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Zinc in PDB 5lpi: Structure of the Zinc Finger Array of CEP104

Protein crystallography data

The structure of Structure of the Zinc Finger Array of CEP104, PDB code: 5lpi was solved by M.Van Breugel, M.Yu, C.Al Jassar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.25 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.149, 80.320, 118.130, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 22.9

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Structure of the Zinc Finger Array of CEP104 (pdb code 5lpi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Structure of the Zinc Finger Array of CEP104, PDB code: 5lpi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 5lpi

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Zinc binding site 1 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn901

b:41.1
occ:1.00
NE2 D:HIS827 2.1 36.0 1.0
SG D:CYS833 2.3 37.4 1.0
SG D:CYS815 2.4 36.2 1.0
SG D:CYS812 2.4 40.7 1.0
CD2 D:HIS827 2.9 37.9 1.0
CB D:CYS833 3.0 38.7 1.0
CB D:CYS812 3.1 37.4 1.0
CE1 D:HIS827 3.1 38.8 1.0
CB D:CYS815 3.3 35.7 1.0
N D:CYS815 3.6 42.8 1.0
O D:HOH1071 3.8 43.9 1.0
CA D:CYS815 4.0 41.0 1.0
CG D:HIS827 4.1 33.5 1.0
ND1 D:HIS827 4.2 33.1 1.0
CB D:ARG814 4.2 46.3 1.0
O D:HOH1033 4.4 40.0 1.0
CA D:CYS833 4.5 39.2 1.0
CA D:CYS812 4.5 39.0 1.0
C D:ARG814 4.6 48.2 1.0
CA D:ARG814 4.8 51.2 1.0
N D:ARG814 4.9 52.7 1.0
CG D:ARG814 4.9 44.5 1.0
C D:CYS812 4.9 45.2 1.0
O D:CYS812 4.9 44.5 1.0
N D:CYS833 5.0 42.2 1.0
CD D:ARG814 5.0 48.0 1.0
C D:CYS815 5.0 37.1 1.0

Zinc binding site 2 out of 16 in 5lpi

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Zinc binding site 2 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn902

b:28.8
occ:1.00
NE2 D:HIS798 2.1 26.3 1.0
SG D:CYS803 2.3 28.1 1.0
SG D:CYS783 2.3 25.8 1.0
SG D:CYS786 2.4 24.5 1.0
CE1 D:HIS798 3.1 29.4 1.0
CD2 D:HIS798 3.1 28.9 1.0
CB D:CYS783 3.1 25.1 1.0
CB D:CYS803 3.2 25.2 1.0
CB D:CYS786 3.2 23.9 1.0
N D:CYS786 3.8 23.8 1.0
CA D:CYS803 3.9 27.2 1.0
CA D:CYS786 4.1 27.5 1.0
ND1 D:HIS798 4.2 28.7 1.0
CG D:HIS798 4.2 30.8 1.0
O D:HOH1051 4.2 30.1 1.0
CD2 D:LEU799 4.5 26.8 1.0
CA D:CYS783 4.5 28.6 1.0
CB D:HIS785 4.6 25.3 1.0
C D:HIS785 4.7 26.9 1.0
N D:ASP804 4.8 32.6 1.0
C D:CYS803 4.8 29.9 1.0
C D:CYS786 4.9 25.8 1.0
N D:CYS803 4.9 32.1 1.0
N D:HIS785 4.9 26.8 1.0
CA D:HIS785 5.0 25.7 1.0
C D:CYS783 5.0 25.5 1.0

Zinc binding site 3 out of 16 in 5lpi

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Zinc binding site 3 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn903

b:33.3
occ:1.00
NE2 D:HIS772 2.1 26.4 1.0
SG D:CYS754 2.3 29.1 1.0
SG D:CYS757 2.3 34.8 1.0
SG D:CYS777 2.3 28.0 1.0
CD2 D:HIS772 3.0 23.6 1.0
CB D:CYS777 3.1 27.6 1.0
CB D:CYS757 3.2 29.3 1.0
CE1 D:HIS772 3.2 28.6 1.0
CB D:CYS754 3.2 30.0 1.0
N D:CYS757 3.6 32.3 1.0
CA D:CYS777 3.8 27.7 1.0
O D:HOH1064 3.9 31.0 1.0
CA D:CYS757 3.9 30.1 1.0
CG D:HIS772 4.2 27.3 1.0
ND1 D:HIS772 4.2 27.9 1.0
CB D:PHE756 4.6 33.2 1.0
CA D:CYS754 4.6 33.2 1.0
C D:PHE756 4.6 38.6 1.0
C D:CYS757 4.8 39.0 1.0
C D:CYS777 4.8 27.0 1.0
N D:CYS777 4.9 29.5 1.0
O D:CYS754 4.9 32.8 1.0
N D:LEU778 5.0 28.8 1.0
N D:GLY758 5.0 38.6 1.0
CA D:PHE756 5.0 35.8 1.0

