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Zinc in PDB 8xv8: Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)

Enzymatic activity of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)

All present enzymatic activity of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121):
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121), PDB code: 8xv8 was solved by X.Du, Q.Gan, J.Xu, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.23 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.029, 46.02, 82.91, 90, 112.76, 90
R / Rfree (%) 18.6 / 20.7

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) (pdb code 8xv8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121), PDB code: 8xv8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 8xv8

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Zinc binding site 1 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


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 Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:35.4
occ:1.00
 SG A:CYS313 2.3 30.3 1.0
SG A:CYS305 2.3 34.3 1.0
SG A:CYS316 2.3 35.4 1.0
SG A:CYS302 2.3 37.6 1.0
CB A:CYS302 3.1 42.0 1.0
CB A:CYS313 3.2 33.1 1.0
CB A:CYS305 3.2 39.4 1.0
CB A:CYS316 3.4 30.1 1.0
N A:CYS316 3.7 29.2 1.0
N A:CYS305 3.7 44.9 1.0
CA A:CYS305 4.0 44.6 1.0
CA A:CYS316 4.1 29.3 1.0
NH2 A:ARG324 4.2 36.2 1.0
CA A:CYS302 4.6 47.3 1.0
CB A:VAL315 4.6 34.9 1.0
CA A:CYS313 4.6 28.4 1.0
C A:VAL315 4.7 31.1 1.0
C A:HIS304 4.7 45.4 1.0
CB A:HIS304 4.9 52.4 1.0
C A:CYS305 4.9 45.5 1.0
NH1 A:ARG324 4.9 31.6 1.0
C A:CYS316 4.9 29.0 1.0
CA A:VAL315 5.0 30.3 1.0
N A:VAL315 5.0 26.8 1.0
C A:CYS302 5.0 48.8 1.0
O A:CYS302 5.0 42.8 1.0
N A:LYS306 5.0 47.9 1.0

Zinc binding site 2 out of 14 in 8xv8

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Zinc binding site 2 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


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 Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:27.5
occ:1.00
 ND1 A:HIS341 2.1 23.3 1.0
SG A:CYS321 2.3 27.4 1.0
SG A:CYS318 2.3 24.5 1.0
SG A:CYS344 2.3 29.2 1.0
CB A:CYS318 3.1 27.1 1.0
CE1 A:HIS341 3.1 24.7 1.0
CG A:HIS341 3.1 23.8 1.0
CB A:CYS344 3.3 25.6 1.0
CB A:CYS321 3.3 27.1 1.0
CB A:HIS341 3.4 23.9 1.0
N A:CYS321 3.8 27.2 1.0
O A:HOH517 4.0 37.6 1.0
CA A:CYS321 4.1 27.0 1.0
NE2 A:HIS341 4.2 24.0 1.0
O A:HOH518 4.2 54.3 1.0
CD2 A:HIS341 4.3 24.0 1.0
N A:HIS341 4.3 22.1 1.0
CA A:HIS341 4.5 26.1 1.0
CA A:CYS318 4.5 28.3 1.0
CA A:CYS344 4.7 28.7 1.0
CB A:LEU320 4.7 28.5 1.0
C A:CYS321 4.8 28.9 1.0
C A:LEU320 4.8 29.6 1.0
CE1 A:TYR343 4.9 30.0 1.0
N A:GLY322 4.9 28.8 1.0
N A:GLY323 4.9 27.7 1.0

Zinc binding site 3 out of 14 in 8xv8

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Zinc binding site 3 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


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 Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:31.0
occ:1.00
 SG A:CYS333 2.3 30.1 1.0
SG A:CYS360 2.3 28.9 1.0
SG A:CYS336 2.3 34.1 1.0
SG A:CYS363 2.3 34.5 1.0
CB A:CYS333 3.2 30.4 1.0
CB A:CYS363 3.2 36.1 1.0
CB A:CYS336 3.3 33.1 1.0
CB A:CYS360 3.4 28.0 1.0
N A:CYS336 3.7 40.4 1.0
N A:CYS360 4.0 28.5 1.0
N A:CYS363 4.1 33.0 1.0
CA A:CYS336 4.1 36.7 1.0
NH2 G:ARG314 4.2 41.5 1.0
CA A:CYS360 4.2 30.6 1.0
O G:HOH507 4.2 41.0 1.0
CA A:CYS363 4.2 34.2 1.0
CB A:GLU335 4.5 47.8 1.0
CA A:CYS333 4.6 30.6 1.0
C A:CYS360 4.7 29.3 1.0
C A:GLU335 4.8 40.9 1.0
O A:CYS360 4.8 29.1 1.0
CE1 A:PHE340 4.9 25.4 1.0
C A:CYS336 4.9 32.2 1.0
CG A:GLU335 4.9 55.4 1.0
N A:GLU335 5.0 39.6 1.0
N A:ASP337 5.0 31.3 1.0
CA A:GLU335 5.0 39.3 1.0

Zinc binding site 4 out of 14 in 8xv8

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Zinc binding site 4 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


