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Zinc in PDB 3zvy: Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail

Protein crystallography data

The structure of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail, PDB code: 3zvy was solved by N.Lallous, C.Birck, A.G.Mc Ewen, P.Legrand, J.P.Samama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.21 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 42.300, 42.300, 182.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.7

Other elements in 3zvy:

The structure of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail (pdb code 3zvy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail, PDB code: 3zvy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3zvy

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Zinc binding site 1 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1365

b:52.1
occ:0.90
SG A:CYS316 2.3 45.6 1.0
SG A:CYS313 2.4 39.0 1.0
SG A:CYS305 2.4 43.3 1.0
SG A:CYS302 2.4 47.0 1.0
CB A:CYS302 3.0 58.4 1.0
CB A:CYS313 3.1 32.7 1.0
CB A:CYS316 3.2 42.6 1.0
CB A:CYS305 3.3 38.5 1.0
N A:CYS316 3.7 36.3 1.0
N A:CYS305 3.8 42.5 0.5
N A:CYS305 3.8 42.5 0.5
CA A:CYS316 4.0 36.1 1.0
CA A:CYS305 4.1 42.4 1.0
O A:HOH2004 4.4 48.3 1.0
NH2 A:ARG324 4.4 50.1 1.0
CB A:HIS304 4.4 42.1 0.6
CA A:CYS302 4.5 60.0 1.0
CA A:CYS313 4.6 34.4 1.0
NH1 A:ARG324 4.6 47.0 1.0
CB A:VAL315 4.6 39.6 1.0
CB A:HIS304 4.6 42.9 0.5
C A:HIS304 4.7 45.2 0.5
C A:HIS304 4.8 45.7 0.6
C A:VAL315 4.8 36.0 1.0
C A:CYS316 4.8 39.8 1.0
C A:CYS302 4.8 53.3 1.0
O A:CYS302 4.9 52.7 1.0
C A:CYS305 4.9 46.0 1.0
CD2 A:HIS304 4.9 51.4 0.6
N A:HIS304 5.0 45.0 0.5
CA A:HIS304 5.0 44.0 0.6
N A:HIS304 5.0 45.0 0.6
CZ A:ARG324 5.0 49.8 1.0
CA A:HIS304 5.0 43.9 0.5

Zinc binding site 2 out of 8 in 3zvy

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Zinc binding site 2 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1366

b:36.4
occ:0.90
ND1 A:HIS341 2.2 23.1 1.0
SG A:CYS344 2.3 27.5 1.0
SG A:CYS318 2.3 28.5 1.0
SG A:CYS321 2.5 28.5 1.0
CB A:CYS318 3.0 23.8 1.0
CG A:HIS341 3.1 29.8 1.0
CE1 A:HIS341 3.2 28.5 1.0
CB A:CYS344 3.3 26.1 1.0
CB A:CYS321 3.3 25.1 1.0
CB A:HIS341 3.3 26.8 1.0
N A:CYS321 3.8 25.9 1.0
CA A:CYS321 4.1 28.4 1.0
N A:HIS341 4.2 29.1 1.0
CD2 A:HIS341 4.2 26.5 1.0
NE2 A:HIS341 4.3 30.8 1.0
CA A:HIS341 4.4 23.6 1.0
CE1 A:TYR343 4.5 29.3 1.0
CA A:CYS318 4.5 27.6 1.0
CB A:LEU320 4.7 30.8 1.0
CA A:CYS344 4.7 25.7 1.0
O A:HOH2029 4.7 28.4 1.0
C A:CYS321 4.8 28.4 1.0
NE2 B:GLN325 4.8 31.3 1.0
C A:LEU320 4.8 30.9 1.0
N A:GLY322 4.8 27.7 1.0
CD1 A:TYR343 4.9 27.0 1.0
N A:GLY323 5.0 31.3 1.0
C A:CYS318 5.0 25.2 1.0
N A:CYS344 5.0 27.1 1.0

