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Zinc in PDB 3sou: Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide

Protein crystallography data

The structure of Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide, PDB code: 3sou 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) 19.95 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.218, 43.218, 184.347, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 24.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of UHRF1 Phd Finger in Complex with Histone H3 1-9 Peptide (pdb code 3sou). 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 H3 1-9 Peptide, PDB code: 3sou:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3sou

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Zinc binding site 1 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:35.2
occ:1.00
 SG A:CYS326 2.3 25.4 1.0
SG A:CYS315 2.4 31.0 1.0
SG A:CYS329 2.4 27.6 1.0
SG A:CYS318 2.4 29.9 1.0
CB A:CYS315 3.1 34.1 1.0
CB A:CYS326 3.1 25.9 1.0
CB A:CYS329 3.3 27.7 1.0
CB A:CYS318 3.4 28.8 1.0
N A:CYS329 3.8 24.6 1.0
N A:CYS318 3.9 29.5 1.0
CA A:CYS329 4.2 28.4 1.0
CA A:CYS318 4.2 30.0 1.0
O A:HOH24 4.5 34.1 1.0
CA A:CYS315 4.5 35.5 1.0
CA A:CYS326 4.6 25.7 1.0
NH2 A:ARG337 4.6 32.5 1.0
CB A:HIS317 4.6 29.2 1.0
CB A:VAL328 4.7 27.0 1.0
C A:HIS317 4.8 30.5 1.0
C A:VAL328 4.9 25.0 1.0
NH1 A:ARG337 4.9 34.3 1.0
C A:CYS315 4.9 33.1 1.0
O A:CYS315 4.9 32.9 1.0
C A:CYS329 4.9 27.3 1.0

Zinc binding site 2 out of 8 in 3sou

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Zinc binding site 2 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:27.5
occ:1.00
 ND1 A:HIS354 2.2 19.4 1.0
SG A:CYS357 2.3 20.6 1.0
SG A:CYS331 2.4 21.0 1.0
SG A:CYS334 2.4 19.8 1.0
CB A:CYS331 3.1 22.3 1.0
CE1 A:HIS354 3.1 21.9 1.0
CG A:HIS354 3.2 19.9 1.0
CB A:CYS334 3.2 23.5 1.0
CB A:CYS357 3.3 22.3 1.0
CB A:HIS354 3.4 19.9 1.0
N A:CYS334 3.8 20.1 1.0
CA A:CYS334 4.1 22.3 1.0
N A:HIS354 4.2 19.6 1.0
NE2 A:HIS354 4.3 21.6 1.0
CD2 A:HIS354 4.3 21.4 1.0
CA A:HIS354 4.4 18.7 1.0
CA A:CYS331 4.6 20.4 1.0
CE1 A:TYR356 4.6 21.3 1.0
CA A:CYS357 4.7 20.7 1.0
CB A:LEU333 4.8 22.2 1.0
C A:CYS334 4.8 24.2 1.0
C A:LEU333 4.8 23.9 1.0
N A:GLY335 4.9 21.1 1.0
N A:GLY336 5.0 22.5 1.0

Zinc binding site 3 out of 8 in 3sou

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Zinc binding site 3 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:35.5
occ:1.00
 SG A:CYS349 2.3 29.6 1.0
SG A:CYS373 2.4 25.8 1.0
SG A:CYS346 2.4 25.8 1.0
SG A:CYS376 2.4 30.9 1.0
CB A:CYS346 3.2 25.4 1.0
CB A:CYS376 3.3 30.4 1.0
CB A:CYS349 3.3 34.4 1.0
CB A:CYS373 3.4 26.4 1.0
N A:CYS349 3.7 29.5 1.0
CA A:CYS349 4.1 31.0 1.0
N A:CYS373 4.1 25.8 1.0
N A:CYS376 4.2 31.6 1.0
CA A:CYS373 4.3 25.8 1.0
CA A:CYS376 4.3 31.9 1.0
O A:HOH52 4.5 36.0 1.0
CA A:CYS346 4.6 25.0 1.0
CB A:GLU348 4.6 34.7 1.0
C A:GLU348 4.7 33.5 1.0
CB A:GLU375 4.8 30.2 1.0
CE1 A:PHE353 4.8 25.0 1.0
C A:CYS373 4.8 28.9 1.0
C A:CYS349 4.9 28.8 1.0
C A:GLU375 4.9 31.6 1.0
CZ A:PHE353 4.9 25.2 1.0
N A:GLU348 5.0 31.7 1.0
O A:CYS373 5.0 28.6 1.0
CA A:GLU348 5.0 30.7 1.0

