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Zinc in PDB 8xv6: Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119)

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

All present enzymatic activity of Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119), PDB code: 8xv6 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) 19.95 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 70.94, 75.72, 96.48, 90, 90, 90
R / Rfree (%) 15.2 / 16.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) (pdb code 8xv6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119), PDB code: 8xv6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8xv6

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Zinc binding site 1 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:22.0
occ:1.00
 SG A:CYS313 2.3 20.4 1.0
SG A:CYS305 2.3 22.1 1.0
SG A:CYS302 2.3 23.1 1.0
SG A:CYS316 2.4 22.5 1.0
CB A:CYS302 3.1 24.3 1.0
CB A:CYS313 3.2 19.8 1.0
CB A:CYS316 3.3 22.3 1.0
CB A:CYS305 3.4 21.2 1.0
N A:CYS305 3.8 21.8 1.0
N A:CYS316 3.9 19.7 1.0
ZN A:ZN406 4.1 26.2 1.0
CA A:CYS305 4.1 22.1 1.0
CA A:CYS316 4.3 21.1 1.0
CB A:HIS304 4.3 22.7 1.0
OD1 A:ASP307 4.5 27.1 1.0
CA A:CYS302 4.6 26.6 1.0
CA A:CYS313 4.6 19.7 1.0
C A:HIS304 4.8 22.6 1.0
CB A:VAL315 4.8 24.8 1.0
C A:CYS305 4.8 22.5 1.0
N A:ASP307 4.9 24.1 1.0
N A:LYS306 4.9 23.1 1.0
C A:VAL315 4.9 23.2 1.0
CA A:HIS304 5.0 23.5 1.0
NH2 A:ARG324 5.0 27.5 1.0

Zinc binding site 2 out of 10 in 8xv6

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Zinc binding site 2 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:26.2
occ:1.00
 OD1 A:ASP307 1.9 27.1 1.0
N A:SCN403 2.0 27.5 1.0
N A:SCN401 2.0 27.9 1.0
SG A:CYS316 2.2 22.5 1.0
CG A:ASP307 2.9 25.3 1.0
C A:SCN401 3.1 33.2 1.0
C A:SCN403 3.1 28.1 1.0
OD2 A:ASP307 3.2 27.3 1.0
CB A:CYS316 3.3 22.3 1.0
CB A:CYS302 3.7 24.3 1.0
O A:HOH508 3.7 30.9 1.0
CD2 B:LEU105 3.8 34.5 1.0
CD1 B:ILE108 4.0 29.5 1.0
ZN A:ZN405 4.1 22.0 1.0
CB A:ASP307 4.2 28.3 1.0
CA A:CYS316 4.3 21.1 1.0
SG A:CYS302 4.6 23.1 1.0
N A:CYS302 4.7 27.2 1.0
S A:SCN401 4.7 34.4 1.0
CA A:CYS302 4.7 26.6 1.0
SG A:CYS305 4.7 22.1 1.0
CA A:ASP307 4.7 25.9 1.0
S A:SCN403 4.7 29.1 1.0
CG2 B:ILE108 4.8 30.1 1.0

Zinc binding site 3 out of 10 in 8xv6

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Zinc binding site 3 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:21.2
occ:1.00
 ND1 A:HIS341 2.1 23.3 1.0
SG A:CYS344 2.3 24.3 1.0
SG A:CYS321 2.3 19.7 1.0
SG A:CYS318 2.3 19.3 1.0
CE1 A:HIS341 3.1 22.1 1.0
CB A:CYS318 3.1 22.0 1.0
CG A:HIS341 3.1 23.4 1.0
CB A:CYS321 3.2 21.1 1.0
CB A:CYS344 3.3 21.3 1.0
CB A:HIS341 3.5 21.5 1.0
N A:CYS321 3.7 19.7 1.0
CA A:CYS321 4.0 19.4 1.0
NE2 A:HIS341 4.2 23.1 1.0
N A:HIS341 4.2 19.8 1.0
CD2 A:HIS341 4.2 21.9 1.0
CA A:HIS341 4.5 21.4 1.0
CA A:CYS318 4.6 19.6 1.0
C A:LEU320 4.6 20.7 1.0
CA A:CYS344 4.7 22.3 1.0
CB A:LEU320 4.7 21.7 1.0
C A:CYS321 4.7 20.4 1.0
CE1 A:TYR343 4.8 27.9 1.0
N A:GLY322 4.9 18.2 1.0
O A:HOH545 5.0 41.2 1.0
NE2 A:GLN325 5.0 24.4 1.0

