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Zinc in PDB 8xv4: Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)

Enzymatic activity of Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)

All present enzymatic activity of Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119):
2.3.2.27;

Protein crystallography data

The structure of Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119), PDB code: 8xv4 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) 19.99 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.713, 72.365, 63.065, 90, 108.05, 90
R / Rfree (%) 22.7 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) (pdb code 8xv4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119), PDB code: 8xv4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8xv4

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Zinc binding site 1 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:48.1
occ:1.00
 ND1 A:HIS341 2.1 52.8 1.0
SG A:CYS321 2.3 45.6 1.0
SG A:CYS318 2.3 57.7 1.0
SG A:CYS344 2.3 48.9 1.0
CE1 A:HIS341 3.1 52.2 1.0
CG A:HIS341 3.1 53.4 1.0
CB A:CYS318 3.2 58.3 1.0
CB A:CYS321 3.3 46.7 1.0
CB A:CYS344 3.3 52.3 1.0
CB A:HIS341 3.4 55.2 1.0
N A:CYS321 3.7 47.1 1.0
CA A:CYS321 4.1 47.8 1.0
NE2 A:HIS341 4.2 51.6 1.0
CD2 A:HIS341 4.2 51.6 1.0
N A:HIS341 4.3 57.2 1.0
CA A:HIS341 4.5 55.0 1.0
CA A:CYS318 4.6 54.3 1.0
CA A:CYS344 4.7 53.8 1.0
N A:GLY322 4.7 52.2 1.0
CB A:LEU320 4.7 48.8 1.0
C A:CYS321 4.8 50.6 1.0
CE1 A:TYR343 4.8 56.6 1.0
N A:GLY323 4.9 51.4 1.0
C A:LEU320 4.9 49.0 1.0

Zinc binding site 2 out of 7 in 8xv4

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Zinc binding site 2 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:46.3
occ:1.00
 NE2 A:HIS304 2.0 53.3 1.0
NE2 B:HIS304 2.0 46.8 1.0
OE1 C:GLU109 2.0 48.3 1.0
OE1 D:GLU109 2.0 54.6 1.0
CD D:GLU109 2.8 56.6 1.0
CD C:GLU109 2.8 49.3 1.0
OE2 D:GLU109 2.8 56.7 1.0
OE2 C:GLU109 2.9 48.6 1.0
CE1 A:HIS304 3.0 54.9 1.0
CD2 B:HIS304 3.0 46.8 1.0
CE1 B:HIS304 3.0 46.5 1.0
CD2 A:HIS304 3.0 55.3 1.0
ND1 A:HIS304 4.1 57.0 1.0
CD A:LYS303 4.1 63.0 1.0
ND1 B:HIS304 4.1 45.8 1.0
CG B:HIS304 4.1 46.9 1.0
CG A:HIS304 4.1 55.5 1.0
CD B:LYS303 4.1 77.5 1.0
CG D:GLU109 4.2 57.6 1.0
CG C:GLU109 4.3 49.7 1.0
CG B:LYS303 4.4 75.4 1.0
CB C:GLU109 4.9 51.9 1.0
CB D:GLU109 4.9 61.0 1.0
CE A:LYS303 4.9 63.5 1.0
NZ A:LYS303 5.0 65.0 1.0
CG A:LYS303 5.0 64.2 1.0

Zinc binding site 3 out of 7 in 8xv4

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Zinc binding site 3 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:59.1
occ:1.00
 SG A:CYS333 2.3 55.8 1.0
SG A:CYS360 2.3 62.6 1.0
SG A:CYS336 2.3 51.6 1.0
SG A:CYS363 2.4 61.5 1.0
CB A:CYS333 3.4 53.8 1.0
CB A:CYS336 3.4 52.3 1.0
CB A:CYS360 3.4 65.3 1.0
CB A:CYS363 3.5 68.6 1.0
N A:CYS336 3.9 56.0 1.0
N A:CYS360 3.9 63.2 1.0
CA A:CYS336 4.2 55.7 1.0
CA A:CYS360 4.2 65.4 1.0
N A:CYS363 4.3 78.2 1.0
CA A:CYS363 4.5 73.2 1.0
CB A:GLU335 4.6 69.6 1.0
CA A:CYS333 4.8 53.8 1.0
C A:CYS360 4.8 66.3 1.0
O A:CYS360 4.9 62.9 1.0
C A:GLU335 4.9 58.1 1.0
C A:CYS336 5.0 58.5 1.0