Zinc binding site 4 out of 8 in 3sou

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Zinc binding site 4 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn7

b:41.3
occ:1.00
 OE2 A:GLU375 2.0 30.8 1.0
ND1 B:HIS317 2.0 33.0 1.0
NE2 A:HIS332 2.2 30.9 1.0
O B:HOH101 2.3 39.1 1.0
CD A:GLU375 2.8 29.9 1.0
OE1 A:GLU375 2.9 31.0 1.0
CD2 A:HIS332 3.0 28.1 1.0
CE1 B:HIS317 3.0 32.9 1.0
CG B:HIS317 3.0 31.8 1.0
CE1 A:HIS332 3.2 29.8 1.0
CB B:HIS317 3.4 29.4 1.0
O B:HOH120 3.8 40.6 1.0
CA B:HIS317 3.9 28.8 1.0
O A:HOH81 4.0 38.7 1.0
NE2 B:HIS317 4.1 33.2 1.0
CD2 B:HIS317 4.1 33.8 1.0
CG A:HIS332 4.2 25.5 1.0
CG A:GLU375 4.2 27.6 1.0
ND1 A:HIS332 4.3 27.0 1.0
O A:HOH52 4.3 36.0 1.0
O B:HIS317 4.8 29.9 1.0
C B:HIS317 4.8 28.2 1.0
N B:HIS317 4.8 31.1 1.0

Zinc binding site 5 out of 8 in 3sou

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Zinc binding site 5 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:29.1
occ:1.00
 ND1 B:HIS354 2.2 19.6 1.0
SG B:CYS334 2.3 22.4 1.0
SG B:CYS331 2.3 19.5 1.0
SG B:CYS357 2.4 21.2 1.0
CB B:CYS331 3.0 23.2 1.0
CE1 B:HIS354 3.1 21.8 1.0
CG B:HIS354 3.1 20.5 1.0
CB B:CYS334 3.3 24.7 1.0
CB B:CYS357 3.4 22.0 1.0
CB B:HIS354 3.4 21.9 1.0
N B:CYS334 3.8 23.9 1.0
CA B:CYS334 4.1 24.2 1.0
N B:HIS354 4.2 18.6 1.0
NE2 B:HIS354 4.2 20.6 1.0
CD2 B:HIS354 4.3 21.7 1.0
CA B:HIS354 4.4 18.3 1.0
CA B:CYS331 4.5 22.5 1.0
CE1 B:TYR356 4.6 21.5 1.0
O B:HOH86 4.7 28.3 1.0
CA B:CYS357 4.8 22.6 1.0
C B:CYS334 4.8 24.8 1.0
CB B:LEU333 4.8 24.4 1.0
N B:GLY335 4.8 21.3 1.0
C B:LEU333 4.8 24.8 1.0
N B:GLY336 5.0 21.9 1.0

