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Zinc in PDB 3shb: Crystal Structure of Phd Domain of UHRF1

Protein crystallography data

The structure of Crystal Structure of Phd Domain of UHRF1, PDB code: 3shb was solved by L.Hu, Z.Li, P.Wang, Y.Lin, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.70 / 1.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 36.609, 36.609, 219.765, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Phd Domain of UHRF1 (pdb code 3shb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Phd Domain of UHRF1, PDB code: 3shb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3shb

Go back to Zinc Binding Sites List in 3shb
Zinc binding site 1 out of 4 in the Crystal Structure of Phd Domain of UHRF1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:37.5
occ:0.86
SG A:CYS326 2.3 30.9 1.0
SG A:CYS329 2.4 36.7 1.0
SG A:CYS315 2.4 35.8 1.0
SG A:CYS318 2.4 33.4 1.0
CB A:CYS315 3.2 40.3 1.0
CB A:CYS326 3.2 30.3 1.0
CB A:CYS318 3.3 32.2 1.0
CB A:CYS329 3.4 34.7 1.0
N A:CYS329 3.7 29.3 1.0
N A:CYS318 3.8 35.8 1.0
CA A:CYS329 4.1 32.8 1.0
CA A:CYS318 4.2 39.8 1.0
NH2 A:ARG337 4.3 32.7 1.0
CB A:HIS317 4.3 37.5 1.0
O A:HOH2031 4.5 46.9 1.0
CB A:VAL328 4.6 32.1 1.0
CA A:CYS315 4.6 42.8 1.0
CA A:CYS326 4.6 29.0 1.0
C A:HIS317 4.7 40.8 1.0
C A:VAL328 4.7 32.0 1.0
N A:HIS317 4.9 40.0 1.0
C A:CYS315 4.9 42.3 1.0
CA A:HIS317 4.9 36.7 1.0
O A:HOH2039 4.9 42.3 1.0
O A:CYS315 4.9 41.7 1.0
C A:CYS329 4.9 31.4 1.0
NH1 A:ARG337 4.9 35.3 1.0
N A:VAL328 5.0 30.1 1.0
CA A:VAL328 5.0 28.9 1.0

Zinc binding site 2 out of 4 in 3shb

Go back to Zinc Binding Sites List in 3shb
Zinc binding site 2 out of 4 in the Crystal Structure of Phd Domain of UHRF1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:32.8
occ:0.79
ND1 A:HIS354 2.2 27.0 1.0
SG A:CYS357 2.3 31.8 1.0
SG A:CYS331 2.3 28.1 1.0
SG A:CYS334 2.4 29.6 1.0
CB A:CYS331 3.0 27.1 1.0
CE1 A:HIS354 3.1 29.0 1.0
CG A:HIS354 3.2 29.4 1.0
CB A:CYS357 3.3 29.4 1.0
CB A:CYS334 3.3 29.2 1.0
CB A:HIS354 3.5 27.9 1.0
N A:CYS334 3.8 29.4 1.0
CA A:CYS334 4.1 30.0 1.0
N A:HIS354 4.2 27.8 1.0
NE2 A:HIS354 4.3 29.3 1.0
CD2 A:HIS354 4.3 28.6 1.0
CA A:HIS354 4.4 25.9 1.0
CA A:CYS331 4.5 25.6 1.0
O A:HOH2003 4.5 32.8 1.0
CA A:CYS357 4.7 32.0 1.0
CB A:LEU333 4.7 31.8 1.0
CE1 A:TYR356 4.8 31.6 1.0
C A:LEU333 4.8 29.9 1.0
C A:CYS334 4.9 29.6 1.0
N A:GLY335 4.9 26.1 1.0
N A:GLY336 4.9 26.7 1.0
C A:CYS331 5.0 27.1 1.0

Zinc binding site 3 out of 4 in 3shb

Go back to Zinc Binding Sites List in 3shb
Zinc binding site 3 out of 4 in the Crystal Structure of Phd Domain of UHRF1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1003

b:35.5
occ:0.81
SG A:CYS346 2.3 31.7 1.0
SG A:CYS376 2.3 31.9 1.0
SG A:CYS349 2.4 31.4 1.0
SG A:CYS373 2.4 32.6 1.0
CB A:CYS346 3.1 30.7 1.0
CB A:CYS376 3.2 34.8 1.0
CB A:CYS349 3.3 31.6 1.0
CB A:CYS373 3.5 33.0 1.0
N A:CYS349 3.7 31.9 1.0
N A:CYS373 4.0 31.2 1.0
CA A:CYS349 4.1 33.9 1.0
N A:CYS376 4.1 33.0 1.0
CA A:CYS373 4.2 32.1 1.0
CA A:CYS376 4.3 36.2 1.0
CA A:CYS346 4.6 30.6 1.0
CB A:GLU348 4.6 35.0 1.0
O A:HOH2005 4.6 34.0 1.0
C A:GLU375 4.7 34.8 1.0
O A:CYS373 4.7 35.1 1.0
C A:CYS373 4.7 33.5 1.0
CB A:GLU375 4.7 32.2 1.0
C A:GLU348 4.8 37.6 1.0
C A:CYS349 4.8 31.6 1.0
CE2 A:PHE353 4.9 29.6 1.0
N A:ASP350 4.9 27.4 1.0
N A:GLU375 5.0 34.4 1.0

Zinc binding site 4 out of 4 in 3shb

Go back to Zinc Binding Sites List in 3shb
Zinc binding site 4 out of 4 in the Crystal Structure of Phd Domain of UHRF1


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:36.0
occ:0.85
NE2 A:HIS332 2.1 30.3 1.0
OE2 A:GLU375 2.2 36.9 1.0
OE1 A:GLU375 2.4 36.9 1.0
CD A:GLU375 2.6 36.6 1.0
CD2 A:HIS332 3.0 31.6 1.0
CE1 A:HIS332 3.1 29.3 1.0
O A:HOH2005 4.0 34.0 1.0
CG A:GLU375 4.1 35.8 1.0
CG A:HIS332 4.2 29.4 1.0
ND1 A:HIS332 4.2 28.0 1.0
O A:HOH2012 4.2 35.8 1.0
O A:HOH2050 4.7 45.8 1.0

Reference:

L.Hu, Z.Li, P.Wang, Y.Lin, Y.Xu. Crystal Structure of Phd Domain of UHRF1 and Insights Into Recognition of Unmodified Histone H3 Arginine Residue 2. Cell Res. 2011.
ISSN: ISSN 1001-0602
PubMed: 21808300
DOI: 10.1038/CR.2011.124
Page generated: Wed Dec 16 04:50:08 2020

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