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Zinc in PDB 5b76: Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14

Enzymatic activity of Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14

All present enzymatic activity of Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14, PDB code: 5b76 was solved by H.Li, X.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.06 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.120, 47.633, 76.109, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14 (pdb code 5b76). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14, PDB code: 5b76:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5b76

Go back to Zinc Binding Sites List in 5b76
Zinc binding site 1 out of 4 in the Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14


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 Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:23.2
occ:1.00
 SG A:CYS310 2.3 26.7 1.0
SG A:CYS307 2.3 24.5 1.0
SG A:CYS281 2.3 22.6 1.0
SG A:CYS284 2.3 20.5 1.0
HB2 A:CYS310 3.0 54.4 1.0
H A:CYS307 3.1 29.0 1.0
CB A:CYS281 3.2 21.6 1.0
H A:CYS284 3.2 28.7 1.0
HB3 A:CYS281 3.2 25.9 1.0
HB2 A:CYS281 3.2 25.9 1.0
HB3 A:CYS284 3.3 26.0 1.0
CB A:CYS310 3.3 45.3 1.0
HB3 A:SER283 3.4 31.8 1.0
HB3 A:CYS307 3.4 31.3 1.0
CB A:CYS284 3.4 21.7 1.0
CB A:CYS307 3.5 26.1 1.0
H A:CYS310 3.6 34.9 1.0
N A:CYS284 3.7 23.9 1.0
HH11 A:ARG286 3.8 32.8 1.0
N A:CYS307 3.9 24.1 1.0
HB3 A:CYS310 3.9 54.4 1.0
HB A:ILE309 3.9 35.2 1.0
N A:CYS310 4.1 29.1 1.0
HB2 A:ARG286 4.1 23.8 1.0
CA A:CYS284 4.1 22.8 1.0
CA A:CYS307 4.2 22.9 1.0
H A:SER283 4.2 27.9 1.0
HB2 A:CYS284 4.2 26.0 1.0
HB2 A:CYS307 4.2 31.3 1.0
CA A:CYS310 4.3 30.2 1.0
CB A:SER283 4.3 26.5 1.0
H A:ARG286 4.4 20.6 1.0
HD2 A:ARG286 4.4 29.0 1.0
HG A:SER283 4.5 46.8 1.0
NH1 A:ARG286 4.5 27.4 1.0
HE1 A:PHE288 4.6 32.9 1.0
HH12 A:ARG286 4.6 32.8 1.0
C A:SER283 4.6 33.0 1.0
HA A:CYS310 4.6 36.2 1.0
HA A:ILE306 4.6 31.4 1.0
CA A:CYS281 4.6 18.6 1.0
H A:ASP285 4.6 24.2 1.0
H A:ILE309 4.7 30.8 1.0
C A:CYS307 4.7 22.9 1.0
OG A:SER283 4.8 39.0 1.0
O A:CYS307 4.8 25.1 1.0
HB A:ILE306 4.8 42.5 1.0
CA A:SER283 4.8 23.6 1.0
C A:CYS284 4.8 22.3 1.0
N A:SER283 4.9 23.2 1.0
CB A:ILE309 4.9 29.3 1.0
HG3 A:ARG286 4.9 23.1 1.0
HB2 A:SER283 4.9 31.8 1.0
HA A:CYS281 4.9 22.3 1.0
HA A:CYS284 5.0 27.4 1.0
N A:ASP285 5.0 20.2 1.0
C A:ILE306 5.0 24.5 1.0

Zinc binding site 2 out of 4 in 5b76

Go back to Zinc Binding Sites List in 5b76
Zinc binding site 2 out of 4 in the Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14


