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Zinc in PDB 3sow: Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide

Protein crystallography data

The structure of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide, PDB code: 3sow was solved by E.Rajakumara, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.78 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.622, 42.622, 183.489, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide (pdb code 3sow). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide, PDB code: 3sow:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3sow

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Zinc binding site 1 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:25.5
occ:1.00
 SG A:CYS326 2.3 22.0 1.0
SG A:CYS329 2.3 27.5 1.0
SG A:CYS315 2.4 26.9 1.0
SG A:CYS318 2.5 24.4 1.0
CB A:CYS326 3.1 24.1 1.0
CB A:CYS315 3.2 27.9 1.0
CB A:CYS318 3.4 24.7 1.0
CB A:CYS329 3.4 23.0 1.0
N A:CYS318 3.8 23.6 1.0
N A:CYS329 3.8 20.5 1.0
CA A:CYS318 4.2 25.3 1.0
CA A:CYS329 4.2 23.7 1.0
NH2 A:ARG337 4.5 28.0 1.0
CB A:HIS317 4.5 23.9 1.0
CA A:CYS326 4.5 22.1 1.0
CA A:CYS315 4.6 33.7 1.0
CB A:VAL328 4.7 23.5 1.0
C A:HIS317 4.7 26.5 1.0
NH1 A:ARG337 4.7 27.8 1.0
C A:VAL328 4.9 22.9 1.0
CA A:HIS317 4.9 26.2 1.0
N A:HIS317 4.9 26.2 1.0
C A:CYS329 4.9 25.2 1.0
C A:CYS315 4.9 28.4 1.0
C A:CYS318 5.0 25.8 1.0
O A:CYS315 5.0 29.8 1.0
CG1 A:VAL328 5.0 26.4 1.0
C A:CYS326 5.0 21.4 1.0

Zinc binding site 2 out of 8 in 3sow

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Zinc binding site 2 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:19.3
occ:1.00
 ND1 A:HIS354 2.1 18.7 1.0
SG A:CYS331 2.3 18.7 1.0
SG A:CYS357 2.3 17.6 1.0
SG A:CYS334 2.4 19.4 1.0
CB A:CYS331 3.0 18.4 1.0
CG A:HIS354 3.1 20.1 1.0
CE1 A:HIS354 3.2 20.5 1.0
CB A:CYS334 3.3 19.5 1.0
CB A:HIS354 3.3 18.3 1.0
CB A:CYS357 3.3 20.0 1.0
N A:CYS334 3.8 19.1 1.0
CA A:CYS334 4.1 23.1 1.0
N A:HIS354 4.1 15.1 1.0
CD2 A:HIS354 4.2 19.8 1.0
NE2 A:HIS354 4.2 22.0 1.0
CA A:HIS354 4.3 16.9 1.0
CA A:CYS331 4.5 18.9 1.0
CE1 A:TYR356 4.6 22.6 1.0
CB A:LEU333 4.7 20.0 1.0
CA A:CYS357 4.7 19.9 1.0
C A:LEU333 4.8 22.7 1.0
C A:CYS334 4.8 20.4 1.0
N A:GLY335 4.9 17.6 1.0
C A:CYS331 5.0 20.1 1.0

Zinc binding site 3 out of 8 in 3sow

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Zinc binding site 3 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:30.0
occ:1.00
 SG A:CYS373 2.4 23.4 1.0
SG A:CYS349 2.4 28.8 1.0
SG A:CYS376 2.4 38.6 1.0
SG A:CYS346 2.5 28.2 1.0
CB A:CYS349 3.2 34.7 1.0
CB A:CYS346 3.2 27.4 1.0
CB A:CYS376 3.3 33.2 1.0
CB A:CYS373 3.4 27.0 1.0
N A:CYS349 3.6 32.1 1.0
CA A:CYS349 4.0 31.9 1.0
N A:CYS373 4.0 28.9 1.0
N A:CYS376 4.1 31.3 1.0
CA A:CYS373 4.3 28.3 1.0
CA A:CYS376 4.3 34.2 1.0
CA A:CYS346 4.7 26.9 1.0
CB A:GLU348 4.7 36.9 1.0
C A:CYS373 4.8 30.0 1.0
O A:CYS373 4.8 32.6 1.0
C A:CYS349 4.8 30.1 1.0
C A:GLU348 4.8 34.9 1.0
CE1 A:PHE353 4.8 21.4 1.0
N A:ASP350 4.9 29.9 1.0
CB A:GLU375 4.9 28.6 1.0
CZ A:PHE353 5.0 20.2 1.0
C A:GLU375 5.0 33.2 1.0

