Zinc in PDB 5xna: Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)

The structure of Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample), PDB code: 5xna was solved by Y.Fukuda, Y.Miura, E.Mizohata, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.14 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.672, 57.799, 110.903, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.9

The structure of Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) (pdb code 5xna). 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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample), PDB code: 5xna:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)


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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:14.6 occ:1.00 NE2 A:HIS138 1.9 13.6 0.7 NE2 A:HIS138 1.9 9.1 0.3 OE2 B:GLU127 2.0 12.3 1.0 NE2 B:HIS138 2.0 17.4 1.0 OE2 A:GLU127 2.0 14.9 1.0 CD A:GLU127 2.7 15.8 1.0 OE1 A:GLU127 2.7 16.1 1.0 CD B:GLU127 2.8 18.9 1.0 CD2 A:HIS138 2.8 15.5 0.3 CE1 A:HIS138 2.9 23.9 0.7 OE1 B:GLU127 2.9 15.8 1.0 CE1 B:HIS138 2.9 27.5 1.0 CD2 A:HIS138 3.0 14.7 0.7 CD2 B:HIS138 3.0 15.4 1.0 CE1 A:HIS138 3.0 22.0 0.3 CG1 B:VAL136 3.8 16.4 1.0 CG A:HIS138 4.0 17.6 0.3 ND1 A:HIS138 4.0 21.2 0.7 ND1 B:HIS138 4.0 21.6 1.0 ND1 A:HIS138 4.0 20.4 0.3 CG A:HIS138 4.1 18.1 0.7 CG B:HIS138 4.1 16.6 1.0 NE2 B:HIS129 4.1 13.1 1.0 CG A:GLU127 4.2 15.2 1.0 CG1 A:VAL136 4.2 18.2 1.0 CG B:GLU127 4.2 13.7 1.0 CE1 B:HIS129 4.7 15.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)


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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:35.8 occ:0.62 OE2 A:GLU48 2.3 40.4 1.0 CD A:GLU48 3.0 35.2 1.0 OE1 A:GLU48 3.0 38.4 1.0 CG A:GLU48 4.4 31.5 1.0 CD A:LYS160 4.5 39.2 1.0 CG A:LYS160 4.8 35.0 1.0 CE A:LYS160 4.9 31.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)


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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:22.9 occ:1.00 N B:SER30 2.1 21.1 1.0 OE1 B:GLU77 2.1 17.1 1.0 OG B:SER30 2.3 23.1 1.0 CA B:SER30 2.9 21.2 1.0 CD B:GLU77 3.0 25.0 1.0 CB B:SER30 3.1 23.5 1.0 OE2 B:GLU77 3.3 23.8 1.0 C B:SER30 4.4 30.1 1.0 CG B:GLU77 4.4 17.8 1.0 O B:HOH318 4.6 22.1 1.0 CB B:GLU77 4.8 17.9 1.0 O B:SER30 4.9 23.7 1.0 CA B:GLU77 4.9 16.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)


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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:24.1 occ:1.00 NE2 B:HIS82 2.0 18.9 0.6 NE2 B:HIS80 2.1 19.6 1.0 NE2 B:HIS82 2.2 24.4 0.4 OD1 B:ASN97 2.3 28.2 1.0 CE1 B:HIS82 2.9 25.9 0.6 CD2 B:HIS82 3.0 18.6 0.4 CD2 B:HIS80 3.0 20.2 1.0 CE1 B:HIS80 3.0 18.6 1.0 CD2 B:HIS82 3.1 18.5 0.6 CE1 B:HIS82 3.4 26.9 0.4 CG B:ASN97 3.4 34.4 1.0 ND2 B:ASN97 3.8 31.1 1.0 ND1 B:HIS82 4.1 24.1 0.6 ND1 B:HIS80 4.1 23.8 1.0 CG B:HIS82 4.2 19.9 0.6 CG B:HIS80 4.2 21.7 1.0 CG B:HIS82 4.2 19.4 0.4 ND1 B:HIS82 4.4 27.8 0.4 CB B:GLU77 4.4 17.9 1.0 CG B:GLU77 4.5 17.8 1.0 CB B:ASN97 4.7 22.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)


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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:18.3 occ:1.00 NE2 A:HIS129 2.0 19.3 1.0 ND1 B:HIS129 2.1 15.8 1.0 CL A:CL212 2.2 24.1 1.0 CL B:CL212 2.3 20.8 1.0 CD2 A:HIS129 2.9 18.1 1.0 CE1 A:HIS129 3.0 17.8 1.0 CE1 B:HIS129 3.0 15.6 1.0 CG B:HIS129 3.1 17.6 1.0 CB B:HIS129 3.4 15.4 1.0 CG2 B:VAL136 4.1 15.4 1.0 ND1 A:HIS129 4.1 19.0 1.0 CG A:HIS129 4.1 16.3 1.0 NE2 B:HIS129 4.2 13.1 1.0 CD2 B:HIS129 4.2 15.7 1.0 O A:HOH376 4.3 18.6 0.6 CA B:HIS129 4.6 16.0 1.0 CG2 A:VAL136 4.9 24.3 1.0 CG B:PRO131 5.0 28.7 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample)


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 A Secretary Abundant Heat Soluble (Sahs) Protein From Ramazzottius Varieornatus (From Dimer Sample) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:56.2 occ:1.00 NE2 B:HIS68 2.2 38.7 1.0 O B:HOH312 2.4 54.9 1.0 CD2 B:HIS68 2.9 45.1 1.0 CE1 B:HIS68 3.2 51.6 1.0 O B:HOH377 3.9 49.0 1.0 CG B:HIS68 4.1 47.9 1.0 ND1 B:HIS68 4.2 42.0 1.0 NZ B:LYS90 4.3 47.7 1.0 O B:GLY65 4.3 38.9 1.0 CE B:LYS90 4.5 55.7 1.0 CA B:GLY66 4.6 33.6 1.0 O B:GLU62 4.6 60.4 1.0

Y.Fukuda, Y.Miura, E.Mizohata, T.Inoue. Structural Insights Into A Secretory Abundant Heat-Soluble Protein From An Anhydrobiotic Tardigrade, Ramazzottius Varieornatus Febs Lett. V. 591 2458 2017.
ISSN: ISSN 1873-3468
PubMed: 28703282
DOI: 10.1002/1873-3468.12752