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 Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:28.4
occ:1.00
 OE2 G:GLU362 2.0 31.6 1.0
OE2 A:GLU362 2.0 28.7 1.0
NE2 G:HIS319 2.1 29.0 1.0
NE2 A:HIS319 2.1 30.3 1.0
OE1 A:GLU362 2.2 30.5 1.0
OE1 G:GLU362 2.2 32.9 1.0
CD A:GLU362 2.4 29.5 1.0
CD G:GLU362 2.5 33.4 1.0
CD2 G:HIS319 3.0 27.7 1.0
CE1 G:HIS319 3.1 29.0 1.0
CD2 A:HIS319 3.1 24.8 1.0
CE1 A:HIS319 3.1 27.9 1.0
O A:HOH502 3.9 40.2 1.0
CG A:GLU362 4.0 29.3 1.0
CG G:GLU362 4.0 35.7 1.0
ND1 G:HIS319 4.2 30.8 1.0
CG G:HIS319 4.2 31.4 1.0
O A:HOH512 4.2 35.7 1.0
CG A:HIS319 4.2 25.2 1.0
ND1 A:HIS319 4.2 24.5 1.0
NH2 A:ARG314 4.4 35.9 1.0
O G:HOH507 4.5 41.0 1.0
NH1 G:ARG314 4.9 33.9 1.0

Zinc binding site 5 out of 14 in 8xv8

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Zinc binding site 5 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:35.1
occ:1.00
 SG C:CYS313 2.3 35.0 1.0
SG C:CYS305 2.3 31.4 1.0
SG C:CYS316 2.3 34.5 1.0
SG C:CYS302 2.3 37.4 1.0
CB C:CYS302 3.1 40.2 1.0
CB C:CYS313 3.2 32.8 1.0
CB C:CYS305 3.3 41.0 1.0
CB C:CYS316 3.4 30.9 1.0
N C:CYS316 3.6 29.5 1.0
N C:CYS305 3.7 51.1 1.0
CA C:CYS305 4.1 41.0 1.0
CA C:CYS316 4.1 30.9 1.0
NH2 C:ARG324 4.3 28.6 1.0
O C:HOH506 4.4 48.3 1.0
CA C:CYS302 4.6 40.3 1.0
CA C:CYS313 4.6 32.7 1.0
CB C:VAL315 4.6 35.6 1.0
C C:VAL315 4.7 29.0 1.0
C C:HIS304 4.8 51.7 1.0
C C:CYS305 4.8 42.6 1.0
CB C:HIS304 4.9 48.8 1.0
NH1 C:ARG324 4.9 27.4 1.0
C C:CYS316 4.9 30.8 1.0
C C:CYS302 5.0 38.5 1.0
CA C:VAL315 5.0 32.8 1.0
N C:VAL315 5.0 31.7 1.0
N C:LYS306 5.0 44.6 1.0
O C:CYS302 5.0 39.1 1.0

Zinc binding site 6 out of 14 in 8xv8

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Zinc binding site 6 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:26.7
occ:1.00
 ND1 C:HIS341 2.1 23.0 1.0
SG C:CYS321 2.2 27.7 1.0
SG C:CYS344 2.3 28.7 1.0
SG C:CYS318 2.3 25.7 1.0
CE1 C:HIS341 3.0 23.0 1.0
CG C:HIS341 3.1 23.2 1.0
CB C:CYS318 3.1 22.7 1.0
CB C:CYS321 3.3 30.9 1.0
CB C:CYS344 3.4 30.6 1.0
CB C:HIS341 3.5 23.7 1.0
N C:CYS321 3.8 33.0 1.0
CA C:CYS321 4.1 30.8 1.0
NE2 C:HIS341 4.2 21.1 1.0
CD2 C:HIS341 4.2 23.9 1.0
N C:HIS341 4.3 25.6 1.0
CA C:HIS341 4.5 25.8 1.0
CA C:CYS318 4.6 24.7 1.0
CA C:CYS344 4.7 32.2 1.0
CB C:LEU320 4.7 34.0 1.0
C C:CYS321 4.8 28.5 1.0
C C:LEU320 4.8 31.8 1.0
CE1 C:TYR343 4.8 29.4 1.0
N C:GLY322 4.9 28.0 1.0
N C:GLY323 4.9 27.9 1.0

Zinc binding site 7 out of 14 in 8xv8

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Zinc binding site 7 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:34.7
occ:1.00
 SG C:CYS336 2.3 32.5 1.0
SG C:CYS333 2.3 33.3 1.0
SG C:CYS360 2.3 31.7 1.0
SG C:CYS363 2.4 35.7 1.0
CB C:CYS333 3.1 29.4 1.0
CB C:CYS363 3.3 38.9 1.0
CB C:CYS336 3.3 32.6 1.0
CB C:CYS360 3.4 31.5 1.0
N C:CYS336 3.7 34.2 1.0
N C:CYS360 4.0 32.5 1.0
CA C:CYS336 4.1 32.8 1.0
N C:CYS363 4.1 45.4 1.0
NH2 E:ARG314 4.2 45.3 1.0
CA C:CYS360 4.3 34.7 1.0
CA C:CYS363 4.3 44.9 1.0
CB C:GLU335 4.6 41.5 1.0
CA C:CYS333 4.6 33.3 1.0
C C:GLU335 4.8 37.9 1.0
O C:CYS360 4.8 39.5 1.0
C C:CYS360 4.8 36.7 1.0
CE1 C:PHE340 4.9 31.6 1.0
C C:CYS336 4.9 29.6 1.0
N C:ASP337 4.9 31.1 1.0
CB C:GLU362 5.0 33.9 1.0
N C:GLU335 5.0 40.8 1.0
CG C:GLU335 5.0 55.9 1.0
C C:GLU362 5.0 41.3 1.0