Zinc binding site 4 out of 8 in 3sow

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Zinc binding site 4 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn7

b:29.1
occ:1.00
 ND1 B:HIS317 1.9 27.0 1.0
OE2 A:GLU375 2.0 26.8 1.0
NE2 A:HIS332 2.1 26.4 1.0
CD A:GLU375 2.7 26.4 1.0
OE1 A:GLU375 2.7 26.0 1.0
CE1 B:HIS317 2.9 28.4 1.0
CG B:HIS317 2.9 28.1 1.0
CE1 A:HIS332 3.0 24.2 1.0
CD2 A:HIS332 3.1 21.8 1.0
CB B:HIS317 3.3 26.9 1.0
O B:HOH42 3.3 33.7 1.0
CA B:HIS317 3.8 27.0 1.0
NE2 B:HIS317 4.0 29.6 1.0
CD2 B:HIS317 4.0 30.2 1.0
CG A:GLU375 4.1 27.3 1.0
ND1 A:HIS332 4.2 25.4 1.0
CG A:HIS332 4.2 23.8 1.0
C B:HIS317 4.8 29.4 1.0
O B:HIS317 4.8 27.5 1.0
N B:HIS317 4.8 26.4 1.0

Zinc binding site 5 out of 8 in 3sow

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Zinc binding site 5 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:19.7
occ:1.00
 ND1 B:HIS354 2.1 17.9 1.0
SG B:CYS357 2.3 18.4 1.0
SG B:CYS331 2.4 19.2 1.0
SG B:CYS334 2.4 19.4 1.0
CG B:HIS354 3.0 20.1 1.0
CB B:CYS331 3.1 18.4 1.0
CE1 B:HIS354 3.1 19.1 1.0
CB B:CYS334 3.3 21.4 1.0
CB B:HIS354 3.3 18.3 1.0
CB B:CYS357 3.3 18.5 1.0
N B:CYS334 3.8 21.8 1.0
CA B:CYS334 4.1 21.3 1.0
N B:HIS354 4.2 17.7 1.0
CD2 B:HIS354 4.2 17.1 1.0
NE2 B:HIS354 4.2 20.6 1.0
CA B:HIS354 4.4 19.3 1.0
CA B:CYS331 4.6 20.4 1.0
CE1 B:TYR356 4.6 21.2 1.0
CB B:LEU333 4.6 18.7 1.0
CA B:CYS357 4.7 19.0 1.0
C B:LEU333 4.8 23.4 1.0
C B:CYS334 4.8 21.1 1.0
N B:GLY335 4.9 21.2 1.0

Zinc binding site 6 out of 8 in 3sow

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Zinc binding site 6 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:24.6
occ:1.00
 SG B:CYS318 2.3 23.6 1.0
SG B:CYS329 2.3 25.8 1.0
SG B:CYS326 2.4 22.2 1.0
SG B:CYS315 2.4 26.5 1.0
CB B:CYS326 3.2 23.1 1.0
CB B:CYS315 3.2 29.6 1.0
CB B:CYS318 3.3 27.3 1.0
CB B:CYS329 3.4 24.4 1.0
N B:CYS318 3.7 26.2 1.0
N B:CYS329 3.8 24.0 1.0
CA B:CYS318 4.1 28.8 1.0
CA B:CYS329 4.1 25.0 1.0
O B:HOH32 4.3 31.7 1.0
NH2 B:ARG337 4.4 29.6 1.0
CB B:HIS317 4.6 26.9 1.0
CA B:CYS326 4.6 22.3 1.0
CA B:CYS315 4.6 33.2 1.0
CB B:VAL328 4.7 25.1 1.0
C B:HIS317 4.7 29.4 1.0
NH1 B:ARG337 4.7 22.9 1.0
C B:VAL328 4.8 23.0 1.0
C B:CYS315 4.9 29.4 1.0
C B:CYS318 4.9 25.4 1.0
C B:CYS329 4.9 22.2 1.0
O B:CYS315 4.9 28.9 1.0
N B:HIS317 5.0 26.4 1.0
CA B:HIS317 5.0 27.0 1.0

