Zinc in PDB 3ayv: TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2

The structure of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2, PDB code: 3ayv was solved by S.Nakane, T.Wakamatsu, K.Fukui, N.Nakagawa, R.Masui, S.Kuramitsu, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.085, 93.375, 87.379, 90.00, 95.86, 90.00
R / Rfree (%)	17.2 / 20.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 (pdb code 3ayv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2, PDB code: 3ayv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn255 b:67.7 occ:1.00 OE1 A:GLU136 1.9 18.4 1.0 O A:HOH547 2.1 27.1 1.0 NE2 A:HIS55 2.3 17.5 1.0 NE2 A:HIS96 2.4 18.4 1.0 O A:HOH623 2.5 30.8 1.0 CD A:GLU136 2.6 19.0 1.0 OE2 A:GLU136 2.7 24.8 1.0 CD2 A:HIS55 3.2 17.5 1.0 CD2 A:HIS96 3.3 17.7 1.0 CE1 A:HIS55 3.3 16.2 1.0 CE1 A:HIS96 3.4 17.2 1.0 ZN A:ZN256 3.4 71.8 1.0 CE1 A:HIS187 4.0 18.0 1.0 ND1 A:HIS187 4.0 15.7 1.0 CG A:GLU136 4.1 14.8 1.0 O A:HOH560 4.1 20.8 1.0 CE1 A:HIS165 4.2 14.7 1.0 CG A:HIS55 4.4 13.3 1.0 ND1 A:HIS55 4.4 15.6 1.0 CG A:HIS96 4.5 14.0 1.0 ND1 A:HIS96 4.5 16.5 1.0 CB A:GLU136 4.6 12.3 1.0 OE1 A:GLU223 4.6 30.1 1.0 OE2 A:GLU223 4.7 31.0 1.0 CG1 A:VAL94 4.9 14.0 1.0

Zinc binding site 2 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn256 b:71.8 occ:1.00 OE2 A:GLU136 2.1 24.8 1.0 OD2 A:ASP162 2.1 16.6 1.0 ND1 A:HIS187 2.4 15.7 1.0 O A:HOH560 2.4 20.8 1.0 OE2 A:GLU223 2.4 31.0 1.0 O A:HOH547 2.5 27.1 1.0 CD A:GLU136 3.1 19.0 1.0 CG A:ASP162 3.1 14.9 1.0 CG A:HIS187 3.3 15.6 1.0 CB A:HIS187 3.4 15.7 1.0 CE1 A:HIS165 3.4 14.7 1.0 ZN A:ZN255 3.4 67.7 1.0 CD A:GLU223 3.5 28.9 1.0 CE1 A:HIS187 3.5 18.0 1.0 CB A:ASP162 3.5 13.3 1.0 OE1 A:GLU136 3.6 18.4 1.0 OE1 A:GLU223 3.9 30.1 1.0 NE2 A:HIS165 4.0 12.0 1.0 ND1 A:HIS165 4.0 11.4 1.0 CG A:GLU136 4.1 14.8 1.0 OD1 A:ASP162 4.2 14.1 1.0 ZN A:ZN257 4.3 62.8 1.0 O A:HOH528 4.3 15.4 1.0 O A:HOH623 4.3 30.8 1.0 CD2 A:HIS187 4.5 15.7 1.0 NE2 A:HIS187 4.5 17.1 1.0 CG A:GLU223 4.6 22.9 1.0 CA A:ASP162 4.8 12.7 1.0 CD2 A:HIS165 4.8 11.5 1.0 CA A:HIS187 4.9 15.6 1.0 CG A:HIS165 4.9 10.4 1.0