Zinc binding site 4 out of 16 in 5lpi

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Zinc binding site 4 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn904

b:33.8
occ:1.00
NE2 D:HIS862 2.1 29.3 1.0
SG D:CYS869 2.3 32.3 1.0
SG D:CYS845 2.3 29.8 1.0
SG D:CYS848 2.4 33.6 1.0
CE1 D:HIS862 3.1 31.9 1.0
CD2 D:HIS862 3.1 30.2 1.0
CB D:CYS845 3.1 25.0 1.0
CB D:CYS869 3.2 29.3 1.0
CB D:CYS848 3.3 35.2 1.0
N D:CYS848 3.7 36.9 1.0
CA D:CYS869 3.9 39.8 1.0
CA D:CYS848 4.1 33.6 1.0
O D:HOH1053 4.2 37.4 1.0
ND1 D:HIS862 4.2 33.5 1.0
CG D:HIS862 4.2 32.6 1.0
CB D:LEU847 4.5 29.1 1.0
CA D:CYS845 4.6 31.0 1.0
CD2 D:LEU863 4.6 26.4 1.0
C D:LEU847 4.7 33.5 1.0
C D:CYS848 4.9 30.2 1.0
C D:CYS869 4.9 43.4 1.0
N D:LEU847 5.0 32.3 1.0
CA D:LEU847 5.0 29.3 1.0
N D:CYS869 5.0 45.9 1.0

Zinc binding site 5 out of 16 in 5lpi

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Zinc binding site 5 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn901

b:32.5
occ:1.00
NE2 C:HIS862 2.1 30.4 1.0
SG C:CYS845 2.2 28.8 1.0
SG C:CYS869 2.3 30.4 1.0
SG C:CYS848 2.3 30.9 1.0
CE1 C:HIS862 3.0 29.5 1.0
CB C:CYS845 3.1 29.2 1.0
CB C:CYS848 3.2 38.0 1.0
CD2 C:HIS862 3.2 27.1 1.0
CB C:CYS869 3.2 29.4 1.0
N C:CYS848 3.7 27.7 1.0
CA C:CYS869 3.9 44.9 1.0
CA C:CYS848 4.0 26.9 1.0
O C:HOH1086 4.1 42.5 1.0
ND1 C:HIS862 4.2 30.5 1.0
CG C:HIS862 4.3 29.5 1.0
CB C:LEU847 4.4 27.3 1.0
CA C:CYS845 4.5 29.7 1.0
CD2 C:LEU863 4.6 26.4 1.0
C C:LEU847 4.7 32.0 1.0
C C:CYS848 4.8 34.4 1.0
C C:CYS869 4.9 46.8 1.0
CA C:LEU847 4.9 29.2 1.0
N C:LEU847 5.0 34.7 1.0
N C:CYS869 5.0 48.3 1.0
N C:HIS849 5.0 30.2 1.0

Zinc binding site 6 out of 16 in 5lpi

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Zinc binding site 6 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:27.9
occ:1.00
NE2 C:HIS772 2.1 21.8 1.0
SG C:CYS777 2.3 24.9 1.0
SG C:CYS757 2.3 26.9 1.0
SG C:CYS754 2.3 24.5 1.0
CD2 C:HIS772 3.0 22.0 1.0
CE1 C:HIS772 3.1 28.1 1.0
CB C:CYS777 3.2 22.2 1.0
CB C:CYS757 3.2 32.9 1.0
CB C:CYS754 3.2 21.2 1.0
N C:CYS757 3.6 28.7 1.0
CA C:CYS777 3.8 22.2 1.0
O C:HOH1080 3.9 27.7 1.0
CA C:CYS757 4.0 28.6 1.0
CG C:HIS772 4.2 24.2 1.0
ND1 C:HIS772 4.2 26.0 1.0
CB C:PHE756 4.6 29.2 1.0
CA C:CYS754 4.6 25.4 1.0
C C:PHE756 4.7 30.8 1.0
C C:CYS777 4.8 20.2 1.0
C C:CYS757 4.8 32.4 1.0
N C:CYS777 4.9 23.2 1.0
N C:LEU778 4.9 25.9 1.0
N C:GLY758 5.0 31.6 1.0
N C:PHE756 5.0 26.0 1.0
CA C:PHE756 5.0 29.9 1.0

Zinc binding site 7 out of 16 in 5lpi

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Zinc binding site 7 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn903

b:49.3
occ:1.00
NE2 C:HIS827 2.2 52.1 1.0
SG C:CYS815 2.3 44.0 1.0
SG C:CYS812 2.3 53.5 1.0
SG C:CYS833 2.4 42.3 1.0
CB C:CYS812 3.0 42.4 1.0
CD2 C:HIS827 3.1 55.0 1.0
CB C:CYS815 3.2 43.1 1.0
CB C:CYS833 3.2 33.5 1.0
CE1 C:HIS827 3.2 52.9 1.0
N C:CYS815 3.6 42.4 1.0
CA C:CYS815 4.0 47.3 1.0
CG C:HIS827 4.3 53.6 1.0
ND1 C:HIS827 4.3 54.4 1.0
O C:HOH1047 4.3 47.6 1.0
CB C:ARG814 4.4 48.0 1.0
CA C:CYS812 4.5 48.7 1.0
C C:ARG814 4.5 44.4 1.0
CA C:CYS833 4.6 45.5 1.0
CA C:ARG814 4.8 50.9 1.0
N C:ARG814 4.8 59.2 1.0
C C:CYS815 4.9 47.1 1.0
C C:CYS812 4.9 43.5 1.0
CG C:ARG814 5.0 46.3 1.0

