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Zinc in PDB 6oie: The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR

Enzymatic activity of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR

All present enzymatic activity of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR:
2.3.1.48;

Protein crystallography data

The structure of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR, PDB code: 6oie was solved by B.J.Klein, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.60 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.583, 69.535, 70.187, 90.00, 97.28, 90.00
R / Rfree (%) 16.6 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR (pdb code 6oie). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR, PDB code: 6oie:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6oie

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Zinc binding site 1 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.4
occ:1.00
 ND1 A:HIS296 2.2 24.0 1.0
SG A:CYS299 2.3 18.7 1.0
SG A:CYS275 2.3 16.3 1.0
SG A:CYS272 2.4 16.7 1.0
CB A:CYS272 3.0 15.8 1.0
CE1 A:HIS296 3.1 26.1 1.0
CG A:HIS296 3.2 19.5 1.0
CB A:CYS275 3.2 23.1 1.0
CB A:CYS299 3.3 21.0 1.0
CB A:HIS296 3.5 23.6 1.0
NH2 B:ARG276 3.5 26.7 1.0
N A:CYS275 3.8 15.6 1.0
N A:HIS296 4.1 14.8 1.0
CA A:CYS275 4.1 18.5 1.0
NE2 A:HIS296 4.2 21.2 1.0
CD2 A:HIS296 4.3 20.4 1.0
CA A:HIS296 4.4 22.1 1.0
CA A:CYS272 4.5 16.4 1.0
CZ B:ARG276 4.6 23.2 1.0
CA A:CYS299 4.7 18.6 1.0
C A:CYS275 4.8 23.1 1.0
CB A:ALA274 4.8 14.5 1.0
OE2 A:GLU298 4.9 25.5 1.0
C A:ALA274 4.9 17.6 1.0
N A:ARG276 4.9 16.6 1.0

Zinc binding site 2 out of 8 in 6oie

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Zinc binding site 2 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:23.9
occ:1.00
 SG A:CYS266 2.2 18.8 1.0
SG A:CYS237 2.3 22.9 1.0
SG A:CYS240 2.3 22.5 1.0
SG A:CYS269 2.4 23.9 1.0
CB A:CYS269 3.1 23.4 1.0
CB A:CYS237 3.2 25.6 1.0
CB A:CYS240 3.2 26.0 1.0
CB A:CYS266 3.5 17.1 1.0
N A:CYS240 3.8 28.6 1.0
N A:CYS266 3.9 17.4 1.0
CA A:CYS240 4.1 31.0 1.0
N A:CYS269 4.2 20.1 1.0
CA A:CYS266 4.2 18.4 1.0
CA A:CYS269 4.3 23.2 1.0
CA A:CYS237 4.7 23.6 1.0
CB A:ASP239 4.7 27.6 1.0
C A:CYS240 4.7 29.6 1.0
C A:ASP239 4.8 30.7 1.0
C A:CYS266 4.8 19.0 1.0
N A:GLY241 4.9 29.0 1.0
CB A:SER242 4.9 26.4 1.0
O A:CYS266 4.9 19.7 1.0

Zinc binding site 3 out of 8 in 6oie

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Zinc binding site 3 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:22.5
occ:1.00
 ND1 A:HIS245 2.1 19.5 1.0
SG A:CYS248 2.3 22.7 1.0
SG A:CYS216 2.4 18.5 1.0
SG A:CYS219 2.4 24.4 1.0
CE1 A:HIS245 3.1 21.9 1.0
CB A:CYS216 3.1 24.2 1.0
CG A:HIS245 3.2 21.8 1.0
CB A:CYS219 3.3 27.0 1.0
CB A:CYS248 3.3 22.9 1.0
CB A:HIS245 3.5 22.1 1.0
N A:CYS219 3.7 18.9 1.0
N A:HIS245 4.0 17.9 1.0
CA A:CYS219 4.1 22.2 1.0
NE2 A:HIS245 4.2 23.9 1.0
CD2 A:HIS245 4.3 21.8 1.0
O A:HOH506 4.4 35.6 1.0
CA A:HIS245 4.4 20.6 1.0
CA A:CYS216 4.6 20.9 1.0
CA A:CYS248 4.7 20.4 1.0
CB A:PHE218 4.7 18.2 1.0
C A:PHE218 4.8 26.9 1.0
C A:CYS219 4.8 22.1 1.0
CA A:ASN226 4.8 21.4 1.0
N A:ARG227 4.8 20.7 1.0
N A:CYS248 5.0 25.3 1.0
N A:LEU220 5.0 18.0 1.0

