Zinc in PDB 6wxk: PHF23 Phd Domain Apo

Protein crystallography data

The structure of PHF23 Phd Domain Apo, PDB code: 6wxk was solved by K.R.Vann, J.Zhang, Y.Zhang, T.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.23 / 2.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.916, 66.916, 151.048, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 29.4

Zinc Binding Sites:

The binding sites of Zinc atom in the PHF23 Phd Domain Apo (pdb code 6wxk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the PHF23 Phd Domain Apo, PDB code: 6wxk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6wxk

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Zinc binding site 1 out of 10 in the PHF23 Phd Domain Apo


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:96.4
occ:1.00
 ND1 A:HIS364 2.3 67.2 1.0
CB A:HIS364 2.4 61.7 1.0
CG A:HIS364 2.4 65.1 1.0
SG A:CYS342 2.8 44.0 1.0
SG A:CYS367 2.9 72.0 1.0
SG A:CYS344 3.1 78.7 1.0
CE1 A:HIS364 3.3 68.6 1.0
CB A:CYS367 3.5 64.8 1.0
CD2 A:HIS364 3.5 63.4 1.0
CB A:CYS342 3.5 55.6 1.0
CA A:HIS364 3.7 47.3 1.0
N A:HIS364 3.7 44.9 1.0
NE2 A:HIS364 3.9 64.6 1.0
NH2 A:ARG351 4.2 72.7 1.0
NH1 A:ARG351 4.2 57.5 1.0
CB A:CYS344 4.2 54.5 1.0
CZ A:ARG351 4.4 56.0 1.0
C A:HIS364 4.6 50.2 1.0
O A:HIS364 4.6 53.8 1.0
N A:CYS367 4.7 60.3 1.0
CA A:CYS367 4.7 55.2 1.0
OG A:SER366 4.9 70.2 1.0
CA A:CYS342 5.0 50.8 1.0
N A:CYS344 5.0 49.4 1.0
C A:ILE363 5.0 47.4 1.0

Zinc binding site 2 out of 10 in 6wxk

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Zinc binding site 2 out of 10 in the PHF23 Phd Domain Apo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:92.5
occ:1.00
 SG A:CYS356 1.6 69.4 1.0
SG A:CYS359 2.0 47.3 1.0
CB A:CYS356 2.4 53.4 1.0
SG A:CYS381 2.8 74.1 1.0
SG A:CYS384 3.0 65.5 1.0
CB A:CYS359 3.3 52.4 1.0
CB A:CYS384 3.3 82.4 1.0
N A:CYS359 3.6 57.9 1.0
N A:CYS381 3.6 59.3 1.0
CB A:CYS381 3.6 77.5 1.0
CA A:CYS356 3.8 54.1 1.0
CA A:CYS359 3.9 55.3 1.0
CA A:CYS381 4.2 72.0 1.0
OG1 A:THR361 4.3 60.1 1.0
N A:CYS384 4.4 79.7 1.0
C A:CYS356 4.4 52.4 1.0
N A:GLY360 4.5 52.3 1.0
CA A:CYS384 4.5 89.5 1.0
C A:CYS359 4.6 51.2 1.0
C A:TYR380 4.7 60.2 1.0
C A:LEU358 4.7 55.2 1.0
N A:LEU358 4.8 51.9 1.0
O A:CYS381 4.8 84.8 1.0
C A:CYS381 4.8 75.0 1.0
CA A:TYR380 4.9 60.8 1.0
OH A:TYR343 4.9 51.5 1.0
CB A:LEU358 4.9 51.3 1.0
N A:CYS356 4.9 55.9 1.0
N A:THR361 4.9 50.1 1.0
N A:SER357 5.0 48.8 1.0
O A:CYS356 5.0 51.2 1.0

Zinc binding site 3 out of 10 in 6wxk

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Zinc binding site 3 out of 10 in the PHF23 Phd Domain Apo


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:46.8
occ:1.00
 ND1 B:HIS364 2.1 40.4 1.0
SG B:CYS367 2.3 40.1 1.0
SG B:CYS342 2.3 31.9 1.0
SG B:CYS344 2.4 37.4 1.0
CG B:HIS364 2.6 38.4 1.0
CB B:HIS364 2.6 38.5 1.0
CB B:CYS367 3.2 39.3 1.0
CE1 B:HIS364 3.3 39.0 1.0
CB B:CYS342 3.3 43.7 1.0
CB B:CYS344 3.5 41.2 1.0
N B:HIS364 3.7 40.1 1.0
CA B:HIS364 3.7 36.9 1.0
CD2 B:HIS364 3.8 31.3 1.0
NE2 B:HIS364 4.1 31.8 1.0
N B:CYS344 4.4 41.7 1.0
CA B:CYS367 4.5 45.9 1.0
CA B:CYS344 4.6 46.4 1.0
NH2 B:ARG351 4.6 40.9 1.0
CA B:CYS342 4.7 39.2 1.0
C B:HIS364 4.7 44.8 1.0
O B:HIS364 4.7 43.8 1.0
N B:CYS367 4.8 43.1 1.0
C B:CYS342 4.9 41.9 1.0
C B:ILE363 4.9 39.4 1.0

Zinc binding site 4 out of 10 in 6wxk

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Zinc binding site 4 out of 10 in the PHF23 Phd Domain Apo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:65.3
occ:1.00
 SG B:CYS359 1.9 51.0 1.0
SG B:CYS384 2.2 59.4 1.0
CB B:CYS359 2.3 42.5 1.0
SG B:CYS356 2.4 45.9 1.0
SG B:CYS381 2.5 42.0 1.0
N B:CYS359 3.1 57.1 1.0
CA B:CYS359 3.3 47.2 1.0
CB B:CYS356 3.5 50.1 1.0
CB B:CYS381 4.0 51.8 1.0
CB B:CYS384 4.0 58.0 1.0
N B:CYS381 4.2 49.1 1.0
C B:CYS359 4.3 48.5 1.0
C B:LEU358 4.3 53.3 1.0
CB B:LEU358 4.4 53.8 1.0
OH B:TYR343 4.4 60.4 1.0
N B:GLY360 4.6 49.5 1.0
CA B:CYS381 4.6 55.5 1.0
CA B:LEU358 4.8 52.4 1.0
CG B:LEU358 4.8 56.4 1.0
CA B:CYS356 4.9 53.5 1.0
N B:CYS384 4.9 63.1 1.0
N B:LEU358 5.0 56.5 1.0
CD2 B:LEU358 5.0 58.0 1.0

Zinc binding site 5 out of 10 in 6wxk

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Zinc binding site 5 out of 10 in the PHF23 Phd Domain Apo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:43.4
occ:1.00
 ND1 C:HIS364 2.0 53.5 1.0
SG C:CYS342 2.2 32.3 1.0
SG C:CYS367 2.3 37.4 1.0
SG C:CYS344 2.3 31.4 1.0
CG C:HIS364 2.5 48.9 1.0
CB C:HIS364 2.6 44.1 1.0
CE1 C:HIS364 3.2 48.6 1.0
CB C:CYS342 3.2 41.6 1.0
CB C:CYS367 3.3 39.7 1.0
CD2 C:HIS364 3.7 41.0 1.0
CB C:CYS344 3.8 55.1 1.0
N C:HIS364 3.8 39.6 1.0
CA C:HIS364 3.8 32.8 1.0
NE2 C:HIS364 4.0 41.9 1.0
NH2 C:ARG351 4.2 37.9 1.0
N C:CYS344 4.3 46.3 1.0
CA C:CYS342 4.6 38.5 1.0
CA C:CYS344 4.6 43.4 1.0
CA C:CYS367 4.6 39.3 1.0
O C:CYS344 4.6 58.1 1.0
N C:TYR343 4.7 44.8 1.0
C C:HIS364 4.7 39.7 1.0
CZ C:ARG351 4.7 39.2 1.0
O C:HIS364 4.8 43.1 1.0
N C:CYS367 4.8 42.7 1.0
C C:CYS342 4.8 41.3 1.0
NH1 C:ARG351 4.9 43.9 1.0

Zinc binding site 6 out of 10 in 6wxk

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Zinc binding site 6 out of 10 in the PHF23 Phd Domain Apo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:29.7
occ:1.00
 SG C:CYS381 2.2 35.7 1.0
SG C:CYS359 2.2 25.2 1.0
SG C:CYS384 2.3 38.7 1.0
SG C:CYS356 2.4 33.5 1.0
CB C:CYS359 3.0 33.4 1.0
CB C:CYS384 3.3 41.5 1.0
CB C:CYS356 3.4 36.9 1.0
N C:CYS359 3.6 36.5 1.0
CB C:CYS381 3.6 44.3 1.0
CA C:CYS359 3.9 35.3 1.0
N C:CYS381 4.0 40.1 1.0
N C:CYS384 4.1 40.5 1.0
CG2 C:THR361 4.3 39.6 1.0
CA C:CYS384 4.3 43.7 1.0
CA C:CYS381 4.3 40.7 1.0
C C:CYS359 4.7 34.5 1.0
O C:CYS381 4.7 39.9 1.0
C C:LEU358 4.8 35.6 1.0
CB C:LEU358 4.8 36.3 1.0
C C:CYS381 4.8 40.1 1.0
N C:GLY360 4.8 33.3 1.0
CA C:CYS356 4.8 35.0 1.0
C C:LYS383 4.9 38.9 1.0
CB C:LYS383 5.0 46.5 1.0

Zinc binding site 7 out of 10 in 6wxk

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Zinc binding site 7 out of 10 in the PHF23 Phd Domain Apo


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:49.4
occ:1.00
 ND1 D:HIS364 2.0 60.8 1.0
SG D:CYS367 2.4 58.4 1.0
SG D:CYS342 2.5 67.9 1.0
SG D:CYS344 2.6 54.7 1.0
CB D:CYS342 2.8 37.2 1.0
CG D:HIS364 2.9 52.5 1.0
CB D:CYS367 3.0 47.8 1.0
CE1 D:HIS364 3.0 51.6 1.0
CB D:HIS364 3.2 39.4 1.0
CB D:CYS344 3.5 58.5 1.0
N D:HIS364 3.8 41.5 1.0
N D:CYS344 4.1 44.8 1.0
CA D:HIS364 4.1 41.1 1.0
CD2 D:HIS364 4.1 49.9 1.0
NE2 D:HIS364 4.1 47.6 1.0
CA D:CYS342 4.3 41.9 1.0
CA D:CYS344 4.4 44.1 1.0
CA D:CYS367 4.5 47.6 1.0
C D:CYS342 4.5 48.3 1.0
N D:TYR343 4.6 52.7 1.0
N D:CYS367 4.9 48.3 1.0
C D:ILE363 4.9 44.3 1.0
O D:HIS364 4.9 58.6 1.0
CG2 D:ILE363 4.9 42.6 1.0
C D:HIS364 5.0 50.0 1.0

Zinc binding site 8 out of 10 in 6wxk

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Zinc binding site 8 out of 10 in the PHF23 Phd Domain Apo


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:1.0
occ:1.00
 SG D:CYS359 2.0 76.0 1.0
SG D:CYS381 2.4 48.2 1.0
SG D:CYS356 2.6 65.8 1.0
O D:CYS381 3.0 0.5 1.0
N D:CYS381 3.4 68.2 1.0
C D:CYS381 3.4 89.9 1.0
CB D:CYS359 3.5 44.9 1.0
CA D:CYS381 3.6 73.6 1.0
CB D:CYS381 3.6 63.0 1.0
N D:CYS359 3.7 75.1 1.0
CB D:LEU358 4.0 63.1 1.0
CA D:CYS359 4.2 64.9 1.0
CB D:CYS356 4.2 66.6 1.0
N D:GLN382 4.3 91.8 1.0
C D:TYR380 4.4 68.9 1.0
C D:GLN382 4.5 89.5 1.0
O D:GLN382 4.5 83.2 1.0
C D:LEU358 4.6 72.2 1.0
CA D:TYR380 4.7 69.2 1.0
CD1 D:LEU358 4.7 65.8 0.0
CA D:LEU358 4.8 64.8 1.0
CG D:LEU358 4.9 65.8 0.0
N D:LEU358 5.0 75.1 1.0

Zinc binding site 9 out of 10 in 6wxk

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Zinc binding site 9 out of 10 in the PHF23 Phd Domain Apo


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:74.9
occ:1.00
 ND1 E:HIS364 2.1 71.8 1.0
SG E:CYS344 2.1 51.5 1.0
SG E:CYS342 2.2 55.5 1.0
SG E:CYS367 2.3 54.9 1.0
CB E:CYS344 2.9 71.7 1.0
CG E:HIS364 3.0 65.4 1.0
CE1 E:HIS364 3.1 68.9 1.0
CB E:CYS342 3.2 58.8 1.0
CB E:CYS367 3.3 65.1 1.0
CB E:HIS364 3.3 60.9 1.0
N E:CYS344 3.9 58.5 1.0
N E:HIS364 4.0 59.8 1.0
CA E:CYS344 4.0 56.4 1.0
CD2 E:HIS364 4.2 60.5 1.0
NE2 E:HIS364 4.2 63.3 1.0
CA E:HIS364 4.2 60.9 1.0
CA E:CYS342 4.5 56.8 1.0
C E:CYS342 4.7 57.6 1.0
CA E:CYS367 4.7 76.5 1.0
NH1 E:ARG351 4.7 56.1 1.0
N E:TYR343 4.8 60.1 1.0
C E:CYS344 4.8 56.0 1.0
O E:HIS364 4.9 77.3 1.0
CG2 E:ILE363 4.9 62.8 1.0
N E:CYS367 5.0 77.6 1.0

Zinc binding site 10 out of 10 in 6wxk

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Zinc binding site 10 out of 10 in the PHF23 Phd Domain Apo


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of PHF23 Phd Domain Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:0.1
occ:1.00
 CD2 E:LEU358 2.1 0.2 1.0
SG E:CYS359 2.2 0.2 1.0
SG E:CYS381 2.3 0.6 1.0
SG E:CYS356 2.3 0.5 1.0
N E:CYS359 2.5 0.8 1.0
CB E:LEU358 3.0 0.2 1.0
CB E:CYS359 3.1 0.4 1.0
CG E:LEU358 3.2 0.9 1.0
CA E:CYS359 3.2 0.1 1.0
C E:LEU358 3.3 0.4 1.0
CA E:LEU358 3.6 0.5 1.0
CB E:CYS381 3.8 96.5 1.0
CB E:CYS356 3.8 0.1 1.0
N E:CYS381 4.0 96.9 1.0
N E:LEU358 4.2 0.4 1.0
CD1 E:LEU358 4.2 0.8 1.0
O E:LEU358 4.3 0.2 1.0
CA E:CYS381 4.4 0.2 1.0
C E:CYS359 4.6 0.5 1.0
C E:TYR380 5.0 90.0 1.0
C E:CYS381 5.0 0.7 1.0

Reference:

Y.Zhang, Y.Guo, S.M.Gough, J.Zhang, K.R.Vann, K.Li, L.Cai, X.Shi, P.D.Aplan, G.G.Wang, T.G.Kutateladze. Mechanistic Insights Into Chromatin Targeting By Leukemic NUP98-PHF23 Fusion. Nat Commun V. 11 3339 2020.
ISSN: ESSN 2041-1723
PubMed: 32620764
DOI: 10.1038/S41467-020-17098-4
Page generated: Wed Dec 16 13:07:34 2020

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