Zinc binding site 7 out of 8 in 3sow

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Zinc binding site 7 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:27.7
occ:1.00
 SG B:CYS373 2.3 24.9 1.0
SG B:CYS376 2.4 29.9 1.0
SG B:CYS349 2.4 27.9 1.0
SG B:CYS346 2.4 26.7 1.0
CB B:CYS376 3.1 29.3 1.0
CB B:CYS346 3.2 26.3 1.0
CB B:CYS349 3.3 28.4 1.0
CB B:CYS373 3.5 23.4 1.0
N B:CYS349 3.7 28.7 1.0
N B:CYS373 4.1 26.8 1.0
N B:CYS376 4.1 31.3 1.0
CA B:CYS349 4.1 29.6 1.0
CA B:CYS376 4.2 31.2 1.0
CA B:CYS373 4.3 26.4 1.0
CB B:GLU348 4.5 30.8 1.0
CA B:CYS346 4.7 24.8 1.0
C B:GLU348 4.8 32.1 1.0
CE A:LYS316 4.8 40.2 1.0
C B:CYS373 4.8 26.9 1.0
O B:CYS373 4.8 28.5 1.0
CE1 B:PHE353 4.9 21.6 1.0
C B:CYS349 4.9 28.6 1.0
CA B:GLU348 4.9 30.2 1.0
N B:GLU348 4.9 32.5 1.0
N B:ASP350 5.0 26.9 1.0
C B:GLU375 5.0 31.8 1.0
NZ A:LYS316 5.0 41.9 1.0

Zinc binding site 8 out of 8 in 3sow

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Zinc binding site 8 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of UHRF1 Phd Finger in Complex with Histone H3K4ME3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:26.6
occ:1.00
 ND1 A:HIS317 2.0 25.8 1.0
OE2 B:GLU375 2.0 26.5 1.0
NE2 B:HIS332 2.1 26.4 1.0
CD B:GLU375 2.7 25.9 1.0
OE1 B:GLU375 2.7 26.7 1.0
CE1 A:HIS317 2.9 27.1 1.0
CE1 B:HIS332 3.0 23.2 1.0
CG A:HIS317 3.0 27.4 1.0
O B:HOH43 3.0 27.6 1.0
CD2 B:HIS332 3.1 23.5 1.0
CB A:HIS317 3.4 23.9 1.0
CA A:HIS317 3.9 26.2 1.0
NE2 A:HIS317 4.1 28.1 1.0
CD2 A:HIS317 4.1 29.8 1.0
ND1 B:HIS332 4.1 23.0 1.0
CG B:GLU375 4.2 23.9 1.0
CG B:HIS332 4.2 24.8 1.0
O A:HIS317 4.8 28.3 1.0
C A:HIS317 4.8 26.5 1.0
N A:HIS317 4.9 26.2 1.0

Reference:

E.Rajakumara, Z.Wang, H.Ma, L.Hu, H.Chen, Y.Lin, R.Guo, F.Wu, H.Li, F.Lan, Y.G.Shi, Y.Xu, D.J.Patel, Y.Shi. Phd Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression. Mol.Cell V. 43 275 2011.
ISSN: ISSN 1097-2765
PubMed: 21777816
DOI: 10.1016/J.MOLCEL.2011.07.006
Page generated: Sat Oct 26 15:59:49 2024

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