Zinc binding site 6 out of 8 in 3sou

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Zinc binding site 6 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:33.9
occ:1.00
 SG B:CYS329 2.3 26.3 1.0
SG B:CYS318 2.4 27.7 1.0
SG B:CYS326 2.4 25.2 1.0
SG B:CYS315 2.4 27.9 1.0
CB B:CYS326 3.1 28.1 1.0
CB B:CYS315 3.1 31.8 1.0
CB B:CYS329 3.3 27.1 1.0
CB B:CYS318 3.3 30.2 1.0
N B:CYS329 3.8 22.6 1.0
N B:CYS318 3.8 27.7 1.0
CA B:CYS329 4.1 25.7 1.0
CA B:CYS318 4.2 29.3 1.0
O B:HOH45 4.3 35.0 1.0
NH2 B:ARG337 4.4 34.0 1.0
CB B:HIS317 4.5 29.4 1.0
CA B:CYS326 4.6 26.2 1.0
CA B:CYS315 4.6 35.1 1.0
CB B:VAL328 4.7 27.7 1.0
NH1 B:ARG337 4.7 31.8 1.0
C B:HIS317 4.7 28.2 1.0
C B:VAL328 4.8 26.0 1.0
C B:CYS329 4.9 26.2 1.0
O B:CYS315 4.9 28.9 1.0
C B:CYS315 4.9 31.7 1.0
CA B:HIS317 5.0 28.8 1.0

Zinc binding site 7 out of 8 in 3sou

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Zinc binding site 7 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:33.0
occ:1.00
 SG B:CYS376 2.3 28.4 1.0
SG B:CYS349 2.4 27.2 1.0
SG B:CYS373 2.4 25.1 1.0
SG B:CYS346 2.4 27.4 1.0
CB B:CYS376 3.2 28.8 1.0
CB B:CYS346 3.2 25.8 1.0
CB B:CYS349 3.3 29.5 1.0
CB B:CYS373 3.4 26.6 1.0
N B:CYS349 3.8 28.2 1.0
N B:CYS373 4.1 25.1 1.0
CA B:CYS349 4.1 24.9 1.0
N B:CYS376 4.1 29.7 1.0
CA B:CYS376 4.3 30.9 1.0
CA B:CYS373 4.3 25.8 1.0
CB B:GLU348 4.6 31.4 1.0
CA B:CYS346 4.7 24.9 1.0
C B:CYS373 4.8 28.6 1.0
O B:CYS373 4.8 30.3 1.0
C B:GLU348 4.8 30.9 1.0
CB B:GLU375 4.8 28.6 1.0
C B:GLU375 4.8 30.0 1.0
CE1 B:PHE353 4.9 24.1 1.0
C B:CYS349 4.9 29.0 1.0
N B:ASP350 5.0 25.9 1.0

Zinc binding site 8 out of 8 in 3sou

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Zinc binding site 8 out of 8 in the Structure of UHRF1 Phd Finger in Complex with Histone H3 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 H3 1-9 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn8

b:38.8
occ:1.00
 ND1 A:HIS317 2.0 29.6 1.0
OE2 B:GLU375 2.0 28.5 1.0
NE2 B:HIS332 2.1 31.6 1.0
O B:HOH102 2.1 35.7 1.0
CD B:GLU375 2.7 30.5 1.0
OE1 B:GLU375 2.8 29.5 1.0
CE1 A:HIS317 3.0 31.5 1.0
CD2 B:HIS332 3.0 27.7 1.0
CG A:HIS317 3.0 29.5 1.0
CE1 B:HIS332 3.1 30.3 1.0
CB A:HIS317 3.4 29.2 1.0
O B:HOH108 3.7 25.8 1.0
CA A:HIS317 3.8 31.0 1.0
NE2 A:HIS317 4.1 28.7 1.0
O B:HOH66 4.1 35.0 1.0
CD2 A:HIS317 4.1 30.3 1.0
O B:HOH42 4.1 34.5 1.0
CG B:HIS332 4.2 27.6 1.0
ND1 B:HIS332 4.2 27.8 1.0
CG B:GLU375 4.2 29.2 1.0
N A:HIS317 4.7 31.5 1.0
C A:HIS317 4.9 30.5 1.0
O A:HIS317 4.9 31.6 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 15:58:45 2024

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