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Zinc in PDB 5u2j: Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU

Enzymatic activity of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU

All present enzymatic activity of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU:
2.3.1.48;

Protein crystallography data

The structure of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU, PDB code: 5u2j was solved by F.H.Andrews, 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) 34.69 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.540, 69.190, 69.930, 90.00, 97.16, 90.00
R / Rfree (%) 19.1 / 23.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU (pdb code 5u2j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU, PDB code: 5u2j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5u2j

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Zinc binding site 1 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.1
occ:0.81
 SG A:CYS281 2.3 19.0 0.8
SG A:CYS307 2.3 18.1 0.8
SG A:CYS284 2.3 21.7 1.0
SG A:CYS310 2.3 19.8 0.8
CB A:CYS281 3.1 18.4 1.0
CB A:CYS284 3.4 22.8 1.0
CB A:CYS310 3.4 20.8 0.8
CB A:CYS307 3.5 15.4 0.9
N A:CYS284 3.8 20.9 0.8
N A:CYS307 3.9 19.0 1.0
N A:CYS310 4.0 20.8 1.0
CA A:CYS284 4.1 22.0 1.0
CA A:CYS307 4.2 17.0 1.0
CA A:CYS310 4.3 20.9 0.8
CB A:SER283 4.4 26.0 1.0
NH1 A:ARG286 4.6 24.7 0.8
O A:HOH594 4.6 45.7 1.0
O A:CYS307 4.6 15.0 0.7
CA A:CYS281 4.6 18.9 1.0
C A:SER283 4.6 22.6 1.0
C A:CYS307 4.6 18.1 0.9
OG A:SER283 4.7 26.7 0.6
CG2 A:ILE306 4.8 21.1 1.0
C A:CYS284 4.8 21.5 1.0
CB A:ARG286 4.9 19.5 1.0
N A:SER283 4.9 22.8 1.0
CA A:SER283 4.9 23.9 1.0
CB A:VAL309 4.9 22.4 1.0
N A:ASP285 5.0 20.6 1.0

Zinc binding site 2 out of 8 in 5u2j

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Zinc binding site 2 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:17.4
occ:0.79
 ND1 A:HIS289 2.2 21.3 1.0
SG A:CYS292 2.3 18.2 0.8
SG A:CYS268 2.3 20.4 1.0
SG A:CYS265 2.4 16.7 0.8
CB A:CYS265 3.0 18.7 1.0
CE1 A:HIS289 3.1 20.6 0.9
CG A:HIS289 3.2 21.0 0.8
CB A:CYS292 3.2 18.1 0.8
CB A:CYS268 3.2 20.0 1.0
CB A:HIS289 3.5 19.8 0.8
NH2 B:ARG269 3.6 21.8 0.8
N A:CYS268 3.8 19.1 1.0
N A:HIS289 4.1 19.7 1.0
CA A:CYS268 4.1 19.2 1.0
NE2 A:HIS289 4.3 21.0 0.8
CD2 A:HIS289 4.3 21.8 0.7
CA A:HIS289 4.4 19.8 1.0
CA A:CYS265 4.5 18.5 1.0
CA A:CYS292 4.6 18.8 0.9
CZ B:ARG269 4.7 21.0 0.8
CB A:ALA267 4.7 20.2 1.0
O B:HOH590 4.8 43.8 1.0
C A:CYS268 4.8 19.0 0.9
C A:ALA267 4.9 18.8 0.9
N A:CYS292 4.9 20.4 1.0
OE1 A:GLU291 5.0 26.2 0.8

