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Zinc in PDB 3t6r: Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail

Protein crystallography data

The structure of Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail, PDB code: 3t6r was solved by S.Xie, J.Jakoncic, C.M.Qian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.50 / 1.95
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 41.028, 41.028, 183.010, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.9

Other elements in 3t6r:

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

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail (pdb code 3t6r). 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 in Complex with Unmodified H3 N-Terminal Tail, PDB code: 3t6r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3t6r

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Zinc binding site 1 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:27.3
occ:1.00
SG A:CYS302 2.3 22.4 1.0
SG A:CYS313 2.3 21.4 1.0
SG A:CYS316 2.3 26.0 1.0
SG A:CYS305 2.3 22.1 1.0
CB A:CYS302 3.0 25.4 1.0
CB A:CYS313 3.2 22.5 1.0
CB A:CYS316 3.3 24.4 1.0
CB A:CYS305 3.3 21.9 1.0
N A:CYS305 3.7 23.4 1.0
N A:CYS316 3.8 23.6 1.0
CA A:CYS316 4.1 24.2 1.0
O A:HOH70 4.1 40.0 1.0
CA A:CYS305 4.1 23.8 1.0
NH2 A:ARG324 4.4 29.1 1.0
CA A:CYS302 4.5 25.6 1.0
CB A:HIS304 4.6 23.2 1.0
CA A:CYS313 4.6 22.6 1.0
NH1 A:ARG324 4.7 31.2 1.0
CB A:VAL315 4.7 23.8 1.0
C A:HIS304 4.7 24.0 1.0
C A:VAL315 4.8 24.3 1.0
C A:CYS305 4.9 24.8 1.0
C A:CYS316 4.9 23.8 1.0
N A:HIS304 4.9 22.8 1.0
CA A:HIS304 5.0 23.2 1.0

Zinc binding site 2 out of 8 in 3t6r

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Zinc binding site 2 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:25.2
occ:1.00
ND1 A:HIS341 2.2 19.3 1.0
SG A:CYS321 2.3 22.4 1.0
SG A:CYS344 2.3 24.3 1.0
SG A:CYS318 2.3 19.9 1.0
CB A:CYS318 3.1 18.2 1.0
CG A:HIS341 3.1 19.8 1.0
CE1 A:HIS341 3.2 22.4 1.0
CB A:CYS321 3.2 20.4 1.0
CB A:CYS344 3.4 24.1 1.0
CB A:HIS341 3.4 17.8 1.0
N A:CYS321 3.8 20.6 1.0
CA A:CYS321 4.1 22.0 1.0
N A:HIS341 4.2 18.5 1.0
NE2 A:HIS341 4.3 22.5 1.0
CD2 A:HIS341 4.3 20.2 1.0
CA A:HIS341 4.4 19.0 1.0
CA A:CYS318 4.6 19.0 1.0
CE1 A:TYR343 4.6 21.9 1.0
CA A:CYS344 4.7 23.9 1.0
O A:HOH42 4.7 33.4 1.0
C A:CYS321 4.8 21.4 1.0
CB A:LEU320 4.8 22.7 1.0
N A:GLY322 4.9 20.6 1.0
C A:LEU320 4.9 21.8 1.0
N A:GLY323 4.9 21.4 1.0
CD1 A:TYR343 5.0 18.2 1.0

Zinc binding site 3 out of 8 in 3t6r

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Zinc binding site 3 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:31.5
occ:1.00
SG A:CYS336 2.3 28.3 1.0
SG A:CYS333 2.3 23.4 1.0
SG A:CYS360 2.4 24.9 1.0
SG A:CYS363 2.4 32.1 1.0
CB A:CYS363 3.1 34.2 1.0
CB A:CYS333 3.1 22.7 1.0
CB A:CYS336 3.4 29.2 1.0
CB A:CYS360 3.4 25.6 1.0
N A:CYS336 3.8 29.8 1.0
N A:CYS360 4.0 25.6 1.0
N A:CYS363 4.1 32.9 1.0
CA A:CYS336 4.2 28.3 1.0
CA A:CYS363 4.2 34.7 1.0
CA A:CYS360 4.3 26.7 1.0
CA A:CYS333 4.6 23.5 1.0
CB A:GLU335 4.7 31.6 1.0
C A:CYS360 4.8 27.1 1.0
C A:GLU335 4.8 31.5 1.0
O A:CYS360 4.8 26.5 1.0
C A:CYS336 4.9 27.8 1.0
CB A:GLU362 5.0 30.5 1.0
C A:GLU362 5.0 32.7 1.0

Zinc binding site 4 out of 8 in 3t6r

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Zinc binding site 4 out of 8 in the Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn8

b:33.9
occ:1.00
NE2 A:HIS319 2.0 22.2 1.0
OE2 A:GLU362 2.1 26.2 1.0
O A:HOH57 2.4 42.9 1.0
OE1 A:GLU362 2.6 32.5 1.0
CD A:GLU362 2.7 27.4 1.0
CD2 A:HIS319 3.0 19.8 1.0
CE1 A:HIS319 3.0 22.4 1.0
ND1 A:HIS319 4.1 21.2 1.0
CG A:HIS319 4.1 19.7 1.0
CG A:GLU362 4.1 31.2 1.0
O A:HOH69 4.4 38.3 1.0