Zinc binding site 3 out of 8 in 3zvy

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Zinc binding site 3 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1367

b:51.3
occ:0.90
SG A:CYS360 2.3 35.9 1.0
SG A:CYS363 2.4 44.0 1.0
SG A:CYS336 2.4 40.2 1.0
SG A:CYS333 2.5 42.0 1.0
CB A:CYS363 3.2 45.0 1.0
CB A:CYS333 3.2 34.2 1.0
CB A:CYS336 3.3 36.6 1.0
CB A:CYS360 3.4 30.3 1.0
N A:CYS336 3.7 43.3 1.0
N A:CYS360 4.0 42.9 1.0
N A:CYS363 4.0 42.8 1.0
CA A:CYS336 4.1 45.6 1.0
CA A:CYS363 4.2 47.6 1.0
CA A:CYS360 4.2 34.4 1.0
O A:HOH2023 4.3 51.9 1.0
CA A:CYS333 4.7 34.3 1.0
CB A:GLU335 4.7 54.6 1.0
C A:CYS360 4.8 32.2 1.0
O A:CYS360 4.8 37.3 1.0
C A:GLU335 4.8 49.0 1.0
CB A:GLU362 4.9 35.5 1.0
CE1 A:PHE340 4.9 35.4 1.0
C A:GLU362 4.9 37.7 1.0
C A:CYS336 4.9 46.6 1.0

Zinc binding site 4 out of 8 in 3zvy

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Zinc binding site 4 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1368

b:48.3
occ:0.90
NE2 A:HIS319 2.0 32.8 1.0
OE2 A:GLU362 2.2 36.7 1.0
OE1 A:GLU362 2.6 43.1 1.0
CD A:GLU362 2.7 35.5 1.0
CD2 A:HIS319 2.9 32.8 1.0
CE1 A:HIS319 3.1 31.1 1.0
O A:HOH2023 4.1 51.9 1.0
CG A:HIS319 4.1 33.4 1.0
ND1 A:HIS319 4.2 33.1 1.0
CG A:GLU362 4.2 31.7 1.0
O A:HOH2008 4.3 49.9 1.0

Zinc binding site 5 out of 8 in 3zvy

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Zinc binding site 5 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1366

b:51.4
occ:0.90
SG B:CYS305 2.3 40.2 1.0
SG B:CYS316 2.4 40.9 1.0
SG B:CYS313 2.4 38.0 1.0
SG B:CYS302 2.5 44.0 1.0
CB B:CYS313 3.1 30.3 1.0
CB B:CYS302 3.2 51.9 1.0
CB B:CYS305 3.2 34.0 1.0
CB B:CYS316 3.3 40.4 1.0
N B:CYS305 3.7 43.2 1.0
N B:CYS316 3.8 37.1 1.0
CA B:CYS305 4.1 37.5 1.0
CA B:CYS316 4.1 39.6 1.0
NH2 B:ARG324 4.2 37.2 1.0
O B:HOH2001 4.5 49.7 1.0
CA B:CYS313 4.6 35.2 1.0
CB B:HIS304 4.6 40.7 1.0
CA B:CYS302 4.6 51.7 1.0
CB B:VAL315 4.7 44.9 1.0
NH1 B:ARG324 4.7 41.8 1.0
C B:HIS304 4.7 45.3 1.0
C B:CYS305 4.8 44.3 1.0
C B:VAL315 4.8 39.9 1.0
O B:CYS302 4.9 46.2 1.0
C B:CYS316 4.9 38.6 1.0
C B:CYS302 4.9 46.7 1.0
CZ B:ARG324 4.9 41.1 1.0