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 Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:26.1
occ:1.00
 ND1 A:HIS289 2.2 28.4 1.0
SG A:CYS292 2.3 28.2 1.0
SG A:CYS268 2.3 30.6 1.0
SG A:CYS265 2.4 21.9 1.0
HB2 A:HIS289 2.7 27.4 1.0
HB3 A:CYS265 2.8 27.4 1.0
CB A:CYS265 3.0 22.8 1.0
HB2 A:CYS265 3.0 27.4 1.0
HB3 A:CYS268 3.0 32.5 1.0
HB2 A:CYS292 3.0 30.2 1.0
H A:CYS268 3.1 31.3 1.0
CG A:HIS289 3.2 24.0 1.0
CB A:CYS292 3.2 25.1 1.0
CE1 A:HIS289 3.2 29.6 1.0
CB A:CYS268 3.3 27.1 1.0
HB3 A:CYS292 3.3 30.2 1.0
H A:HIS289 3.3 23.6 1.0
HE1 A:HIS289 3.4 35.5 1.0
CB A:HIS289 3.4 22.8 1.0
N A:CYS268 3.8 26.1 1.0
HB3 A:SER267 3.8 41.9 1.0
O A:HOH619 4.0 48.9 1.0
HB2 A:CYS268 4.0 32.5 1.0
HB3 A:HIS289 4.1 27.4 1.0
N A:HIS289 4.1 19.7 1.0
CA A:CYS268 4.1 27.4 1.0
NE2 A:HIS289 4.3 28.9 1.0
CD2 A:HIS289 4.3 24.4 1.0
CA A:HIS289 4.4 22.5 1.0
H A:ASP270 4.5 36.5 1.0
CA A:CYS265 4.5 21.0 1.0
H A:SER267 4.5 28.8 1.0
CA A:CYS292 4.6 26.3 1.0
H A:ARG269 4.7 33.0 1.0
CB A:SER267 4.7 34.9 1.0
HG2 A:GLU291 4.7 51.3 1.0
H A:CYS292 4.8 33.7 1.0
HA A:PHE288 4.8 25.3 1.0
HB3 A:ASP270 4.8 38.8 1.0
HA A:CYS265 4.9 25.2 1.0
C A:CYS268 4.9 29.4 1.0
HA A:CYS268 4.9 32.8 1.0
C A:SER267 4.9 28.8 1.0
HA A:CYS292 4.9 31.6 1.0

Zinc binding site 3 out of 4 in 5b76

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Zinc binding site 3 out of 4 in the Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14


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 Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:20.4
occ:1.00
 ND1 A:HIS238 2.1 18.2 1.0
SG A:CYS241 2.3 23.1 1.0
SG A:CYS209 2.3 19.4 1.0
SG A:CYS212 2.3 19.8 1.0
CE1 A:HIS238 3.0 25.6 1.0
HB2 A:HIS238 3.0 24.1 1.0
HB3 A:CYS209 3.1 22.2 1.0
H A:CYS212 3.1 21.3 1.0
HE1 A:HIS238 3.1 30.8 1.0
CB A:CYS209 3.1 18.5 1.0
HB3 A:CYS212 3.1 27.5 1.0
CG A:HIS238 3.2 22.2 1.0
HB2 A:CYS209 3.2 22.2 1.0
HB2 A:CYS241 3.2 26.1 1.0
H A:HIS238 3.2 23.2 1.0
CB A:CYS212 3.3 22.9 1.0
CB A:CYS241 3.4 21.7 1.0
CB A:HIS238 3.6 20.1 1.0
HB3 A:CYS241 3.7 26.1 1.0
N A:CYS212 3.7 17.8 1.0
HB2 A:PHE211 3.7 21.8 1.0
HG3 A:ARG220 4.0 34.7 1.0
N A:HIS238 4.0 19.3 1.0
CA A:CYS212 4.1 21.7 1.0
HA A:ASN219 4.1 33.1 1.0
HB2 A:CYS212 4.1 27.5 1.0
NE2 A:HIS238 4.1 24.2 1.0
H A:GLY214 4.2 26.1 1.0
CD2 A:HIS238 4.3 24.6 1.0
HB3 A:HIS238 4.3 24.1 1.0
O A:HOH507 4.4 37.3 1.0
H A:PHE211 4.4 19.7 1.0
CA A:HIS238 4.4 20.3 1.0
H A:CYS241 4.5 23.2 1.0
HB2 A:ASN219 4.5 29.9 1.0
CA A:CYS209 4.6 19.9 1.0
HA2 A:GLY237 4.7 21.2 1.0
H A:LEU213 4.7 22.1 1.0
H A:ARG220 4.7 32.0 1.0
CB A:PHE211 4.7 18.1 1.0
HD2 A:PHE211 4.7 24.1 1.0
CA A:CYS241 4.7 21.6 1.0
C A:PHE211 4.8 19.4 1.0
C A:CYS212 4.8 19.4 1.0
HE2 A:HIS238 4.9 29.1 1.0
HA A:CYS212 4.9 26.1 1.0
CA A:ASN219 4.9 27.6 1.0
HD2 A:ARG220 4.9 27.5 1.0
HA A:CYS209 4.9 23.9 1.0
N A:CYS241 4.9 19.3 1.0
N A:LEU213 5.0 18.4 1.0
CG A:ARG220 5.0 28.9 1.0

