Atomistry » Zinc » PDB 5u0d-5ubi » 5u2j
Atomistry »
  Zinc »
    PDB 5u0d-5ubi »
      5u2j »

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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Go back to Zinc Binding Sites List in 5u2j
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy