA A:CYS244 4.3 61.5 1.0
O A:CYS308 4.3 79.9 1.0
CA A:CYS308 4.3 75.6 1.0
CD2 A:HIS242 4.3 49.6 1.0
C A:SER243 4.6 51.7 1.0
CA A:CYS306 4.6 67.5 1.0
C A:CYS308 4.8 81.5 1.0
N A:CYS313 4.8 74.6 1.0
CB A:THR310 4.8 81.5 1.0
C A:CYS306 4.8 65.6 1.0

Zinc binding site 5 out of 8 in 1peg

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Zinc binding site 5 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:70.7
occ:1.00
 CB B:CYS132 3.2 76.3 1.0
ZN B:ZN6 3.5 77.0 1.0
CA B:CYS128 3.7 91.1 1.0
ZN B:ZN7 4.0 98.6 1.0
CA B:CYS66 4.3 92.5 1.0
CA B:CYS132 4.5 84.0 1.0
CA B:CYS81 4.6 96.9 1.0

Zinc binding site 6 out of 8 in 1peg

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Zinc binding site 6 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:77.0
occ:1.00
 SG B:CYS134 2.8 64.6 1.0
SG B:CYS138 3.1 88.0 1.0
ZN B:ZN7 3.4 98.6 1.0
ZN B:ZN5 3.5 70.7 1.0
CB B:CYS134 4.0 75.0 1.0
CB B:CYS132 4.2 76.3 1.0
CA B:CYS128 4.3 91.1 1.0
CB B:CYS138 4.4 74.3 1.0
CB B:ASN140 4.9 48.8 1.0

Zinc binding site 7 out of 8 in 1peg

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Zinc binding site 7 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn7

b:98.6
occ:1.00
 ZN B:ZN6 3.4 77.0 1.0
CA B:CYS74 4.0 72.6 1.0
ZN B:ZN5 4.0 70.7 1.0
CA B:CYS79 4.1 0.0 1.0
CA B:CYS68 4.9 0.0 1.0

Zinc binding site 8 out of 8 in 1peg

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Zinc binding site 8 out of 8 in the Structural Basis For the Product Specificity of Histone Lysine Methyltransferases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For the Product Specificity of Histone Lysine Methyltransferases within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:56.4
occ:1.00
 SG B:CYS308 2.3 60.8 1.0
SG B:CYS306 2.3 59.7 1.0
SG B:CYS244 2.4 73.8 1.0
SG B:CYS313 2.4 69.4 1.0
CB B:CYS244 3.3 60.1 1.0
CB B:CYS308 3.3 44.4 1.0
CB B:CYS313 3.3 55.8 1.0
CB B:CYS306 3.4 63.1 1.0
CA B:CYS313 3.6 59.5 1.0
N B:CYS244 4.1 55.2 1.0
N B:ARG314 4.2 53.4 1.0
CA B:CYS244 4.3 55.4 1.0
CA B:CYS308 4.3 51.2 1.0
N B:CYS308 4.3 60.0 1.0
C B:CYS313 4.3 55.0 1.0
O B:CYS308 4.3 57.0 1.0
NE2 B:HIS242 4.5 67.8 1.0
CD2 B:HIS242 4.6 58.5 1.0
CB B:THR310 4.7 48.5 1.0
C B:SER243 4.7 52.0 1.0
C B:CYS308 4.7 57.3 1.0
CA B:CYS306 4.7 67.2 1.0
N B:CYS313 4.8 59.1 1.0
C B:CYS306 4.9 71.8 1.0
O B:THR310 5.0 53.2 1.0

Reference:

X.Zhang, Z.Yang, S.I.Khan, J.R.Horton, H.Tamaru, E.U.Selker, X.Cheng. Structural Basis For the Product Specificity of Histone Lysine Methyltransferases Mol.Cell V. 12 177 2003.
ISSN: ISSN 1097-2765
PubMed: 12887903
DOI: 10.1016/S1097-2765(03)00224-7
Page generated: Wed Oct 16 17:48:29 2024

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