Zinc binding site 3 out of 8 in 5u2j

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Zinc binding site 3 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:21.1
occ:0.84
 SG A:CYS212 2.3 19.2 0.8
ND1 A:HIS238 2.3 24.5 1.0
SG A:CYS209 2.4 18.7 0.8
SG A:CYS241 2.4 24.0 0.8
CB A:CYS209 3.1 20.2 0.7
CE1 A:HIS238 3.3 25.4 0.9
CG A:HIS238 3.3 23.4 1.0
CB A:CYS212 3.3 22.4 0.7
CB A:CYS241 3.4 23.8 0.8
CB A:HIS238 3.6 23.2 0.9
N A:CYS212 3.8 21.0 1.0
N A:HIS238 4.0 21.6 1.0
CA A:CYS212 4.1 21.1 1.0
O A:HOH519 4.3 20.3 0.6
NE2 A:HIS238 4.4 26.3 1.0
CA A:HIS238 4.4 22.2 1.0
CD2 A:HIS238 4.4 25.0 1.0
CA A:CYS209 4.6 19.7 0.8
CA A:CYS241 4.7 23.6 1.0
CB A:PHE211 4.8 26.0 0.9
CG A:ARG220 4.8 36.7 0.8
CA A:ASN219 4.8 25.0 1.0
N A:ARG220 4.8 28.8 1.0
C A:PHE211 4.8 22.5 0.7
C A:CYS212 4.8 19.9 1.0
N A:CYS241 4.9 23.9 0.8
CB A:ASN219 5.0 27.3 1.0
N A:LEU213 5.0 22.9 0.9

Zinc binding site 4 out of 8 in 5u2j

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Zinc binding site 4 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:19.8
occ:0.78
 SG A:CYS259 2.2 26.8 1.0
SG A:CYS233 2.3 22.5 0.8
SG A:CYS262 2.3 28.3 0.9
SG A:CYS230 2.4 22.1 0.8
CB A:CYS230 3.2 22.3 0.9
CB A:CYS262 3.2 26.6 1.0
CB A:CYS233 3.2 26.8 1.0
CB A:CYS259 3.4 24.9 1.0
N A:CYS233 3.8 28.9 1.0
N A:CYS259 3.9 18.9 1.0
CA A:CYS233 4.1 28.5 1.0
N A:CYS262 4.2 28.2 1.0
CA A:CYS259 4.2 21.6 1.0
CA A:CYS262 4.3 26.2 1.0
CA A:CYS230 4.7 21.0 1.0
C A:CYS259 4.8 23.1 1.0
C A:CYS233 4.8 27.1 0.8
CB A:ASP232 4.8 32.5 0.9
C A:ASP232 4.8 31.5 0.7
O A:CYS259 4.8 24.4 1.0
N A:GLY234 4.9 25.8 0.8
CB A:SER235 4.9 24.8 1.0

Zinc binding site 5 out of 8 in 5u2j

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Zinc binding site 5 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:17.1
occ:0.82
 SG B:CYS307 2.3 17.7 0.7
SG B:CYS284 2.3 14.2 0.7
SG B:CYS310 2.3 17.5 0.8
SG B:CYS281 2.4 16.9 0.8
CB B:CYS281 3.2 18.5 1.0
CB B:CYS284 3.4 17.1 1.0
CB B:CYS310 3.4 17.2 1.0
CB B:CYS307 3.4 18.7 1.0
N B:CYS284 3.8 16.0 0.8
N B:CYS307 3.9 18.7 1.0
N B:CYS310 4.0 18.5 0.9
CA B:CYS307 4.1 19.5 0.8
CA B:CYS284 4.2 15.7 0.9
NH1 B:ARG286 4.2 19.8 0.8
CA B:CYS310 4.3 18.1 1.0
CB B:SER283 4.4 20.1 1.0
O B:CYS307 4.6 20.7 0.9
C B:CYS307 4.6 20.5 0.9
CA B:CYS281 4.6 17.7 0.9
O B:HOH574 4.7 22.4 0.8
C B:SER283 4.7 16.8 0.8
CG2 B:ILE306 4.8 19.2 1.0
C B:CYS284 4.9 15.3 0.8
CA B:SER283 4.9 18.5 1.0
CB B:ARG286 4.9 16.4 0.9
OG B:SER283 4.9 21.5 0.4
N B:SER283 4.9 17.9 0.9
C B:ILE306 5.0 19.1 0.9