Zinc binding site 4 out of 10 in 8xv6

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Zinc binding site 4 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:23.2
occ:1.00
 SG A:CYS363 2.2 23.3 1.0
SG A:CYS333 2.3 22.5 1.0
SG A:CYS360 2.4 23.2 1.0
SG A:CYS336 2.4 23.8 1.0
CB A:CYS333 3.2 21.2 1.0
CB A:CYS336 3.3 25.6 1.0
CB A:CYS363 3.3 25.5 1.0
CB A:CYS360 3.4 22.0 1.0
N A:CYS336 3.7 25.9 1.0
N A:CYS360 4.0 22.0 1.0
N A:CYS363 4.0 23.8 1.0
CA A:CYS336 4.1 25.2 1.0
O A:HOH538 4.2 43.2 1.0
CA A:CYS360 4.2 22.8 1.0
CA A:CYS363 4.2 23.9 1.0
CB A:GLU335 4.6 27.6 1.0
CA A:CYS333 4.7 21.3 1.0
C A:CYS360 4.7 21.8 1.0
O A:CYS360 4.8 21.6 1.0
C A:GLU335 4.8 26.4 1.0
C A:CYS336 4.9 24.2 1.0
CE1 A:PHE340 4.9 20.2 1.0

Zinc binding site 5 out of 10 in 8xv6

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Zinc binding site 5 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:22.1
occ:1.00
 N A:SCN402 1.9 24.8 1.0
OE1 A:GLU362 2.0 26.3 1.0
NE2 A:HIS319 2.0 19.7 1.0
CD A:GLU362 2.7 27.1 1.0
OE2 A:GLU362 2.8 28.1 1.0
CE1 A:HIS319 2.9 21.8 1.0
CD2 A:HIS319 3.1 22.4 1.0
C A:SCN402 3.1 21.0 1.0
O A:HOH538 4.0 43.2 1.0
ND1 A:HIS319 4.1 21.1 1.0
CG A:GLU362 4.1 25.7 1.0
CG A:HIS319 4.1 19.8 1.0
S A:SCN402 4.7 31.5 1.0
CB A:GLU362 4.8 25.1 1.0
O A:HOH544 4.9 44.0 1.0

Zinc binding site 6 out of 10 in 8xv6

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Zinc binding site 6 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn403

b:27.1
occ:1.00
 N C:SCN401 2.0 29.4 1.0
OD1 C:ASP307 2.0 26.2 1.0
N D:SCN201 2.0 28.5 1.0
SG C:CYS316 2.3 24.2 1.0
CG C:ASP307 2.9 29.4 1.0
C C:SCN401 3.1 27.1 1.0
C D:SCN201 3.2 32.1 1.0
OD2 C:ASP307 3.3 30.7 1.0
CB C:CYS316 3.3 23.6 1.0
CB C:CYS302 3.7 24.4 1.0
O C:HOH515 3.7 35.0 1.0
CD2 D:LEU105 3.8 36.4 1.0
ZN C:ZN404 4.1 22.8 1.0
CD1 D:ILE108 4.1 28.4 1.0
CB C:ASP307 4.3 29.3 1.0
CA C:CYS316 4.3 21.9 1.0
SG C:CYS302 4.6 25.2 1.0
S C:SCN401 4.7 34.6 1.0
N C:CYS302 4.7 30.4 1.0
CA C:CYS302 4.7 27.7 1.0
S D:SCN201 4.7 29.4 1.0
SG C:CYS305 4.8 23.6 1.0
CA C:ASP307 4.8 28.4 1.0
CG2 D:ILE108 4.9 29.5 1.0

Zinc binding site 7 out of 10 in 8xv6

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Zinc binding site 7 out of 10 in the Crystal Structure of 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 Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn404

b:22.8
occ:1.00
 SG C:CYS305 2.3 23.6 1.0
SG C:CYS313 2.3 21.9 1.0
SG C:CYS302 2.3 25.2 1.0
SG C:CYS316 2.4 24.2 1.0
CB C:CYS302 3.1 24.4 1.0
CB C:CYS313 3.2 21.6 1.0
CB C:CYS316 3.3 23.6 1.0
CB C:CYS305 3.3 24.8 1.0
N C:CYS305 3.8 24.5 1.0
N C:CYS316 4.0 21.4 1.0
CA C:CYS305 4.1 24.0 1.0
ZN C:ZN403 4.1 27.1 1.0
CA C:CYS316 4.3 21.9 1.0
CB C:HIS304 4.4 27.3 1.0
OD1 C:ASP307 4.5 26.2 1.0
CA C:CYS302 4.6 27.7 1.0
CB C:VAL315 4.6 24.4 1.0
CA C:CYS313 4.7 20.7 1.0
C C:HIS304 4.7 27.2 1.0
C C:CYS305 4.8 27.3 1.0
NH2 C:ARG324 4.9 29.3 1.0
N C:ASP307 4.9 27.1 1.0
C C:VAL315 4.9 22.9 1.0
CA C:HIS304 4.9 27.1 1.0
N C:LYS306 5.0 27.6 1.0
N C:HIS304 5.0 27.1 1.0