Zinc binding site 3 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn257 b:62.8 occ:1.00 OD2 A:ASP196 2.1 12.9 1.0 O A:HOH560 2.2 20.8 1.0 O A:HOH582 2.2 22.2 1.0 NE2 A:HIS165 2.3 12.0 1.0 NE2 A:HIS198 2.4 19.2 1.0 O A:HOH528 2.4 15.4 1.0 CG A:ASP196 3.0 15.0 1.0 CD2 A:HIS165 3.1 11.5 1.0 CE1 A:HIS198 3.2 21.9 1.0 CE1 A:HIS165 3.2 14.7 1.0 OD1 A:ASP196 3.3 14.6 1.0 CD2 A:HIS198 3.4 19.8 1.0 OD2 A:ASP162 4.0 16.6 1.0 ZN A:ZN256 4.3 71.8 1.0 CG A:HIS165 4.3 10.4 1.0 O A:HOH623 4.3 30.8 1.0 ND1 A:HIS165 4.3 11.4 1.0 ND1 A:HIS198 4.4 21.0 1.0 CB A:ASP196 4.4 14.2 1.0 OE2 A:GLU223 4.5 31.0 1.0 CG A:HIS198 4.5 17.3 1.0 ND2 A:ASN189 4.7 11.5 1.0 CG A:ASP162 4.7 14.9 1.0 O A:HOH547 4.7 27.1 1.0 OD1 A:ASP162 4.8 14.1 1.0

Zinc binding site 4 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn255 b:80.3 occ:1.00 NE2 B:HIS96 2.2 17.6 1.0 OE1 B:GLU136 2.2 21.2 1.0 O B:HOH620 2.2 26.8 1.0 NE2 B:HIS55 2.3 20.8 1.0 O B:HOH685 2.3 31.8 1.0 OE2 B:GLU136 2.6 23.1 1.0 CD B:GLU136 2.7 20.8 1.0 CE1 B:HIS96 3.2 18.8 1.0 CD2 B:HIS96 3.2 19.7 1.0 CD2 B:HIS55 3.3 20.1 1.0 CE1 B:HIS55 3.3 20.2 1.0 ZN B:ZN256 3.5 65.9 1.0 O B:HOH550 4.1 21.6 1.0 CG B:GLU136 4.2 17.7 1.0 CE1 B:HIS187 4.2 18.4 1.0 CE1 B:HIS165 4.2 16.2 1.0 ND1 B:HIS187 4.3 18.6 1.0 ND1 B:HIS96 4.3 17.1 1.0 CG B:HIS96 4.4 17.3 1.0 ND1 B:HIS55 4.4 17.4 1.0 CG B:HIS55 4.4 16.2 1.0 CB B:GLU136 4.7 15.7 1.0 OE2 B:GLU223 4.8 31.6 1.0 OE1 B:GLU223 4.9 29.3 1.0

Zinc binding site 5 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn256 b:65.9 occ:1.00 OE2 B:GLU136 2.2 23.1 1.0 OD2 B:ASP162 2.2 21.4 1.0 OE2 B:GLU223 2.4 31.6 1.0 O B:HOH620 2.5 26.8 1.0 O B:HOH550 2.5 21.6 1.0 ND1 B:HIS187 2.5 18.6 1.0 CD B:GLU136 3.1 20.8 1.0 CG B:ASP162 3.2 17.3 1.0 CG B:HIS187 3.3 19.4 1.0 CE1 B:HIS165 3.4 16.2 1.0 CD B:GLU223 3.4 30.8 1.0 CB B:HIS187 3.5 17.1 1.0 ZN B:ZN255 3.5 80.3 1.0 CE1 B:HIS187 3.5 18.4 1.0 CB B:ASP162 3.6 15.9 1.0 OE1 B:GLU136 3.7 21.2 1.0 OE1 B:GLU223 3.9 29.3 1.0 ND1 B:HIS165 4.0 15.6 1.0 O B:HOH685 4.0 31.8 1.0 NE2 B:HIS165 4.0 15.6 1.0 CG B:GLU136 4.1 17.7 1.0 ZN B:ZN257 4.2 58.6 1.0 O B:HOH525 4.3 16.9 1.0 OD1 B:ASP162 4.3 18.6 1.0 CG B:GLU223 4.5 24.9 1.0 CD2 B:HIS187 4.5 14.8 1.0 NE2 B:HIS187 4.6 18.7 1.0 CA B:ASP162 4.8 15.4 1.0 CG B:HIS165 4.9 13.9 1.0 CD2 B:HIS165 4.9 14.9 1.0 CA B:HIS187 5.0 18.1 1.0

Zinc binding site 6 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn257 b:58.6 occ:1.00 O B:HOH550 2.1 21.6 1.0 OD2 B:ASP196 2.2 18.1 1.0 O B:HOH554 2.3 27.5 1.0 NE2 B:HIS165 2.3 15.6 1.0 O B:HOH525 2.4 16.9 1.0 NE2 B:HIS198 2.4 21.1 1.0 CG B:ASP196 3.2 17.4 1.0 CE1 B:HIS165 3.2 16.2 1.0 CE1 B:HIS198 3.2 23.5 1.0 CD2 B:HIS165 3.2 14.9 1.0 OD1 B:ASP196 3.4 17.4 1.0 CD2 B:HIS198 3.4 22.8 1.0 OD2 B:ASP162 3.9 21.4 1.0 O B:HOH668 4.0 31.2 1.0 O B:HOH685 4.1 31.8 1.0 ZN B:ZN256 4.2 65.9 1.0 OE2 B:GLU223 4.2 31.6 1.0 ND1 B:HIS165 4.3 15.6 1.0 CG B:HIS165 4.3 13.9 1.0 ND1 B:HIS198 4.4 22.6 1.0 CG B:HIS198 4.5 19.5 1.0 CB B:ASP196 4.5 17.4 1.0 O B:HOH620 4.6 26.8 1.0 OD1 B:ASN189 4.6 19.0 1.0 CG B:ASP162 4.6 17.3 1.0 OD1 B:ASP162 4.7 18.6 1.0

Zinc binding site 7 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn255 b:72.0 occ:1.00 OE1 C:GLU136 2.1 24.8 1.0 O C:HOH596 2.2 34.6 1.0 NE2 C:HIS55 2.3 19.1 1.0 NE2 C:HIS96 2.3 20.1 1.0 O C:HOH702 2.4 33.9 1.0 CD C:GLU136 2.8 23.1 1.0 OE2 C:GLU136 2.9 26.6 1.0 CD2 C:HIS55 3.2 19.1 1.0 CE1 C:HIS96 3.3 21.4 1.0 CD2 C:HIS96 3.3 19.4 1.0 CE1 C:HIS55 3.3 19.0 1.0 ZN C:ZN256 3.5 81.3 1.0 O C:HOH539 4.1 19.8 1.0 CE1 C:HIS187 4.1 19.4 1.0 ND1 C:HIS187 4.2 17.5 1.0 CG C:GLU136 4.3 18.9 1.0 CG C:HIS55 4.3 15.5 1.0 CE1 C:HIS165 4.4 14.6 1.0 ND1 C:HIS55 4.4 16.9 1.0 ND1 C:HIS96 4.4 18.7 1.0 CG C:HIS96 4.5 16.4 1.0 OE1 C:GLU223 4.5 29.6 1.0 OE2 C:GLU223 4.7 31.5 1.0 CB C:GLU136 4.8 15.1 1.0