Zinc binding site 6 out of 8 in 5u2j

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Zinc binding site 6 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:23.4
occ:0.85
 CD2 B:HIS289 2.1 27.0 1.0
SG B:CYS292 2.3 26.1 0.8
SG B:CYS265 2.3 20.8 1.0
SG B:CYS268 2.4 25.4 0.9
CB B:CYS265 2.9 20.1 1.0
CG B:HIS289 2.9 26.7 0.8
NE2 B:HIS289 3.1 29.9 1.0
CB B:CYS292 3.3 25.9 1.0
CB B:CYS268 3.3 27.3 1.0
CB B:HIS289 3.4 24.8 1.0
N B:CYS268 3.8 21.7 0.9
N B:HIS289 4.1 22.6 1.0
ND1 B:HIS289 4.1 29.1 1.0
CA B:CYS268 4.1 24.0 1.0
O B:HOH594 4.1 46.0 1.0
CE1 B:HIS289 4.2 29.8 1.0
CA B:HIS289 4.4 23.6 0.9
CA B:CYS265 4.4 20.1 1.0
CA B:CYS292 4.7 26.0 1.0
CB B:ALA267 4.8 22.9 1.0
O A:HOH563 4.9 41.3 1.0
C B:CYS268 4.9 24.1 1.0
C B:ALA267 4.9 22.3 0.8
N B:CYS292 5.0 27.2 1.0

Zinc binding site 7 out of 8 in 5u2j

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Zinc binding site 7 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:23.9
occ:1.00
 ND1 B:HIS238 2.2 23.0 1.0
SG B:CYS212 2.2 19.4 0.8
SG B:CYS241 2.3 20.2 0.7
SG B:CYS209 2.3 19.8 0.8
CE1 B:HIS238 3.0 23.6 0.8
CB B:CYS209 3.1 20.2 1.0
CG B:HIS238 3.2 23.5 0.8
CB B:CYS241 3.3 21.4 1.0
CB B:CYS212 3.3 22.5 1.0
CB B:HIS238 3.6 24.0 1.0
N B:CYS212 3.8 22.3 0.8
N B:HIS238 4.1 20.3 1.0
CA B:CYS212 4.1 22.6 1.0
NE2 B:HIS238 4.2 24.7 1.0
CD2 B:HIS238 4.3 24.8 1.0
CA B:HIS238 4.5 21.7 1.0
O B:HOH517 4.5 31.3 1.0
CA B:CYS209 4.5 19.5 0.7
CA B:CYS241 4.7 22.6 1.0
CG B:ARG220 4.7 36.0 0.8
CB B:PHE211 4.8 26.4 0.8
CA B:ASN219 4.8 25.2 0.9
C B:CYS212 4.8 22.2 1.0
C B:PHE211 4.8 23.2 0.9
N B:ARG220 4.9 29.4 0.8
N B:LEU213 5.0 19.9 0.8
N B:CYS241 5.0 24.0 1.0

Zinc binding site 8 out of 8 in 5u2j

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Zinc binding site 8 out of 8 in the Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Morf Double Phd Finger (Dpf) in Complex with Histone H3K14BU within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:20.0
occ:0.79
 SG B:CYS262 2.2 24.6 0.9
SG B:CYS233 2.3 21.0 0.8
SG B:CYS230 2.4 17.9 0.8
SG B:CYS259 2.4 22.1 0.8
CB B:CYS230 3.2 17.7 1.0
CB B:CYS233 3.2 24.0 1.0
CB B:CYS262 3.2 23.0 0.9
CB B:CYS259 3.5 20.2 0.8
N B:CYS233 3.7 22.3 1.0
N B:CYS259 3.9 19.2 1.0
CA B:CYS233 4.0 24.1 0.9
N B:CYS262 4.1 25.1 0.9
CA B:CYS259 4.2 19.5 0.9
CA B:CYS262 4.3 23.4 1.0
CA B:CYS230 4.6 19.1 1.0
C B:CYS233 4.7 23.9 1.0
C B:CYS259 4.8 20.3 1.0
O B:CYS259 4.8 18.9 0.7
C B:ASP232 4.8 23.1 1.0
N B:GLY234 4.8 23.1 0.9
CB B:ASP232 4.9 23.5 1.0
CB B:SER235 4.9 20.6 1.0

Reference:

B.J.Klein, J.Simithy, X.Wang, J.Ahn, F.H.Andrews, Y.Zhang, J.Cote, X.Shi, B.A.Garcia, T.G.Kutateladze. Recognition of Histone H3K14 Acylation By Morf. Structure V. 25 650 2017.
ISSN: ISSN 1878-4186
PubMed: 28286003
DOI: 10.1016/J.STR.2017.02.003
Page generated: Mon Oct 28 09:06:53 2024

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