Zinc binding site 8 out of 10 in 8xv6

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Zinc binding site 8 out of 10 in the Crystal Structure of 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 8 of Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn405

b:21.7
occ:1.00
 ND1 C:HIS341 2.1 22.6 1.0
SG C:CYS321 2.3 21.3 1.0
SG C:CYS344 2.3 24.5 1.0
SG C:CYS318 2.4 20.0 1.0
CE1 C:HIS341 3.0 22.9 1.0
CB C:CYS318 3.1 21.7 1.0
CG C:HIS341 3.2 21.2 1.0
CB C:CYS321 3.2 23.0 1.0
CB C:CYS344 3.4 20.7 1.0
CB C:HIS341 3.5 22.1 1.0
N C:CYS321 3.7 21.4 1.0
CA C:CYS321 4.0 20.4 1.0
O C:HOH549 4.1 39.6 1.0
NE2 C:HIS341 4.2 23.2 1.0
CD2 C:HIS341 4.2 23.3 1.0
N C:HIS341 4.3 19.8 1.0
CA C:HIS341 4.5 21.3 1.0
CA C:CYS318 4.6 19.9 1.0
CA C:CYS344 4.7 22.1 1.0
CB C:LEU320 4.8 23.3 1.0
C C:LEU320 4.8 22.3 1.0
CE1 C:TYR343 4.8 27.4 1.0
O C:HOH551 4.8 38.1 1.0
C C:CYS321 4.8 20.0 1.0
N C:GLY322 4.9 18.9 1.0

Zinc binding site 9 out of 10 in 8xv6

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Zinc binding site 9 out of 10 in the Crystal Structure of 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 9 of Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn406

b:20.8
occ:1.00
 SG C:CYS363 2.3 21.4 1.0
SG C:CYS360 2.3 21.5 1.0
SG C:CYS336 2.3 20.5 1.0
SG C:CYS333 2.4 20.4 1.0
CB C:CYS333 3.2 18.6 1.0
CB C:CYS363 3.3 22.5 1.0
CB C:CYS336 3.4 22.8 1.0
CB C:CYS360 3.4 19.8 1.0
N C:CYS336 3.7 23.1 1.0
N C:CYS360 3.9 20.1 1.0
N C:CYS363 4.0 22.1 1.0
CA C:CYS336 4.1 22.1 1.0
CA C:CYS360 4.2 21.0 1.0
CA C:CYS363 4.2 23.6 1.0
O C:HOH540 4.3 41.6 1.0
CA C:CYS333 4.6 19.0 1.0
CB C:GLU335 4.7 24.0 1.0
C C:CYS360 4.7 19.6 1.0
O C:CYS360 4.8 19.5 1.0
C C:GLU335 4.8 23.4 1.0
C C:CYS336 4.9 22.4 1.0
CE1 C:PHE340 4.9 16.9 1.0

Zinc binding site 10 out of 10 in 8xv6

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Zinc binding site 10 out of 10 in the Crystal Structure of 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 10 of Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn407

b:24.0
occ:1.00
 OE2 C:GLU362 2.0 42.4 1.0
NE2 C:HIS319 2.1 21.2 1.0
OE1 C:GLU362 2.2 31.6 1.0
S C:SCN402 2.3 38.3 1.0
CD C:GLU362 2.5 28.1 1.0
CD2 C:HIS319 3.0 20.3 1.0
CE1 C:HIS319 3.0 24.1 1.0
C C:SCN402 3.9 34.9 1.0
CG C:GLU362 4.1 26.7 1.0
ND1 C:HIS319 4.1 21.4 1.0
CG C:HIS319 4.1 18.7 1.0
O C:HOH540 4.4 41.6 1.0
N C:SCN402 4.9 20.1 1.0

Reference:

X.Du, Q.Gan, J.Xu, J.Liu. Crystal Structure of Phd Domain of UHRF1 in Complex with Mstella Peptide (Residues 85-119) To Be Published.
Page generated: Wed Nov 13 13:50:18 2024

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