Zinc in PDB 5ly0: Crystal Structure of Lob Domain of RAMOSA2 From Wheat

The structure of Crystal Structure of Lob Domain of RAMOSA2 From Wheat, PDB code: 5ly0 was solved by X.-B.Wei, B.Zhang, W.-F.Chen, S.-H.Fan, S.Rety, X.-G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.345, 85.206, 93.334, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.1

The binding sites of Zinc atom in the Crystal Structure of Lob Domain of RAMOSA2 From Wheat (pdb code 5ly0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Lob Domain of RAMOSA2 From Wheat, PDB code: 5ly0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Lob Domain of RAMOSA2 From Wheat


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 Lob Domain of RAMOSA2 From Wheat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.8 occ:1.00 SG A:CYS31 2.4 28.0 1.0 SG A:CYS42 2.4 27.2 1.0 SG A:CYS38 2.4 27.5 1.0 SG A:CYS28 2.4 26.1 1.0 HB2 A:CYS38 3.1 33.6 1.0 HB2 A:CYS31 3.1 32.7 1.0 CB A:CYS38 3.3 28.0 1.0 HB3 A:CYS28 3.3 31.8 1.0 H A:CYS28 3.3 35.3 1.0 HB2 A:ALA45 3.3 33.4 1.0 HA A:CYS38 3.3 36.4 1.0 HB2 A:CYS42 3.3 33.5 1.0 CB A:CYS42 3.4 27.9 1.0 CB A:CYS31 3.4 27.2 1.0 HB3 A:CYS42 3.5 33.5 1.0 CB A:CYS28 3.5 26.5 1.0 H A:CYS31 3.5 29.0 1.0 HB2 A:PHE44 3.8 32.6 1.0 CA A:CYS38 3.8 30.4 1.0 N A:CYS28 4.0 29.4 1.0 HB3 A:CYS31 4.0 32.7 1.0 H A:ALA45 4.1 33.1 1.0 HB3 A:CYS38 4.1 33.6 1.0 N A:CYS31 4.2 24.2 1.0 HA A:ALA45 4.2 32.0 1.0 CB A:ALA45 4.2 27.9 1.0 HB2 A:CYS28 4.2 31.8 1.0 HB3 A:ALA30 4.2 27.6 1.0 CA A:CYS28 4.3 26.8 1.0 N A:ALA45 4.4 27.6 1.0 CA A:CYS31 4.4 25.6 1.0 HD2 A:PHE44 4.5 38.2 1.0 CA A:ALA45 4.5 26.7 1.0 O A:HOH348 4.6 36.8 1.0 H A:PHE44 4.6 33.4 1.0 HH21 A:ARG36 4.7 67.0 1.0 HB1 A:ALA45 4.7 33.4 1.0 C A:CYS38 4.8 29.8 1.0 CB A:PHE44 4.8 27.1 1.0 HA A:CYS31 4.8 30.7 1.0 H A:LEU39 4.8 38.1 1.0 HE A:ARG36 4.8 63.7 1.0 CA A:CYS42 4.8 30.1 1.0 HB3 A:ALA45 4.8 33.4 1.0 C A:CYS28 4.8 26.0 1.0 O A:CYS28 4.8 25.9 1.0 O A:HOH346 4.8 33.0 1.0 HA A:PRO27 4.9 44.7 1.0 N A:CYS38 5.0 30.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Lob Domain of RAMOSA2 From Wheat


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 Lob Domain of RAMOSA2 From Wheat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:51.7 occ:1.00 SG B:CYS31 2.3 54.6 1.0 SG B:CYS42 2.4 50.3 1.0 SG B:CYS38 2.4 59.1 1.0 SG B:CYS28 2.4 47.8 1.0 HB3 B:CYS28 3.1 56.4 1.0 HB2 B:CYS38 3.1 76.7 1.0 H B:CYS28 3.1 64.1 1.0 HH21 B:ARG36 3.2 95.0 1.0 HB3 B:CYS42 3.2 69.5 1.0 HB2 B:ALA45 3.2 64.9 1.0 CB B:CYS42 3.2 57.9 1.0 HB2 B:CYS31 3.2 68.1 1.0 CB B:CYS38 3.3 64.0 1.0 HB2 B:CYS42 3.3 69.5 1.0 CB B:CYS28 3.3 47.0 1.0 HA B:CYS38 3.3 80.5 1.0 H B:CYS31 3.4 60.6 1.0 CB B:CYS31 3.4 56.7 1.0 CA B:CYS38 3.8 67.0 1.0 H B:ALA45 3.9 62.3 1.0 N B:CYS28 3.9 53.4 1.0 NH2 B:ARG36 4.0 79.2 1.0 HB3 B:ALA30 4.1 52.1 1.0 HB2 B:CYS28 4.1 56.4 1.0 N B:CYS31 4.1 50.5 1.0 CB B:ALA45 4.1 54.1 1.0 HB2 B:PHE44 4.1 60.8 1.0 HB3 B:CYS31 4.1 68.1 1.0 HB3 B:CYS38 4.1 76.7 1.0 CA B:CYS28 4.1 50.1 1.0 HE B:ARG36 4.2 91.8 1.0 HA B:ALA45 4.2 61.5 1.0 N B:ALA45 4.3 51.9 1.0 CA B:CYS31 4.4 54.9 1.0 HH22 B:ARG36 4.4 95.0 1.0 CA B:ALA45 4.5 51.2 1.0 H B:PHE44 4.6 69.5 1.0 HB1 B:ALA45 4.6 64.9 1.0 HB3 B:ALA45 4.6 64.9 1.0 HA B:PRO27 4.6 71.8 1.0 CA B:CYS42 4.7 61.8 1.0 C B:CYS28 4.7 47.5 1.0 C B:CYS38 4.7 73.3 1.0 HD2 B:PHE44 4.8 61.4 1.0 H B:LEU39 4.8 92.9 1.0 HA B:CYS31 4.8 65.8 1.0 O B:CYS28 4.8 50.5 1.0 NE B:ARG36 4.9 76.5 1.0 CZ B:ARG36 4.9 79.6 1.0 H B:ALA30 4.9 53.8 1.0 N B:CYS38 5.0 69.2 1.0 HA B:CYS28 5.0 60.1 1.0

W.F.Chen, X.B.Wei, S.Rety, L.Y.Huang, N.N.Liu, S.X.Dou, X.G.Xi. Structural Analysis Reveals A "Molecular Calipers" Mechanism For A Lateral Organ Boundaries Domain Transcription Factor Protein From Wheat. J. Biol. Chem. V. 294 142 2019.
ISSN: ESSN 1083-351X
PubMed: 30425099
DOI: 10.1074/JBC.RA118.003956