Zinc binding site 4 out of 8 in 6oie

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Zinc binding site 4 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:21.8
occ:1.00
 SG A:CYS288 2.3 20.8 1.0
SG A:CYS317 2.3 22.0 1.0
SG A:CYS291 2.3 20.9 1.0
SG A:CYS314 2.4 17.8 1.0
CB A:CYS288 3.2 16.4 1.0
CB A:CYS291 3.3 21.9 1.0
CB A:CYS317 3.4 24.7 1.0
CB A:CYS314 3.5 14.6 1.0
N A:CYS291 3.7 21.0 1.0
N A:CYS314 3.8 15.7 1.0
N A:CYS317 4.0 22.4 1.0
CA A:CYS291 4.1 19.4 1.0
CA A:CYS314 4.2 15.2 1.0
CA A:CYS317 4.3 24.6 1.0
CB A:SER290 4.3 22.7 1.0
O A:CYS314 4.5 25.7 1.0
C A:CYS314 4.6 20.7 1.0
OG A:SER290 4.6 40.5 1.0
C A:SER290 4.6 19.5 1.0
CA A:CYS288 4.6 22.3 1.0
NH1 A:ARG293 4.7 23.8 1.0
C A:CYS291 4.8 20.1 1.0
CG2 A:ILE313 4.9 17.9 1.0
CA A:SER290 4.9 17.9 1.0
CB A:VAL316 4.9 24.3 1.0
N A:SER290 4.9 17.8 1.0
CB A:ARG293 4.9 17.5 1.0
C A:ILE313 5.0 18.7 1.0
CD A:ARG293 5.0 13.9 1.0

Zinc binding site 5 out of 8 in 6oie

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Zinc binding site 5 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:20.1
occ:1.00
 SG B:CYS291 2.3 16.4 1.0
SG B:CYS288 2.3 18.9 1.0
SG B:CYS314 2.4 21.4 1.0
SG B:CYS317 2.4 18.7 1.0
CB B:CYS288 3.1 12.8 1.0
CB B:CYS317 3.3 18.6 1.0
CB B:CYS291 3.4 14.1 1.0
CB B:CYS314 3.5 18.2 1.0
N B:CYS291 3.9 17.7 1.0
N B:CYS314 3.9 17.0 1.0
N B:CYS317 4.0 21.0 1.0
CA B:CYS314 4.1 17.1 1.0
CA B:CYS291 4.2 18.3 1.0
NH1 B:ARG293 4.2 21.9 1.0
CA B:CYS317 4.2 20.6 1.0
CB B:SER290 4.5 22.2 1.0
O B:CYS314 4.5 21.4 1.0
O B:HOH547 4.5 19.6 1.0
C B:CYS314 4.6 20.1 1.0
CA B:CYS288 4.6 16.2 1.0
C B:SER290 4.6 20.4 1.0
OG B:SER290 4.8 37.4 1.0
CG2 B:ILE313 4.8 16.0 1.0
C B:CYS291 4.9 18.9 1.0
CA B:SER290 4.9 18.4 1.0
N B:SER290 4.9 16.1 1.0

Zinc binding site 6 out of 8 in 6oie

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Zinc binding site 6 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:23.1
occ:1.00
 ND1 B:HIS296 2.1 26.8 1.0
SG B:CYS299 2.2 20.0 1.0
SG B:CYS275 2.3 20.8 1.0
SG B:CYS272 2.4 17.2 1.0
CE1 B:HIS296 3.0 30.6 1.0
CB B:CYS272 3.0 17.0 1.0
CG B:HIS296 3.1 29.2 1.0
CB B:CYS299 3.2 22.2 1.0
CB B:CYS275 3.3 24.7 1.0
CB B:HIS296 3.4 25.6 1.0
N B:CYS275 3.8 21.6 1.0
O B:HOH578 3.9 34.9 1.0
N B:HIS296 4.1 17.2 1.0
NE2 B:HIS296 4.1 24.5 1.0
CA B:CYS275 4.1 20.2 1.0
CD2 B:HIS296 4.2 27.1 1.0
CA B:HIS296 4.4 20.2 1.0
CA B:CYS272 4.5 26.7 1.0
CA B:CYS299 4.6 24.6 1.0
N B:CYS299 4.9 20.9 1.0
C B:CYS275 4.9 20.6 1.0
C B:ALA274 5.0 26.1 1.0
CB B:ALA274 5.0 20.4 1.0
O B:VAL277 5.0 29.9 1.0

