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Zinc in PDB 9jko: Crystal Structure of the Rna- Binding Domain of Human ZAR1

Protein crystallography data

The structure of Crystal Structure of the Rna- Binding Domain of Human ZAR1, PDB code: 9jko was solved by Q.L.Liu, C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.51 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.61, 58.45, 81.5, 90, 90, 90
R / Rfree (%) 18.8 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Rna- Binding Domain of Human ZAR1 (pdb code 9jko). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Rna- Binding Domain of Human ZAR1, PDB code: 9jko:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 9jko

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Zinc binding site 1 out of 6 in the Crystal Structure of the Rna- Binding Domain of Human ZAR1


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 the Rna- Binding Domain of Human ZAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:10.6
occ:1.00
 NE2 A:HIS399 2.1 10.5 1.0
SG A:CYS407 2.3 10.1 1.0
SG A:CYS414 2.3 8.6 1.0
SG A:CYS404 2.3 10.4 1.0
CE1 A:HIS399 3.1 10.0 1.0
CB A:CYS404 3.1 10.6 1.0
CD2 A:HIS399 3.1 9.3 1.0
CB A:CYS414 3.2 9.9 1.0
CB A:CYS407 3.3 10.9 1.0
N A:CYS414 3.7 8.6 1.0
N A:CYS407 3.8 12.2 1.0
CA A:CYS414 4.0 9.9 1.0
CA A:CYS407 4.1 10.1 1.0
ND1 A:HIS399 4.2 10.2 1.0
CG A:HIS399 4.3 9.8 1.0
CB A:ARG406 4.5 10.0 1.0
CA A:CYS404 4.6 10.7 1.0
C A:ARG406 4.7 16.1 1.0
NE1 A:TRP345 4.7 11.0 1.0
O A:HOH637 4.8 9.0 1.0
C A:SER413 4.9 10.8 1.0
CA A:ARG406 4.9 12.7 1.0
N A:ARG406 5.0 10.4 1.0
C A:CYS407 5.0 11.8 1.0

Zinc binding site 2 out of 6 in 9jko

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Zinc binding site 2 out of 6 in the Crystal Structure of the Rna- Binding Domain of Human ZAR1


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 the Rna- Binding Domain of Human ZAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:13.9
occ:1.00
 SG A:CYS332 2.3 14.2 1.0
SG A:CYS335 2.3 14.0 1.0
SG A:CYS359 2.3 11.8 1.0
SG A:CYS362 2.4 13.6 1.0
CB A:CYS359 3.2 14.8 1.0
CB A:CYS362 3.2 14.1 1.0
CB A:CYS335 3.2 16.0 1.0
CB A:CYS332 3.4 15.3 1.0
N A:CYS362 3.6 13.9 1.0
CA A:CYS362 4.0 14.6 1.0
N A:CYS335 4.0 15.8 1.0
CA A:CYS335 4.2 17.4 1.0
OH A:TYR366 4.4 14.5 1.0
CA A:CYS359 4.6 13.9 1.0
CE2 A:TYR366 4.6 13.0 1.0
CB A:THR361 4.7 19.4 1.0
C A:THR361 4.7 15.9 1.0
CA A:CYS332 4.8 13.8 1.0
C A:CYS362 4.8 15.9 1.0
CB A:ASP334 4.9 16.2 1.0
N A:THR361 4.9 15.6 1.0
NZ A:LYS364 4.9 14.9 1.0
N A:GLN363 4.9 13.1 1.0
CZ A:TYR366 4.9 15.0 1.0
C A:ASP334 4.9 20.9 1.0

Zinc binding site 3 out of 6 in 9jko

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Zinc binding site 3 out of 6 in the Crystal Structure of the Rna- Binding Domain of Human ZAR1


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 the Rna- Binding Domain of Human ZAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:17.4
occ:1.00
 SG A:CYS379 2.3 16.5 1.0
SG A:CYS386 2.3 17.8 1.0
SG A:CYS384 2.3 17.1 1.0
SG A:CYS376 2.3 17.6 1.0
CB A:CYS376 3.1 17.0 1.0
CB A:CYS386 3.1 18.1 1.0
CB A:CYS384 3.2 18.7 1.0
CB A:CYS379 3.2 21.0 1.0
N A:CYS379 3.8 22.0 1.0
CA A:CYS379 4.0 21.2 1.0
N A:CYS386 4.1 16.6 1.0
CA A:CYS386 4.2 15.5 1.0
CB A:SER378 4.5 21.0 1.0
O A:HOH650 4.5 23.8 1.0
O A:HOH782 4.5 30.2 1.0
CA A:CYS376 4.5 18.1 1.0
CA A:CYS384 4.6 20.6 1.0
O A:HOH659 4.7 27.4 1.0
C A:CYS379 4.7 28.3 1.0
C A:SER378 4.7 22.3 1.0
O A:GLN381 4.7 22.3 1.0
N A:LYS380 4.9 21.1 1.0
CG A:LYS389 4.9 15.3 1.0
N A:SER385 5.0 14.8 1.0
C A:CYS384 5.0 19.7 1.0
N A:GLN381 5.0 24.4 1.0
CA A:SER378 5.0 20.8 1.0