Zinc binding site 4 out of 4 in 5b76

Go back to Zinc Binding Sites List in 5b76
Zinc binding site 4 out of 4 in the Crystal Structure of Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14


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 Moz Double Phd Finger Domain in Complex with Histone H3 Crotonylation at K14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:19.8
occ:1.00
 SG A:CYS262 2.3 22.6 1.0
SG A:CYS233 2.3 20.5 1.0
SG A:CYS230 2.3 17.6 1.0
SG A:CYS259 2.3 19.4 1.0
HB2 A:CYS262 2.8 25.8 1.0
HB3 A:CYS233 2.9 23.8 1.0
H A:CYS233 3.1 27.5 1.0
HB3 A:CYS230 3.1 20.2 1.0
CB A:CYS262 3.1 21.5 1.0
CB A:CYS230 3.2 16.9 1.0
CB A:CYS233 3.2 19.8 1.0
HB2 A:CYS230 3.2 20.2 1.0
H A:CYS259 3.2 22.1 1.0
HB3 A:CYS259 3.3 21.9 1.0
CB A:CYS259 3.5 18.3 1.0
HB3 A:CYS262 3.7 25.8 1.0
N A:CYS233 3.7 22.9 1.0
H A:CYS262 3.7 25.1 1.0
HB2 A:ASP232 3.9 23.8 1.0
HB2 A:CYS233 4.0 23.8 1.0
N A:CYS259 4.0 18.4 1.0
CA A:CYS233 4.0 20.6 1.0
O A:HOH609 4.2 60.3 1.0
HB2 A:CYS259 4.2 21.9 1.0
N A:CYS262 4.3 20.9 1.0
CA A:CYS259 4.3 18.6 1.0
CA A:CYS262 4.3 19.3 1.0
H A:ASP232 4.3 23.4 1.0
HB2 A:ASN235 4.4 30.8 1.0
H A:GLY234 4.5 22.5 1.0
H A:ASN235 4.5 24.6 1.0
CA A:CYS230 4.6 18.0 1.0
HD22 A:ASN235 4.6 58.2 1.0
HA A:CYS262 4.7 23.1 1.0
C A:ASP232 4.8 20.9 1.0
CB A:ASP232 4.8 19.8 1.0
HA A:GLN258 4.8 24.2 1.0
C A:CYS233 4.8 21.2 1.0
HA A:CYS233 4.8 24.8 1.0
N A:GLY234 4.9 18.8 1.0
C A:CYS259 4.9 19.1 1.0
HA A:CYS230 5.0 21.6 1.0
HB2 A:GLU261 5.0 29.5 1.0

Reference:

X.Xiong, T.Panchenko, S.Yang, S.Zhao, P.Yan, W.Zhang, W.Xie, Y.Li, Y.Zhao, C.D.Allis, H.Li. Selective Recognition of Histone Crotonylation By Double Phd Fingers of Moz and DPF2 Nat.Chem.Biol. V. 12 1111 2016.
ISSN: ESSN 1552-4469
PubMed: 27775714
DOI: 10.1038/NCHEMBIO.2218
Page generated: Sun Oct 27 13:25:24 2024

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