Zinc binding site 7 out of 8 in 6oie

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Zinc binding site 7 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:23.5
occ:1.00
 ND1 B:HIS245 2.2 21.7 1.0
SG B:CYS248 2.3 21.6 1.0
SG B:CYS216 2.3 23.4 1.0
SG B:CYS219 2.3 22.6 1.0
CE1 B:HIS245 3.0 22.0 1.0
CB B:CYS216 3.1 27.1 1.0
CG B:HIS245 3.2 26.4 1.0
CB B:CYS248 3.4 20.7 1.0
CB B:CYS219 3.4 21.1 1.0
CB B:HIS245 3.7 26.8 1.0
N B:CYS219 3.8 25.7 1.0
N B:HIS245 4.1 22.8 1.0
CA B:CYS219 4.1 21.1 1.0
NE2 B:HIS245 4.2 19.8 1.0
CD2 B:HIS245 4.3 22.9 1.0
O B:HOH508 4.5 29.7 1.0
CA B:HIS245 4.5 23.9 1.0
CA B:CYS216 4.6 22.1 1.0
CG B:ARG227 4.6 48.3 1.0
CA B:CYS248 4.7 22.1 1.0
CB B:PHE218 4.8 23.2 1.0
C B:CYS219 4.8 21.3 1.0
N B:ARG227 4.8 32.8 1.0
C B:PHE218 4.8 21.1 1.0
CA B:ASN226 4.8 26.0 1.0
N B:LEU220 5.0 20.5 1.0
NH1 B:ARG227 5.0 46.2 1.0

Zinc binding site 8 out of 8 in 6oie

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Zinc binding site 8 out of 8 in the The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Double Phd Finger (Dpf) of Morf in Complex with Histone H3K14CR within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:22.8
occ:1.00
 SG B:CYS237 2.3 16.7 1.0
SG B:CYS240 2.3 21.3 1.0
SG B:CYS269 2.3 21.4 1.0
SG B:CYS266 2.4 19.7 1.0
CB B:CYS269 3.2 23.4 1.0
CB B:CYS237 3.2 17.8 1.0
CB B:CYS240 3.2 24.4 1.0
CB B:CYS266 3.5 14.9 1.0
N B:CYS240 3.7 18.5 1.0
N B:CYS266 4.0 16.3 1.0
O B:HOH566 4.0 35.4 1.0
CA B:CYS240 4.0 24.1 1.0
N B:CYS269 4.0 19.6 1.0
CA B:CYS269 4.2 21.5 1.0
CA B:CYS266 4.3 24.0 1.0
CA B:CYS237 4.6 14.3 1.0
C B:CYS240 4.7 22.5 1.0
C B:CYS266 4.8 25.4 1.0
C B:ASP239 4.8 22.1 1.0
CB B:ASP239 4.8 21.5 1.0
O B:CYS266 4.8 25.1 1.0
N B:GLY241 4.9 27.5 1.0
CB B:SER242 4.9 26.4 1.0

Reference:

B.J.Klein, S.M.Jang, C.Lachance, W.Mi, J.Lyu, S.Sakuraba, K.Krajewski, W.W.Wang, S.Sidoli, J.Liu, Y.Zhang, X.Wang, B.M.Warfield, A.J.Kueh, A.K.Voss, T.Thomas, B.A.Garcia, W.R.Liu, B.D.Strahl, H.Kono, W.Li, X.Shi, J.Cote, T.G.Kutateladze. Histone H3K23-Specific Acetylation By Morf Is Coupled to H3K14 Acylation. Nat Commun V. 10 4724 2019.
ISSN: ESSN 2041-1723
PubMed: 31624313
DOI: 10.1038/S41467-019-12551-5
Page generated: Tue Oct 29 04:24:35 2024

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