Zinc binding site 4 out of 6 in 9jko

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Zinc binding site 4 out of 6 in the Crystal Structure of the Rna- Binding Domain of Human ZAR1


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 the Rna- Binding Domain of Human ZAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:15.8
occ:1.00
 SG B:CYS386 2.3 12.9 1.0
SG B:CYS384 2.3 17.5 1.0
SG B:CYS379 2.3 20.5 1.0
SG B:CYS376 2.3 14.4 1.0
CB B:CYS384 3.1 20.0 1.0
CB B:CYS379 3.2 23.9 1.0
CB B:CYS386 3.2 13.2 1.0
CB B:CYS376 3.3 15.4 1.0
N B:CYS379 3.7 19.9 1.0
CA B:CYS379 4.0 22.2 1.0
N B:CYS386 4.1 17.5 1.0
CA B:CYS386 4.3 14.7 1.0
CB B:SER378 4.3 16.4 1.0
C B:SER378 4.5 21.5 1.0
CA B:CYS384 4.5 21.2 1.0
O B:HOH703 4.6 21.9 1.0
C B:CYS379 4.7 25.6 1.0
CA B:CYS376 4.7 17.1 1.0
O B:GLN381 4.7 31.2 1.0
N B:LYS380 4.7 20.9 1.0
CG B:LYS389 4.8 15.1 1.0
CA B:SER378 4.8 18.3 1.0
N B:SER385 4.9 19.7 1.0
N B:SER378 4.9 14.9 1.0
C B:CYS384 5.0 21.8 1.0

Zinc binding site 5 out of 6 in 9jko

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Zinc binding site 5 out of 6 in the Crystal Structure of the Rna- Binding Domain of Human ZAR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Rna- Binding Domain of Human ZAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:12.8
occ:1.00
 NE2 B:HIS399 2.1 13.6 1.0
SG B:CYS404 2.3 12.4 1.0
SG B:CYS407 2.3 13.8 1.0
SG B:CYS414 2.3 12.1 1.0
CE1 B:HIS399 3.0 13.6 1.0
CB B:CYS404 3.1 13.8 1.0
CB B:CYS414 3.2 12.8 1.0
CD2 B:HIS399 3.2 14.7 1.0
CB B:CYS407 3.3 14.9 1.0
N B:CYS407 3.7 15.5 1.0
N B:CYS414 3.8 11.6 1.0
CA B:CYS407 4.1 16.1 1.0
CA B:CYS414 4.1 10.7 1.0
ND1 B:HIS399 4.2 13.7 1.0
CG B:HIS399 4.3 13.5 1.0
CB B:ARG406 4.4 11.7 1.0
CA B:CYS404 4.6 13.6 1.0
C B:ARG406 4.7 16.8 1.0
O B:HOH624 4.7 12.3 1.0
NE1 B:TRP345 4.8 13.8 1.0
C B:CYS407 4.9 15.6 1.0
CA B:ARG406 4.9 13.3 1.0
C B:SER413 5.0 11.0 1.0
N B:ARG406 5.0 15.1 1.0
C B:CYS404 5.0 14.6 1.0

Zinc binding site 6 out of 6 in 9jko

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Zinc binding site 6 out of 6 in the Crystal Structure of the Rna- Binding Domain of Human ZAR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Rna- Binding Domain of Human ZAR1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:17.4
occ:1.00
 SG B:CYS359 2.3 14.8 1.0
SG B:CYS335 2.3 19.6 1.0
SG B:CYS362 2.3 17.9 1.0
SG B:CYS332 2.3 15.3 1.0
CB B:CYS362 3.1 20.4 1.0
CB B:CYS359 3.2 17.0 1.0
CB B:CYS335 3.3 19.9 1.0
CB B:CYS332 3.4 16.0 1.0
N B:CYS362 3.6 22.7 1.0
CA B:CYS362 3.9 20.6 1.0
N B:CYS335 4.0 21.0 1.0
CA B:CYS335 4.3 20.2 1.0
C B:THR361 4.7 23.2 1.0
CA B:CYS359 4.7 15.1 1.0
OH B:TYR366 4.7 21.8 1.0
NZ B:LYS364 4.7 27.8 1.0
C B:CYS362 4.7 20.1 1.0
CB B:THR361 4.7 23.8 1.0
CA B:CYS332 4.8 15.6 1.0
CE2 B:TYR366 4.8 16.9 1.0
O B:HOH744 4.8 30.3 1.0
N B:THR361 4.9 20.1 1.0
CB B:ASP334 4.9 25.6 1.0
N B:GLN363 4.9 20.1 1.0
CA B:THR361 5.0 22.3 1.0
C B:ASP334 5.0 24.9 1.0

Reference:

Q.Liu, H.Ma, X.He, C.Xu, J.Zhang. Molecular Insights Into Rna Recognition By the ZAR1 C-Terminal Domain. Febs Lett. 2025.
ISSN: ISSN 0014-5793
PubMed: 40388637
DOI: 10.1002/1873-3468.70080
Page generated: Fri Aug 22 18:23:20 2025

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