Zinc in PDB 7bvw: Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1

The structure of Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1, PDB code: 7bvw was solved by S.Chen, K.B.Wong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.23 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.431, 23.648, 75.699, 90, 94.8, 90
R / Rfree (%)	17.9 / 22.2

The structure of Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1 (pdb code 7bvw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1, PDB code: 7bvw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1


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 Ring-H2 Domain of Arabidopsis RMR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:18.2 occ:1.00 ND1 A:HIS255 2.3 15.0 1.0 SG A:CYS258 2.4 14.6 1.0 SG A:CYS235 2.4 19.1 1.0 SG A:CYS232 2.4 14.2 1.0 CG A:HIS255 3.0 14.5 1.0 CB A:CYS232 3.1 12.9 1.0 CB A:HIS255 3.1 14.9 1.0 CB A:CYS235 3.3 17.9 1.0 CB A:CYS258 3.3 12.3 1.0 CE1 A:HIS255 3.4 16.6 1.0 N A:CYS235 3.8 18.9 1.0 CA A:CYS235 4.2 16.7 1.0 N A:HIS255 4.3 14.0 1.0 CD2 A:HIS255 4.3 14.4 1.0 CA A:HIS255 4.3 15.0 1.0 NE2 A:HIS255 4.4 15.7 1.0 O A:HOH530 4.4 41.9 1.0 CA A:CYS232 4.5 16.4 1.0 CB A:ILE234 4.6 16.6 1.0 C A:ILE234 4.7 19.4 1.0 CA A:CYS258 4.7 12.7 1.0 C A:CYS232 4.9 20.0 1.0 O A:CYS232 4.9 21.7 1.0 N A:ILE234 5.0 20.9 1.0 C A:CYS235 5.0 17.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1


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 Ring-H2 Domain of Arabidopsis RMR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:21.0 occ:1.00 ND1 A:HIS252 2.0 19.6 1.0 SG A:CYS250 2.3 21.3 1.0 SG A:CYS273 2.3 20.2 1.0 SG A:CYS270 2.3 15.8 1.0 CE1 A:HIS252 2.8 22.5 1.0 CB A:CYS270 3.1 15.1 1.0 CG A:HIS252 3.2 19.6 1.0 CB A:CYS250 3.2 19.2 1.0 CB A:CYS273 3.5 21.0 1.0 CB A:HIS252 3.6 19.8 1.0 N A:CYS273 3.8 20.1 1.0 NE2 A:HIS252 4.0 22.6 1.0 CA A:CYS273 4.2 18.7 1.0 CD2 A:HIS252 4.2 20.2 1.0 O A:CYS250 4.5 18.7 1.0 CA A:CYS250 4.5 20.2 1.0 CA A:CYS270 4.6 14.8 1.0 C A:CYS250 4.6 19.0 1.0 CB A:VAL272 4.6 24.5 1.0 N A:HIS252 4.6 22.3 1.0 CB A:HIS275 4.7 26.5 1.0 C A:CYS273 4.8 19.2 1.0 CA A:HIS252 4.8 19.7 1.0 C A:VAL272 4.9 21.6 1.0 N A:LYS274 4.9 17.1 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1


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 Ring-H2 Domain of Arabidopsis RMR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:28.9 occ:0.50 OE1 A:GLU230 2.0 28.0 1.0 NE2 A:HIS225 2.1 25.0 1.0 CD A:GLU230 2.6 29.6 1.0 OE2 A:GLU230 2.7 31.8 1.0 CE1 A:HIS225 2.9 25.4 1.0 CD2 A:HIS225 3.3 23.3 1.0 ND1 A:HIS225 4.1 25.7 1.0 CG A:GLU230 4.1 28.6 1.0 CE1 A:HIS226 4.3 37.2 1.0 CG A:HIS225 4.3 23.4 1.0 O A:HOH516 4.7 20.1 1.0 ND1 A:HIS226 4.7 35.3 1.0 CB A:GLU230 4.8 27.2 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1


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 Ring-H2 Domain of Arabidopsis RMR1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:23.9 occ:1.00 ND1 B:HIS255 2.2 16.1 1.0 SG B:CYS258 2.3 17.4 1.0 SG B:CYS235 2.4 17.5 1.0 SG B:CYS232 2.4 18.2 1.0 CG B:HIS255 3.0 17.8 1.0 CB B:CYS232 3.1 15.6 1.0 CB B:HIS255 3.2 17.1 1.0 CE1 B:HIS255 3.3 17.2 1.0 CB B:CYS235 3.3 20.1 1.0 CB B:CYS258 3.4 15.9 1.0 N B:CYS235 3.9 22.6 1.0 N B:HIS255 4.2 14.2 1.0 CA B:CYS235 4.2 21.4 1.0 CD2 B:HIS255 4.3 17.9 1.0 CA B:HIS255 4.3 15.7 1.0 NE2 B:HIS255 4.4 18.1 1.0 CA B:CYS232 4.5 19.1 1.0 CA B:CYS258 4.8 17.0 1.0 CB B:ILE234 4.8 14.1 1.0 C B:ILE234 4.9 19.1 1.0 C B:CYS232 4.9 20.2 1.0 O B:CYS232 4.9 18.8 1.0 C B:CYS235 5.0 21.1 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Ring-H2 Domain of Arabidopsis RMR1


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 Ring-H2 Domain of Arabidopsis RMR1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:19.1 occ:1.00 ND1 B:HIS252 2.0 16.5 1.0 SG B:CYS250 2.3 17.2 1.0 SG B:CYS273 2.3 20.3 1.0 SG B:CYS270 2.4 21.5 1.0 CE1 B:HIS252 2.9 21.4 1.0 CB B:CYS270 3.1 21.4 1.0 CG B:HIS252 3.2 18.9 1.0 CB B:CYS250 3.2 17.0 1.0 CB B:CYS273 3.4 23.6 1.0 CB B:HIS252 3.6 19.4 1.0 N B:CYS273 3.8 22.8 1.0 NE2 B:HIS252 4.0 21.2 1.0 CA B:CYS273 4.1 22.8 1.0 CD2 B:HIS252 4.2 19.6 1.0 O B:CYS250 4.4 15.4 1.0 CA B:CYS250 4.4 16.7 1.0 CB B:VAL272 4.4 22.9 1.0 CA B:CYS270 4.5 21.3 1.0 C B:CYS250 4.6 17.8 1.0 N B:HIS252 4.7 18.1 1.0 CB B:HIS275 4.8 24.2 1.0 C B:CYS273 4.8 22.8 1.0 CA B:HIS252 4.8 18.7 1.0 C B:VAL272 4.8 24.6 1.0 CG1 B:VAL272 4.9 22.9 1.0 N B:VAL272 5.0 26.4 1.0 N B:LYS274 5.0 21.9 1.0 CA B:VAL272 5.0 25.2 1.0

S.Chen, Y.L.Zeng, H.Y.Wong, L.Yang, F.Luo, L.W.Jiang, K.B.Wong. The Ring-Finger of ATRMR1 (Arabidopsis Receptor-Homology-Transmembrane-Ring-H2 Sorting Receptor 1) Is An E3 Ligase That Mediate Its Trafficking To Be Published.