Atomistry » Zinc » PDB 3sjc-3sub » 3sow
Atomistry »
  Zinc »
    PDB 3sjc-3sub »
      3sow »

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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Go back to Zinc Binding Sites List in 3sow
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy