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Zinc in PDB 6asb: Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna

Protein crystallography data

The structure of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna, PDB code: 6asb was solved by K.Liu, W.Tempel, J.R.Walker, C.H.Arrowsmith, C.Bountra, A.M.Edwards, J.Min, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 2.85
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.729, 64.282, 67.324, 103.53, 104.66, 99.40
R / Rfree (%) 21.3 / 25.1

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna (pdb code 6asb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna, PDB code: 6asb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 6asb

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Zinc binding site 1 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2001

b:72.3
occ:1.00
 SG C:CYS77 2.3 54.0 1.0
SG C:CYS39 2.3 52.4 1.0
SG C:CYS42 2.3 53.3 1.0
SG C:CYS45 2.4 47.8 1.0
CB C:CYS77 3.2 48.0 1.0
CB C:CYS39 3.4 46.2 1.0
CB C:CYS45 3.5 46.9 1.0
CB C:CYS42 3.5 52.1 1.0
N C:CYS39 3.6 44.4 1.0
CA C:CYS77 3.6 48.3 1.0
CA C:CYS39 3.9 45.0 1.0
N C:CYS42 3.9 52.5 1.0
N C:ARG40 3.9 44.1 1.0
N C:THR78 4.1 51.7 1.0
C C:CYS39 4.3 49.1 1.0
C C:CYS77 4.3 54.0 1.0
CA C:CYS42 4.3 53.4 1.0
N C:ARG41 4.5 48.5 1.0
N C:CYS45 4.5 48.2 1.0
CA C:CYS45 4.5 46.6 1.0
C C:ARG38 4.6 48.4 1.0
N C:ALA79 4.7 54.7 1.0
OG1 C:THR78 4.7 57.7 1.0
O C:ALA79 4.7 53.9 1.0
N C:CYS77 4.8 47.5 1.0
CA C:ARG40 4.9 46.6 1.0
CB C:ARG38 4.9 39.8 1.0
CA C:ARG38 5.0 40.8 1.0
NH1 C:ARG38 5.0 31.8 1.0

Zinc binding site 2 out of 16 in 6asb

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Zinc binding site 2 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:84.1
occ:1.00
 SG C:CYS50 2.2 56.9 1.0
SG C:CYS56 2.3 54.0 1.0
SG C:CYS53 2.3 49.4 1.0
SG C:CYS72 2.3 53.3 1.0
CB C:CYS53 3.3 48.0 1.0
CB C:CYS56 3.3 50.8 1.0
CB C:CYS72 3.3 45.9 1.0
CB C:CYS50 3.7 56.1 1.0
CA C:CYS72 3.7 42.3 1.0
N C:CYS50 3.8 54.6 1.0
N C:LEU73 3.8 38.2 1.0
N C:CYS53 3.8 49.9 1.0
N C:GLY51 4.0 50.4 1.0
CA C:CYS53 4.1 48.9 1.0
CA C:CYS50 4.1 56.1 1.0
C C:CYS72 4.2 42.0 1.0
N C:CYS56 4.2 47.5 1.0
CA C:CYS56 4.3 48.7 1.0
C C:CYS50 4.5 58.7 1.0
CD1 C:LEU74 4.5 47.6 1.0
N C:ASP52 4.6 51.2 1.0
N C:LEU74 4.6 39.5 1.0
C C:GLU49 4.8 58.7 1.0
C C:CYS53 4.8 54.1 1.0
CA C:LEU73 4.8 36.3 1.0
O C:CYS53 4.9 54.3 1.0
CA C:GLY51 5.0 50.2 1.0

Zinc binding site 3 out of 16 in 6asb

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Zinc binding site 3 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:96.5
occ:1.00
 ND1 C:HIS122 2.2 72.8 1.0
SG C:CYS88 2.2 70.4 1.0
SG C:CYS125 2.3 72.3 1.0
SG C:CYS91 2.4 76.0 1.0
CB C:CYS88 2.8 65.0 1.0
CE1 C:HIS122 3.2 72.5 1.0
CG C:HIS122 3.2 69.6 1.0
CB C:CYS91 3.4 74.0 1.0
CB C:CYS125 3.4 66.1 1.0
CB C:HIS122 3.5 65.7 1.0
N C:CYS91 3.8 70.9 1.0
CA C:CYS91 4.1 73.4 1.0
N C:HIS122 4.1 61.2 1.0
NE2 C:HIS122 4.3 71.8 1.0
CD2 C:HIS122 4.3 70.8 1.0
CA C:CYS88 4.3 62.7 1.0
CA C:HIS122 4.4 62.3 1.0
C C:CYS91 4.7 77.6 1.0
CA C:CYS125 4.8 67.0 1.0
N C:GLY92 4.8 69.2 1.0
C C:CYS88 4.9 65.8 1.0
O C:GLU93 4.9 63.8 1.0
O C:HIS122 4.9 68.2 1.0
C C:LEU90 5.0 73.2 1.0