Zinc binding site 8 out of 16 in 5lpi

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Zinc binding site 8 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn904

b:45.7
occ:1.00
NE2 C:HIS798 2.1 41.7 1.0
SG C:CYS783 2.3 43.4 1.0
SG C:CYS803 2.3 44.9 1.0
SG C:CYS786 2.4 45.8 1.0
CD2 C:HIS798 3.1 39.4 1.0
CB C:CYS783 3.1 44.0 1.0
CB C:CYS786 3.2 47.3 1.0
CE1 C:HIS798 3.2 42.3 1.0
CB C:CYS803 3.3 49.3 1.0
N C:CYS786 3.7 54.3 1.0
CA C:CYS803 3.9 57.4 1.0
CA C:CYS786 4.0 51.6 1.0
CG C:HIS798 4.2 36.8 1.0
ND1 C:HIS798 4.2 44.2 1.0
N C:ASP804 4.6 70.5 1.0
CA C:CYS783 4.6 42.3 1.0
CD2 C:LEU799 4.7 40.3 1.0
CB C:HIS785 4.7 48.0 1.0
C C:HIS785 4.7 57.3 1.0
C C:CYS786 4.8 48.6 1.0
C C:CYS803 4.8 71.4 1.0

Zinc binding site 9 out of 16 in 5lpi

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Zinc binding site 9 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:27.9
occ:1.00
NE2 A:HIS862 2.1 24.4 1.0
SG A:CYS848 2.3 26.0 1.0
SG A:CYS845 2.3 25.6 1.0
SG A:CYS869 2.3 26.9 1.0
CB A:CYS845 3.0 23.5 1.0
CB A:CYS869 3.1 23.7 1.0
CD2 A:HIS862 3.1 24.4 1.0
CE1 A:HIS862 3.1 28.5 1.0
CB A:CYS848 3.2 27.1 1.0
CA A:CYS869 3.6 23.6 1.0
N A:CYS848 3.7 25.6 1.0
CA A:CYS848 4.0 25.1 1.0
ND1 A:HIS862 4.2 25.0 1.0
CG A:HIS862 4.2 28.3 1.0
O A:HOH1050 4.3 32.3 1.0
CA A:CYS845 4.5 23.8 1.0
CB A:LEU847 4.5 25.5 1.0
CD2 A:LEU863 4.5 27.4 1.0
N A:CYS869 4.6 28.9 1.0
C A:CYS869 4.7 32.4 1.0
C A:LEU847 4.7 30.3 1.0
N A:THR870 4.7 28.7 1.0
C A:CYS848 4.9 29.3 1.0
N A:LEU847 4.9 22.0 1.0
C A:CYS845 4.9 24.9 1.0
CA A:LEU847 5.0 24.7 1.0

Zinc binding site 10 out of 16 in 5lpi

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Zinc binding site 10 out of 16 in the Structure of the Zinc Finger Array of CEP104


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Zinc Finger Array of CEP104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:26.2
occ:1.00
NE2 A:HIS827 2.1 20.8 1.0
SG A:CYS815 2.3 23.2 1.0
SG A:CYS812 2.3 21.8 1.0
SG A:CYS833 2.3 24.8 1.0
CD2 A:HIS827 3.0 22.9 1.0
CB A:CYS833 3.0 23.5 1.0
CE1 A:HIS827 3.1 21.9 1.0
CB A:CYS812 3.1 20.2 1.0
CB A:CYS815 3.2 22.0 1.0
N A:CYS815 3.5 25.0 1.0
CA A:CYS815 3.9 23.9 1.0
O A:HOH1035 4.0 24.8 1.0
CG A:HIS827 4.2 23.7 1.0
ND1 A:HIS827 4.2 24.9 1.0
O A:HOH1082 4.3 32.9 1.0
CB A:ARG814 4.3 24.6 1.0
C A:ARG814 4.5 29.9 1.0
CA A:CYS833 4.5 26.8 1.0
CA A:CYS812 4.5 24.3 1.0
CA A:ARG814 4.8 27.3 1.0
N A:CYS833 4.8 28.6 1.0
N A:ARG814 4.8 26.2 1.0
C A:CYS815 4.9 23.2 1.0
CG A:ARG814 4.9 35.1 1.0
C A:CYS812 4.9 24.5 1.0
O A:CYS812 4.9 24.8 1.0

Reference:

C.Al-Jassar, A.Andreeva, D.D.Barnabas, S.H.Mclaughlin, C.M.Johnson, M.Yu, M.Van Breugel. The Ciliopathy-Associated CEP104 Protein Interacts with Tubulin and NEK1 Kinase. Structure V. 25 146 2017.
ISSN: ISSN 1878-4186
PubMed: 28017521
DOI: 10.1016/J.STR.2016.11.014
Page generated: Wed Dec 16 06:30:24 2020

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