Zinc binding site 4 out of 7 in 8xv4

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Zinc binding site 4 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:62.7
occ:1.00
 SG A:CYS313 2.3 64.7 1.0
SG A:CYS302 2.3 63.1 1.0
SG A:CYS305 2.3 60.1 1.0
SG A:CYS316 2.3 61.0 1.0
CB A:CYS305 3.3 61.8 1.0
CB A:CYS302 3.3 63.5 1.0
CB A:CYS313 3.3 61.7 1.0
CB A:CYS316 3.3 60.5 1.0
N A:CYS316 3.5 54.8 1.0
N A:CYS305 3.7 63.0 1.0
CA A:CYS316 4.0 57.2 1.0
CA A:CYS305 4.1 63.5 1.0
CB A:VAL315 4.3 51.6 1.0
CB A:HIS304 4.6 56.4 1.0
C A:HIS304 4.6 62.4 1.0
C A:VAL315 4.6 53.3 1.0
CA A:CYS302 4.7 63.4 1.0
CA A:CYS313 4.7 59.8 1.0
NH2 A:ARG324 4.7 54.3 1.0
CA A:VAL315 4.8 52.3 1.0
N A:HIS304 4.9 58.6 1.0
N A:VAL315 4.9 52.0 1.0
CA A:HIS304 4.9 58.3 1.0
C A:CYS305 4.9 64.9 1.0
CG1 A:VAL315 5.0 52.5 1.0

Zinc binding site 5 out of 7 in 8xv4

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Zinc binding site 5 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:54.6
occ:1.00
 SG B:CYS316 2.3 58.2 1.0
SG B:CYS302 2.3 59.3 1.0
SG B:CYS313 2.3 53.1 1.0
SG B:CYS305 2.4 51.6 1.0
CB B:CYS316 3.3 58.0 1.0
CB B:CYS302 3.3 60.9 1.0
CB B:CYS305 3.4 52.7 1.0
N B:CYS316 3.4 55.4 1.0
CB B:CYS313 3.4 52.2 1.0
N B:CYS305 3.8 53.1 1.0
CA B:CYS316 3.9 56.5 1.0
CB B:VAL315 4.2 53.3 1.0
CA B:CYS305 4.2 54.8 1.0
C B:VAL315 4.5 54.1 1.0
CB B:HIS304 4.6 48.6 1.0
CA B:VAL315 4.7 53.2 1.0
CA B:CYS302 4.7 62.2 1.0
C B:HIS304 4.7 51.0 1.0
NH2 B:ARG324 4.8 70.5 1.0
N B:VAL315 4.8 54.2 1.0
CA B:CYS313 4.8 52.8 1.0
CG1 B:VAL315 4.8 55.9 1.0
O B:LYS306 4.9 79.0 1.0
CG2 B:VAL315 5.0 52.4 1.0
N B:HIS304 5.0 53.0 1.0

Zinc binding site 6 out of 7 in 8xv4

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Zinc binding site 6 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:50.2
occ:1.00
 ND1 B:HIS341 2.1 48.8 1.0
SG B:CYS344 2.3 51.3 1.0
SG B:CYS321 2.3 47.1 1.0
SG B:CYS318 2.3 52.3 1.0
CG B:HIS341 3.1 49.6 1.0
CE1 B:HIS341 3.1 48.0 1.0
CB B:CYS318 3.3 51.2 1.0
CB B:CYS321 3.3 46.5 1.0
CB B:CYS344 3.3 52.1 1.0
CB B:HIS341 3.4 53.2 1.0
N B:CYS321 3.8 44.4 1.0
CA B:CYS321 4.1 45.0 1.0
NE2 B:HIS341 4.2 47.1 1.0
CD2 B:HIS341 4.2 48.7 1.0
N B:HIS341 4.3 56.0 1.0
CA B:HIS341 4.5 54.7 1.0
CA B:CYS318 4.7 50.3 1.0
CA B:CYS344 4.7 54.2 1.0
CB B:LEU320 4.7 46.9 1.0
CE1 B:TYR343 4.8 60.0 1.0
N B:GLY322 4.8 45.5 1.0
C B:CYS321 4.9 44.5 1.0
C B:LEU320 4.9 46.9 1.0
N B:GLY323 5.0 47.7 1.0

Zinc binding site 7 out of 7 in 8xv4

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Zinc binding site 7 out of 7 in the Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)


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 Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:66.7
occ:1.00
 SG B:CYS336 2.3 65.2 1.0
SG B:CYS360 2.3 69.1 1.0
SG B:CYS333 2.3 54.7 1.0
SG B:CYS363 2.4 85.1 1.0
CB B:CYS336 3.4 63.8 1.0
CB B:CYS333 3.4 58.7 1.0
CB B:CYS360 3.5 72.2 1.0
CB B:CYS363 3.5 86.2 1.0
N B:CYS336 3.8 64.3 1.0
N B:CYS360 4.0 77.6 1.0
CA B:CYS336 4.2 63.3 1.0
CA B:CYS360 4.3 75.7 1.0
N B:CYS363 4.3 84.7 1.0
CA B:CYS363 4.5 88.6 1.0
CB B:GLU335 4.6 76.7 1.0
CA B:CYS333 4.8 63.9 1.0
C B:CYS360 4.9 78.8 1.0
O B:CYS360 4.9 80.2 1.0
C B:GLU335 4.9 69.3 1.0
C B:CYS336 5.0 64.1 1.0

Reference:

X.Du, Q.Gan, J.Xu, J.Liu. Crystal Structure of Ttd-Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) To Be Published.
Page generated: Fri Aug 22 15:40:41 2025

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