Zinc binding site 4 out of 16 in 6asb

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Zinc binding site 4 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2004

b:79.9
occ:1.00
 SG C:CYS117 2.3 62.4 1.0
SG C:CYS148 2.3 59.5 1.0
SG C:CYS145 2.3 61.2 1.0
SG C:CYS114 2.4 60.8 1.0
CB C:CYS117 3.1 59.1 1.0
CB C:CYS114 3.2 55.2 1.0
CB C:CYS148 3.3 56.2 1.0
N C:CYS117 3.6 57.4 1.0
CB C:CYS145 3.6 56.5 1.0
CA C:CYS117 3.9 57.2 1.0
N C:CYS145 4.1 56.9 1.0
NH2 C:ARG147 4.2 60.8 1.0
CA C:CYS145 4.4 57.0 1.0
N C:CYS148 4.4 58.7 1.0
CA C:CYS148 4.4 57.7 1.0
CB C:ILE116 4.5 58.0 1.0
CA C:CYS114 4.6 53.5 1.0
C C:ILE116 4.6 62.2 1.0
C C:CYS117 4.8 59.6 1.0
CZ C:ARG147 4.9 81.9 1.0
CA C:ILE116 4.9 54.6 1.0
O C:CYS145 4.9 63.5 1.0
N C:ILE116 5.0 54.6 1.0

Zinc binding site 5 out of 16 in 6asb

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Zinc binding site 5 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2001

b:69.0
occ:1.00
 SG F:CYS42 2.3 50.8 1.0
SG F:CYS39 2.3 53.4 1.0
SG F:CYS77 2.3 58.6 1.0
SG F:CYS45 2.4 46.8 1.0
CB F:CYS45 3.4 43.0 1.0
CB F:CYS77 3.4 52.3 1.0
CB F:CYS39 3.4 49.8 1.0
CB F:CYS42 3.6 49.9 1.0
N F:CYS39 3.6 45.9 1.0
CA F:CYS77 3.7 51.6 1.0
CA F:CYS39 3.9 47.6 1.0
N F:CYS42 4.0 49.1 1.0
N F:ARG40 4.0 42.6 1.0
N F:THR78 4.2 53.4 1.0
N F:CYS45 4.2 44.0 1.0
CA F:CYS42 4.3 50.0 1.0
CA F:CYS45 4.3 42.3 1.0
C F:CYS39 4.3 50.7 1.0
C F:CYS77 4.3 55.4 1.0
N F:ARG41 4.5 43.7 1.0
N F:ALA79 4.6 57.8 1.0
C F:ARG38 4.7 49.9 1.0
NH1 F:ARG38 4.8 26.1 1.0
O F:ALA79 4.8 62.6 1.0
N F:CYS77 4.9 50.0 1.0
CA F:ARG40 4.9 41.0 1.0
CA F:ARG38 5.0 44.7 1.0

Zinc binding site 6 out of 16 in 6asb

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Zinc binding site 6 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2002

b:76.8
occ:1.00
 SG F:CYS53 2.3 50.8 1.0
SG F:CYS72 2.3 50.5 1.0
SG F:CYS56 2.4 53.8 1.0
SG F:CYS50 2.4 55.9 1.0
CB F:CYS53 3.2 50.7 1.0
CB F:CYS56 3.2 52.5 1.0
CB F:CYS72 3.3 43.5 1.0
N F:CYS50 3.7 48.6 1.0
CB F:CYS50 3.7 52.3 1.0
N F:CYS53 3.7 54.2 1.0
CA F:CYS72 3.8 42.5 1.0
N F:GLY51 3.8 50.8 1.0
N F:LEU73 3.9 43.6 1.0
CA F:CYS53 4.0 53.3 1.0
CA F:CYS50 4.1 51.2 1.0
N F:CYS56 4.2 51.0 1.0
C F:CYS72 4.2 45.9 1.0
CA F:CYS56 4.3 51.1 1.0
C F:CYS50 4.4 55.8 1.0
N F:ASP52 4.4 54.5 1.0
C F:CYS53 4.6 57.2 1.0
C F:GLU49 4.7 52.5 1.0
N F:LEU74 4.7 46.5 1.0
CA F:GLY51 4.8 52.8 1.0
O F:CYS53 4.8 57.0 1.0
C F:ASP52 4.9 61.2 1.0
CA F:GLU49 4.9 48.6 1.0
CA F:LEU73 4.9 43.7 1.0

Zinc binding site 7 out of 16 in 6asb

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Zinc binding site 7 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2003

b:0.6
occ:1.00
 ND1 F:HIS122 2.1 0.4 1.0
SG F:CYS91 2.3 0.2 1.0
SG F:CYS88 2.3 0.1 1.0
SG F:CYS125 2.3 0.9 1.0
CE1 F:HIS122 3.0 0.0 1.0
CB F:CYS88 3.1 0.0 1.0
CG F:HIS122 3.2 1.0 1.0
CB F:CYS125 3.4 0.3 1.0
CB F:CYS91 3.6 0.7 1.0
CB F:HIS122 3.7 0.4 1.0
N F:CYS91 4.0 0.8 1.0
NE2 F:HIS122 4.2 0.1 1.0
CD2 F:HIS122 4.3 0.5 1.0
N F:HIS122 4.3 1.0 1.0
CA F:CYS91 4.4 0.9 1.0
CA F:CYS88 4.6 0.9 1.0
CA F:HIS122 4.6 0.6 1.0
CA F:CYS125 4.8 0.5 1.0
CB F:LEU90 4.9 0.3 1.0

Zinc binding site 8 out of 16 in 6asb

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Zinc binding site 8 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn2004

b:0.6
occ:1.00
 SG F:CYS114 2.3 0.5 1.0
SG F:CYS117 2.4 0.5 1.0
SG F:CYS145 2.4 1.0 1.0
SG F:CYS148 2.4 1.0 1.0
CB F:CYS114 3.1 0.1 1.0
CB F:CYS117 3.4 0.1 1.0
CB F:CYS148 3.8 0.8 1.0
N F:CYS117 3.9 0.6 1.0
CB F:CYS145 4.0 0.7 1.0
CA F:CYS117 4.2 0.8 1.0
N F:CYS145 4.4 0.9 1.0
N F:CYS148 4.4 0.0 1.0
CA F:CYS114 4.6 0.5 1.0
CA F:CYS145 4.7 0.6 1.0
CA F:CYS148 4.7 0.8 1.0
CB F:ARG147 4.8 0.2 1.0
CB F:ILE116 5.0 0.8 1.0

Zinc binding site 9 out of 16 in 6asb

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Zinc binding site 9 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2001

b:0.0
occ:1.00
 SG I:CYS45 2.3 78.0 1.0
SG I:CYS77 2.3 72.5 1.0
SG I:CYS42 2.4 82.1 1.0
SG I:CYS39 2.5 73.7 1.0
CB I:CYS77 3.2 68.6 1.0
CB I:CYS45 3.3 79.2 1.0
CB I:CYS39 3.5 65.3 1.0
CA I:CYS77 3.5 71.6 1.0
CB I:CYS42 3.5 81.3 1.0
N I:CYS39 3.7 62.4 1.0
N I:CYS42 3.9 81.3 1.0
N I:ARG40 4.0 65.6 1.0
CA I:CYS39 4.0 63.4 1.0
N I:THR78 4.0 80.5 1.0
N I:CYS45 4.2 83.5 1.0
C I:CYS77 4.2 78.8 1.0
CA I:CYS42 4.3 84.0 1.0
CA I:CYS45 4.3 81.5 1.0
C I:CYS39 4.4 70.2 1.0
N I:ARG41 4.5 73.3 1.0
C I:ARG38 4.6 64.8 1.0
N I:CYS77 4.7 71.0 1.0
CB I:ARG38 4.8 60.0 1.0
N I:ALA79 4.9 80.6 1.0
CA I:ARG38 4.9 58.1 1.0
CA I:ARG40 4.9 67.2 1.0
C I:CYS42 5.0 93.4 1.0

Zinc binding site 10 out of 16 in 6asb

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Zinc binding site 10 out of 16 in the Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cxxc and Phd-Type Zinc Finger Regions of FBXL19 in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2002

b:90.7
occ:1.00
 SG I:CYS53 2.3 82.2 1.0
SG I:CYS50 2.3 97.6 1.0
SG I:CYS56 2.4 93.1 1.0
SG I:CYS72 2.4 72.8 1.0
CB I:CYS56 3.1 89.8 1.0
CB I:CYS53 3.1 82.9 1.0
CB I:CYS72 3.4 64.4 1.0
CB I:CYS50 3.6 98.0 1.0
N I:CYS53 3.6 90.0 1.0
N I:CYS50 3.6 94.3 1.0
CA I:CYS72 3.9 60.1 1.0
CA I:CYS53 3.9 86.1 1.0
N I:GLY51 3.9 95.4 1.0
CA I:CYS50 4.0 98.1 1.0
N I:LEU73 4.0 62.5 1.0
N I:CYS56 4.2 84.6 1.0
CA I:CYS56 4.2 86.3 1.0
N I:ASP52 4.3 98.3 1.0
C I:CYS50 4.4 0.8 1.0
C I:CYS72 4.4 62.4 1.0
C I:CYS53 4.6 89.6 1.0
O I:CYS53 4.6 89.2 1.0
C I:GLU49 4.6 98.4 1.0
CD1 I:LEU74 4.7 89.0 1.0
C I:ASP52 4.8 97.0 1.0
N I:LEU74 4.8 71.1 1.0
CA I:GLY51 4.8 96.5 1.0
CA I:GLU49 4.9 89.4 1.0

Reference:

C.Xu, K.Liu, M.Lei, A.Yang, Y.Li, T.R.Hughes, J.Min. Dna Sequence Recognition of Human Cxxc Domains and Their Structural Determinants. Structure V. 26 85 2018.
ISSN: ISSN 1878-4186
PubMed: 29276034
DOI: 10.1016/J.STR.2017.11.022
Page generated: Mon Oct 28 17:37:45 2024

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