Zinc binding site 5 out of 8 in 3t6r

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Zinc binding site 5 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:27.9
occ:1.00
SG B:CYS305 2.3 24.8 1.0
SG B:CYS313 2.3 22.4 1.0
SG B:CYS316 2.3 24.9 1.0
SG B:CYS302 2.4 25.1 1.0
CB B:CYS302 3.0 29.6 1.0
CB B:CYS313 3.1 21.0 1.0
CB B:CYS305 3.3 24.7 1.0
CB B:CYS316 3.4 23.7 1.0
N B:CYS305 3.8 25.4 1.0
N B:CYS316 3.9 22.5 1.0
CA B:CYS305 4.2 25.3 1.0
CA B:CYS316 4.2 23.2 1.0
CA B:CYS302 4.5 30.1 1.0
CA B:CYS313 4.6 21.2 1.0
NH2 B:ARG324 4.6 30.0 1.0
C B:HIS304 4.7 26.9 1.0
CB B:VAL315 4.7 22.9 1.0
CB B:HIS304 4.7 27.1 1.0
NH1 B:ARG324 4.8 34.7 1.0
C B:VAL315 4.9 23.1 1.0
C B:CYS302 4.9 28.8 1.0
N B:HIS304 4.9 26.7 1.0
CA B:HIS304 5.0 26.6 1.0

Zinc binding site 6 out of 8 in 3t6r

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Zinc binding site 6 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:22.9
occ:1.00
ND1 B:HIS341 2.1 16.2 1.0
SG B:CYS321 2.3 18.8 1.0
SG B:CYS344 2.3 19.6 1.0
SG B:CYS318 2.3 18.6 1.0
CB B:CYS318 3.0 16.8 1.0
CE1 B:HIS341 3.1 19.9 1.0
CG B:HIS341 3.1 17.1 1.0
CB B:CYS321 3.3 19.9 1.0
CB B:CYS344 3.3 19.0 1.0
CB B:HIS341 3.4 16.5 1.0
N B:CYS321 3.8 19.8 1.0
CA B:CYS321 4.1 20.6 1.0
N B:HIS341 4.1 16.7 1.0
NE2 B:HIS341 4.2 20.9 1.0
CD2 B:HIS341 4.3 19.5 1.0
CA B:HIS341 4.4 16.2 1.0
CA B:CYS318 4.5 18.0 1.0
CE1 B:TYR343 4.6 19.8 1.0
CA B:CYS344 4.7 19.8 1.0
CB B:LEU320 4.8 19.4 1.0
C B:LEU320 4.8 20.6 1.0
C B:CYS321 4.9 21.2 1.0
N B:GLY322 4.9 19.4 1.0
CD1 B:TYR343 5.0 19.9 1.0

Zinc binding site 7 out of 8 in 3t6r

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Zinc binding site 7 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn6

b:28.7
occ:1.00
SG B:CYS363 2.3 27.0 1.0
SG B:CYS336 2.3 24.6 1.0
SG B:CYS333 2.3 23.5 1.0
SG B:CYS360 2.4 23.1 1.0
CB B:CYS333 3.2 21.9 1.0
CB B:CYS363 3.2 29.0 1.0
CB B:CYS336 3.3 26.4 1.0
CB B:CYS360 3.4 22.2 1.0
N B:CYS336 3.7 27.0 1.0
N B:CYS360 4.0 21.4 1.0
N B:CYS363 4.1 28.8 1.0
CA B:CYS336 4.1 26.2 1.0
CA B:CYS360 4.2 23.1 1.0
CA B:CYS363 4.3 30.5 1.0
CB B:GLU335 4.5 29.3 1.0
CA B:CYS333 4.6 23.3 1.0
C B:GLU335 4.8 29.1 1.0
C B:CYS360 4.8 23.2 1.0
O B:CYS360 4.8 22.5 1.0
C B:CYS336 4.9 26.3 1.0
CE2 B:PHE340 4.9 20.0 1.0
N B:GLU335 5.0 29.1 1.0
CB B:GLU362 5.0 26.5 1.0
CA B:GLU335 5.0 28.9 1.0
C B:GLU362 5.0 28.4 1.0

Zinc binding site 8 out of 8 in 3t6r

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Zinc binding site 8 out of 8 in the Structure of UHRF1 in Complex with Unmodified 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 Structure of UHRF1 in Complex with Unmodified H3 N-Terminal Tail within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn7

b:27.6
occ:1.00
OE2 B:GLU362 1.9 25.5 1.0
OE1 A:GLU297 2.0 28.4 1.0
NE2 B:HIS319 2.1 25.6 1.0
CD B:GLU362 2.6 25.4 1.0
OE1 B:GLU362 2.7 27.8 1.0
CD A:GLU297 2.8 25.1 1.0
OE2 A:GLU297 2.9 26.3 1.0
CE1 B:HIS319 3.0 23.8 1.0
CD2 B:HIS319 3.0 22.0 1.0
CG B:GLU362 4.1 28.1 1.0
ND1 B:HIS319 4.1 19.5 1.0
CG B:HIS319 4.2 19.8 1.0
CG A:GLU297 4.2 26.9 1.0
CB A:GLU297 5.0 29.2 1.0

Reference:

S.Xie, J.Jakoncic, C.M.Qian. UHRF1 Double Tudor Domain and the Adjacent Phd Finger Act Together to Recognize K9ME3-Containing Histone H3 Tail J.Mol.Biol. V. 415 318 2012.
ISSN: ISSN 0022-2836
PubMed: 22100450
DOI: 10.1016/J.JMB.2011.11.012
Page generated: Wed Dec 16 04:51:32 2020

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