Zinc binding site 8 out of 14 in 8xv8

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Zinc binding site 8 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn404

b:31.6
occ:1.00
 OE2 C:GLU362 2.0 34.5 1.0
OE2 E:GLU362 2.0 31.5 1.0
NE2 C:HIS319 2.1 32.6 1.0
OE1 C:GLU362 2.1 27.9 1.0
NE2 E:HIS319 2.1 35.0 1.0
OE1 E:GLU362 2.1 28.3 1.0
CD C:GLU362 2.4 27.4 1.0
CD E:GLU362 2.5 29.3 1.0
CD2 C:HIS319 3.0 28.3 1.0
CD2 E:HIS319 3.1 33.0 1.0
CE1 C:HIS319 3.1 34.7 1.0
CE1 E:HIS319 3.1 35.3 1.0
CG C:GLU362 3.9 31.1 1.0
CG E:GLU362 4.0 32.7 1.0
CG C:HIS319 4.1 29.6 1.0
ND1 C:HIS319 4.2 33.3 1.0
CG E:HIS319 4.2 34.4 1.0
ND1 E:HIS319 4.2 33.0 1.0
O C:HOH502 4.4 40.5 1.0
NH1 C:ARG314 4.6 56.8 1.0
NH1 E:ARG314 4.9 39.1 1.0

Zinc binding site 9 out of 14 in 8xv8

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Zinc binding site 9 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:38.0
occ:1.00
 SG E:CYS313 2.3 35.4 1.0
SG E:CYS316 2.3 34.2 1.0
SG E:CYS302 2.3 38.7 1.0
SG E:CYS305 2.3 38.1 1.0
CB E:CYS302 3.2 41.0 1.0
CB E:CYS313 3.2 35.1 1.0
CB E:CYS305 3.3 44.4 1.0
CB E:CYS316 3.4 33.7 1.0
N E:CYS316 3.7 36.2 1.0
N E:CYS305 3.7 49.8 1.0
CA E:CYS316 4.1 36.7 1.0
CA E:CYS305 4.1 48.3 1.0
NH2 E:ARG324 4.3 37.4 1.0
CB E:VAL315 4.5 38.3 1.0
CA E:CYS302 4.6 46.0 1.0
C E:VAL315 4.7 34.4 1.0
CA E:CYS313 4.7 33.8 1.0
C E:HIS304 4.7 54.5 1.0
CB E:HIS304 4.7 55.7 1.0
NH1 E:ARG324 4.9 33.9 1.0
C E:CYS305 4.9 50.5 1.0
C E:CYS316 4.9 36.3 1.0
C E:CYS302 5.0 44.5 1.0
CA E:VAL315 5.0 33.5 1.0
N E:VAL315 5.0 29.4 1.0
O E:CYS302 5.0 41.3 1.0
N E:HIS304 5.0 60.0 1.0

Zinc binding site 10 out of 14 in 8xv8

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Zinc binding site 10 out of 14 in the Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:39.1
occ:1.00
 ND1 E:HIS341 2.1 35.7 1.0
SG E:CYS321 2.2 32.6 1.0
SG E:CYS318 2.3 39.6 1.0
SG E:CYS344 2.4 43.8 1.0
CE1 E:HIS341 3.0 34.3 1.0
CB E:CYS318 3.0 31.6 1.0
CG E:HIS341 3.1 34.2 1.0
CB E:CYS321 3.3 37.5 1.0
CB E:CYS344 3.4 42.0 1.0
CB E:HIS341 3.5 37.0 1.0
N E:CYS321 3.8 38.0 1.0
CA E:CYS321 4.1 35.9 1.0
NE2 E:HIS341 4.2 33.6 1.0
CD2 E:HIS341 4.2 33.1 1.0
N E:HIS341 4.3 34.3 1.0
CA E:HIS341 4.5 37.3 1.0
CA E:CYS318 4.5 31.1 1.0
CB E:LEU320 4.7 40.3 1.0
CA E:CYS344 4.7 47.4 1.0
C E:CYS321 4.8 36.6 1.0
N E:GLY322 4.8 36.0 1.0
C E:LEU320 4.8 39.0 1.0
N E:GLY323 4.9 36.8 1.0
CE1 E:TYR343 4.9 44.8 1.0

Reference:

X.Du, Q.Gan, J.Xu, J.Liu. Crystal Structure of Phd Domain of UHRF1 in Complex with Hstella Peptide (Residues 75-121) To Be Published.
Page generated: Fri Aug 22 15:41:35 2025

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