Zinc in PDB 6krz: Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant

The structure of Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant, PDB code: 6krz was solved by H.Tanabe, Y.Fujii, M.Okada-Iwabu, M.Iwabu, T.Yamauchi, T.Kadowaki, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.90 / 3.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.589, 119.350, 197.814, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 27.3

The binding sites of Zinc atom in the Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant (pdb code 6krz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant, PDB code: 6krz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant


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 Human Adiponectin Receptor 1 D208A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:54.6 occ:1.00 NE2 A:HIS341 1.9 75.6 1.0 NE2 A:HIS191 2.3 59.8 1.0 NE2 A:HIS337 2.4 66.2 1.0 CE1 A:HIS341 2.8 61.4 1.0 CD2 A:HIS341 3.0 61.3 1.0 CD2 A:HIS337 3.1 65.0 1.0 O A:HOH507 3.1 16.5 1.0 CE1 A:HIS191 3.1 59.3 1.0 CD2 A:HIS191 3.4 57.6 1.0 OG A:SER187 3.4 47.2 1.0 CE1 A:HIS337 3.5 68.9 1.0 ND1 A:HIS341 4.0 61.8 1.0 CG A:HIS341 4.1 58.6 1.0 ND1 A:HIS191 4.3 59.1 1.0 CG A:HIS337 4.4 62.7 1.0 CE2 A:PHE340 4.4 57.9 1.0 CG A:HIS191 4.4 54.5 1.0 ND1 A:HIS337 4.5 67.0 1.0 CB A:SER187 4.7 49.6 1.0 CE1 A:HIS141 4.8 51.1 1.0 CD2 A:PHE340 4.8 57.9 1.0 ND1 A:HIS141 4.9 46.9 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant


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 Human Adiponectin Receptor 1 D208A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:61.9 occ:1.00 NE2 B:HIS341 2.0 81.5 1.0 NE2 B:HIS337 2.2 53.1 1.0 NE2 B:HIS191 2.4 63.2 1.0 CE1 B:HIS341 2.8 82.5 1.0 O B:HOH515 3.1 37.2 1.0 CD2 B:HIS341 3.1 79.7 1.0 CE1 B:HIS337 3.1 57.1 1.0 CD2 B:HIS337 3.2 51.9 1.0 CE1 B:HIS191 3.3 64.4 1.0 CD2 B:HIS191 3.3 62.8 1.0 OG B:SER187 3.4 44.0 1.0 ND1 B:HIS341 4.0 82.2 1.0 CG B:HIS341 4.2 78.1 1.0 ND1 B:HIS337 4.2 53.8 1.0 CG B:HIS337 4.3 52.4 1.0 ND1 B:HIS191 4.4 66.0 1.0 CG B:HIS191 4.5 62.6 1.0 CE2 B:PHE340 4.6 47.5 1.0 CB B:SER187 4.7 45.4 1.0 CD2 B:PHE340 4.9 47.1 1.0 ND1 B:HIS141 4.9 66.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Human Adiponectin Receptor 1 D208A Mutant


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 Human Adiponectin Receptor 1 D208A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:84.5 occ:1.00 NE2 C:HIS191 2.1 0.1 1.0 NE2 C:HIS337 2.3 88.7 1.0 NE2 C:HIS341 2.3 90.5 1.0 C4 C:OLB404 2.8 0.4 1.0 CE1 C:HIS341 3.0 91.2 1.0 CE1 C:HIS191 3.1 0.5 1.0 CD2 C:HIS191 3.1 0.7 1.0 CD2 C:HIS337 3.2 86.6 1.0 CE1 C:HIS337 3.2 92.2 1.0 OG C:SER187 3.3 67.8 1.0 C5 C:OLB404 3.4 0.1 1.0 C3 C:OLB404 3.5 0.7 1.0 CD2 C:HIS341 3.5 86.8 1.0 C2 C:OLB404 4.1 0.1 1.0 ND1 C:HIS191 4.2 0.2 1.0 ND1 C:HIS341 4.2 89.5 1.0 CG C:HIS191 4.2 0.3 1.0 C6 C:OLB404 4.2 0.6 1.0 ND1 C:HIS337 4.3 90.2 1.0 CG C:HIS337 4.3 86.3 1.0 CG C:HIS341 4.5 86.5 1.0 CB C:SER187 4.7 71.0 1.0 O20 C:OLB404 4.7 0.4 1.0 C1 C:OLB404 4.9 0.3 1.0

H.Tanabe, Y.Fujii, M.Okada-Iwabu, M.Iwabu, K.Kano, H.Kawana, M.Hato, Y.Nakamura, T.Terada, T.Kimura-Someya, M.Shirouzu, Y.Kawano, M.Yamamoto, J.Aoki, T.Yamauchi, T.Kadowaki, S.Yokoyama. Human Adiponectin Receptor ADIPOR1 Assumes Closed and Open Structures. Commun Biol V. 3 446 2020.
ISSN: ESSN 2399-3642
PubMed: 32796916
DOI: 10.1038/S42003-020-01160-4