Zinc binding site 6 out of 8 in 3zvy

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Zinc binding site 6 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1367

b:34.8
occ:0.90
ND1 B:HIS341 2.1 23.6 1.0
SG B:CYS318 2.3 25.6 1.0
SG B:CYS344 2.3 26.7 1.0
SG B:CYS321 2.4 28.1 1.0
CB B:CYS318 3.0 22.4 1.0
CE1 B:HIS341 3.0 24.2 1.0
CG B:HIS341 3.1 22.0 1.0
CB B:CYS321 3.3 27.4 1.0
CB B:CYS344 3.3 25.2 1.0
CB B:HIS341 3.4 22.4 1.0
N B:CYS321 3.7 26.2 1.0
CA B:CYS321 4.1 31.4 1.0
N B:HIS341 4.1 24.5 1.0
NE2 B:HIS341 4.1 26.4 1.0
CD2 B:HIS341 4.2 22.5 1.0
CA B:HIS341 4.4 21.6 1.0
CA B:CYS318 4.5 26.3 1.0
CE1 B:TYR343 4.6 23.9 1.0
CA B:CYS344 4.7 25.7 1.0
NE2 A:GLN325 4.7 38.4 1.0
CB B:LEU320 4.7 29.0 1.0
C B:LEU320 4.8 35.8 1.0
C B:CYS321 4.8 29.1 1.0
O A:HOH2015 4.8 34.5 1.0
N B:GLY322 4.9 31.2 1.0
N B:GLY323 4.9 26.0 1.0
C B:CYS318 5.0 30.1 1.0

Zinc binding site 7 out of 8 in 3zvy

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Zinc binding site 7 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1368

b:54.5
occ:0.90
SG B:CYS360 2.3 37.6 1.0
SG B:CYS333 2.4 41.6 1.0
SG B:CYS336 2.4 44.1 1.0
SG B:CYS363 2.5 49.2 1.0
CB B:CYS363 3.1 44.0 1.0
CB B:CYS333 3.1 35.5 1.0
CB B:CYS336 3.4 53.7 1.0
CB B:CYS360 3.5 35.9 1.0
N B:CYS336 3.7 50.8 1.0
N B:CYS363 4.0 45.0 1.0
N B:CYS360 4.0 39.0 1.0
CA B:CYS336 4.1 54.7 1.0
CA B:CYS363 4.1 47.4 1.0
CA B:CYS360 4.3 35.2 1.0
CB B:GLU335 4.6 54.8 1.0
CA B:CYS333 4.6 34.8 1.0
C B:GLU335 4.8 53.4 1.0
CB B:GLU362 4.8 39.2 1.0
CE1 B:PHE340 4.8 31.3 1.0
O B:CYS360 4.8 41.9 1.0
C B:CYS360 4.8 38.0 1.0
C B:GLU362 4.8 46.1 1.0
C B:CYS336 4.9 55.4 1.0
N B:ASP337 4.9 49.1 1.0
N B:GLU335 5.0 49.8 1.0
CA B:GLU335 5.0 51.8 1.0
CZ B:PHE340 5.0 32.3 1.0

Zinc binding site 8 out of 8 in 3zvy

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Zinc binding site 8 out of 8 in the Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Phd Finger of Human UHRF1 in Complex with Unmodified Histone H3 N- Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1369

b:50.3
occ:0.90
NE2 B:HIS319 2.1 35.1 1.0
OE2 B:GLU362 2.3 37.3 1.0
OE1 B:GLU362 2.4 43.0 1.0
CL B:CL1370 2.5 48.4 0.5
CL B:CL1370 2.6 41.9 0.6
CD B:GLU362 2.7 41.2 1.0
CE1 B:HIS319 3.1 37.5 1.0
CD2 B:HIS319 3.1 29.8 1.0
CG B:GLU362 4.2 42.9 1.0
ND1 B:HIS319 4.2 33.0 1.0
CG B:HIS319 4.2 29.3 1.0
O B:HOH2006 4.8 59.8 1.0

Reference:

N.Lallous, P.Legrand, A.G.Mcewen, S.Ramon-Maiques, J.P.Samama, C.Birck. The Phd Finger of Human UHRF1 Reveals A New Subgroup of Unmethylated Histone H3 Tail Readers. Plos One V. 6 27599 2011.
ISSN: ESSN 1932-6203
PubMed: 22096602
DOI: 10.1371/JOURNAL.PONE.0027599
Page generated: Wed Dec 16 05:00:05 2020

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