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

Protein crystallography data

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

Other elements in 5xna:

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

Zinc Binding Sites:

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 5xna

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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 5xna

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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 5xna

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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 5xna

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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 5xna

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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 5xna

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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

Reference:

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
Page generated: Mon Oct 28 15:11:23 2024

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