Zinc in PDB 8yva: Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center

The structure of Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center, PDB code: 8yva was solved by F.D.Li, M.L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.99 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.019, 46.351, 59.228, 79.41, 74.33, 72.86
R / Rfree (%)	17.6 / 22.1

The binding sites of Zinc atom in the Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center (pdb code 8yva). 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 Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center, PDB code: 8yva:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center


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 Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:17.1 occ:1.00 NE2 A:HIS501 2.1 14.5 1.0 NE2 A:HIS497 2.1 15.7 1.0 SG A:CYS474 2.2 15.4 1.0 SG A:CYS479 2.3 18.5 1.0 CD2 A:HIS497 3.0 12.5 1.0 CB A:CYS474 3.0 17.8 1.0 CD2 A:HIS501 3.1 15.1 1.0 CB A:CYS479 3.1 20.6 1.0 CE1 A:HIS501 3.1 16.0 1.0 CE1 A:HIS497 3.2 18.2 1.0 CG A:HIS497 4.2 12.0 1.0 ND1 A:HIS501 4.2 19.7 1.0 CG A:HIS501 4.2 17.7 1.0 ND1 A:HIS497 4.2 13.2 1.0 CB A:PHE476 4.3 20.4 1.0 CA A:CYS474 4.4 16.3 1.0 CA A:CYS479 4.5 25.4 1.0 O A:CYS474 4.7 22.5 1.0 C A:CYS474 4.8 20.3 1.0 SG A:CYS557 4.9 14.9 1.0 CB A:ARG481 5.0 25.3 1.0 N A:PHE476 5.0 22.7 1.0 O A:HOH770 5.0 34.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center


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 Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:16.8 occ:1.00 NE2 A:HIS530 2.0 14.5 1.0 NE2 A:HIS525 2.1 18.8 1.0 SG A:CYS509 2.2 14.1 1.0 SG A:CYS512 2.3 18.5 1.0 CD2 A:HIS530 3.0 18.3 1.0 CE1 A:HIS530 3.0 21.6 1.0 CD2 A:HIS525 3.0 16.4 1.0 CE1 A:HIS525 3.1 17.7 1.0 CB A:CYS509 3.2 17.1 1.0 CB A:CYS512 3.4 20.3 1.0 N A:CYS512 3.6 19.7 1.0 CA A:CYS512 4.0 19.3 1.0 ND1 A:HIS530 4.1 20.4 1.0 CG A:HIS530 4.1 19.2 1.0 CB A:TYR514 4.1 17.4 1.0 ND1 A:HIS525 4.2 15.7 1.0 CG A:HIS525 4.2 14.0 1.0 CB A:LYS511 4.5 19.2 1.0 C A:CYS512 4.5 20.0 1.0 C A:LYS511 4.5 23.2 1.0 CA A:CYS509 4.7 13.3 1.0 O A:CYS512 4.7 19.1 1.0 N A:LYS511 4.8 17.2 1.0 CG2 A:ILE529 4.8 25.6 1.0 CA A:LYS511 4.8 19.9 1.0 N A:TYR514 4.8 20.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center


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 Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:16.4 occ:1.00 NE2 B:HIS497 2.0 11.9 1.0 NE2 B:HIS501 2.1 14.0 1.0 SG B:CYS479 2.2 18.9 1.0 SG B:CYS474 2.3 14.5 1.0 CD2 B:HIS497 3.0 12.3 1.0 CB B:CYS474 3.0 14.9 1.0 CD2 B:HIS501 3.0 15.9 1.0 CE1 B:HIS497 3.0 16.8 1.0 CB B:CYS479 3.1 20.0 1.0 CE1 B:HIS501 3.1 17.1 1.0 CG B:HIS497 4.1 14.2 1.0 ND1 B:HIS497 4.1 14.1 1.0 ND1 B:HIS501 4.2 15.7 1.0 CG B:HIS501 4.2 15.3 1.0 CB B:PHE476 4.2 21.6 1.0 CA B:CYS474 4.4 14.2 1.0 CB B:ARG481 4.5 28.7 1.0 CA B:CYS479 4.5 24.0 1.0 C B:CYS474 4.8 16.9 1.0 O B:HOH721 4.8 25.3 1.0 N B:PHE476 4.9 20.5 1.0 SG B:CYS557 4.9 18.6 1.0 N B:ARG481 5.0 24.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center


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 Caenorhabditis Elegans Zim-2 ZF1-2-Ctd Domain in Complex with Chromosome V Pairing Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:14.8 occ:1.00 NE2 B:HIS530 2.0 14.2 1.0 NE2 B:HIS525 2.1 15.0 1.0 SG B:CYS509 2.2 13.5 1.0 SG B:CYS512 2.3 14.0 1.0 CD2 B:HIS530 2.9 16.7 1.0 CD2 B:HIS525 3.0 15.3 1.0 CE1 B:HIS530 3.1 18.1 1.0 CE1 B:HIS525 3.1 13.1 1.0 CB B:CYS509 3.2 12.0 1.0 CB B:CYS512 3.4 15.8 1.0 N B:CYS512 3.7 16.3 1.0 CA B:CYS512 4.0 13.9 1.0 CG B:HIS530 4.1 19.0 1.0 ND1 B:HIS530 4.1 18.1 1.0 CB B:TYR514 4.2 12.4 1.0 CG B:HIS525 4.2 12.9 1.0 ND1 B:HIS525 4.2 13.3 1.0 C B:LYS511 4.2 18.0 1.0 C B:CYS512 4.5 13.0 1.0 O B:CYS512 4.6 12.3 1.0 CB B:LYS511 4.6 19.1 1.0 N B:LYS511 4.6 15.2 1.0 CA B:CYS509 4.7 9.5 1.0 CA B:LYS511 4.7 19.4 1.0 CG2 B:ILE529 4.8 17.6 1.0 O B:LYS511 4.8 19.4 1.0 N B:TYR514 4.9 12.9 1.0

M.Li, C.Zhu, Z.Xu, M.Xu, Y.Kuang, X.Hou, X.Huang, M.Lv, Y.Liu, Y.Zhang, Z.Xu, X.Han, S.Wang, Y.Shi, S.Guang, F.Li. Structural Basis For C. Elegans Pairing Center Dna Binding Specificity By the Zim/Him-8 Family Proteins. Nat Commun V. 15 10355 2024.
ISSN: ESSN 2041-1723
PubMed: 39609407
DOI: 10.1038/S41467-024-54548-9