Zinc binding site 8 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn256 b:81.3 occ:1.00 OE2 C:GLU136 2.0 26.6 1.0 OD2 C:ASP162 2.2 18.3 1.0 OE2 C:GLU223 2.4 31.5 1.0 ND1 C:HIS187 2.5 17.5 1.0 O C:HOH539 2.6 19.8 1.0 O C:HOH596 2.6 34.6 1.0 CD C:GLU136 2.9 23.1 1.0 CG C:ASP162 3.2 15.7 1.0 CE1 C:HIS165 3.3 14.6 1.0 CG C:HIS187 3.4 17.3 1.0 CD C:GLU223 3.4 28.3 1.0 CB C:HIS187 3.5 14.7 1.0 CE1 C:HIS187 3.5 19.4 1.0 ZN C:ZN255 3.5 72.0 1.0 OE1 C:GLU136 3.5 24.8 1.0 CB C:ASP162 3.6 13.6 1.0 OE1 C:GLU223 3.8 29.6 1.0 ND1 C:HIS165 3.9 12.9 1.0 CG C:GLU136 3.9 18.9 1.0 NE2 C:HIS165 3.9 14.2 1.0 ZN C:ZN257 4.3 56.6 1.0 OD1 C:ASP162 4.3 15.6 1.0 O C:HOH524 4.4 13.4 1.0 O C:HOH702 4.5 33.9 1.0 CD2 C:HIS187 4.5 14.6 1.0 NE2 C:HIS187 4.6 15.7 1.0 CG C:GLU223 4.6 23.3 1.0 CG C:HIS165 4.8 11.1 1.0 CD2 C:HIS165 4.8 12.0 1.0 CA C:ASP162 4.9 12.9 1.0 CA C:HIS187 5.0 14.9 1.0

Zinc binding site 9 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn257 b:56.6 occ:1.00 O C:HOH539 2.2 19.8 1.0 O C:HOH540 2.2 25.0 1.0 OD2 C:ASP196 2.3 12.7 1.0 NE2 C:HIS165 2.3 14.2 1.0 NE2 C:HIS198 2.3 17.0 1.0 O C:HOH524 2.4 13.4 1.0 CG C:ASP196 3.1 13.2 1.0 CE1 C:HIS198 3.2 18.0 1.0 CD2 C:HIS165 3.2 12.0 1.0 CE1 C:HIS165 3.2 14.6 1.0 OD1 C:ASP196 3.3 16.0 1.0 CD2 C:HIS198 3.3 17.1 1.0 OD2 C:ASP162 3.9 18.3 1.0 ZN C:ZN256 4.3 81.3 1.0 OE2 C:GLU223 4.3 31.5 1.0 ND1 C:HIS198 4.3 16.5 1.0 ND1 C:HIS165 4.3 12.9 1.0 CG C:HIS165 4.3 11.1 1.0 CG C:HIS198 4.4 15.7 1.0 O C:HOH702 4.4 33.9 1.0 CB C:ASP196 4.5 13.4 1.0 ND2 C:ASN189 4.5 10.8 1.0 O C:HOH596 4.7 34.6 1.0 CG C:ASP162 4.7 15.7 1.0 OD1 C:ASP162 4.8 15.6 1.0

Zinc binding site 10 out of 12 in the TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of TTHB071 Protein From Thermus Thermophilus HB8 Soaking with ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn255 b:61.7 occ:1.00 OE1 D:GLU136 2.0 18.2 1.0 O D:HOH573 2.3 22.2 1.0 NE2 D:HIS55 2.3 17.1 1.0 NE2 D:HIS96 2.3 17.9 1.0 O D:HOH619 2.3 28.1 1.0 CD D:GLU136 2.7 16.6 1.0 OE2 D:GLU136 2.7 22.0 1.0 CD2 D:HIS55 3.2 16.4 1.0 CD2 D:HIS96 3.3 16.1 1.0 CE1 D:HIS55 3.3 17.6 1.0 CE1 D:HIS96 3.3 16.4 1.0 ZN D:ZN256 3.4 57.8 1.0 CE1 D:HIS187 4.0 15.3 1.0 CG D:GLU136 4.1 13.8 1.0 ND1 D:HIS187 4.2 14.3 1.0 O D:HOH536 4.3 20.6 1.0 CE1 D:HIS165 4.3 13.8 1.0 CG D:HIS55 4.3 13.0 1.0 ND1 D:HIS55 4.4 13.6 1.0 ND1 D:HIS96 4.4 13.5 1.0 CG D:HIS96 4.4 12.4 1.0 CB D:GLU136 4.6 10.3 1.0 OE1 D:GLU223 4.6 27.7 1.0 OE2 D:GLU223 4.8 30.0 1.0 CG1 D:VAL94 4.9 9.9 1.0

S.Nakane, T.Wakamatsu, R.Masui, S.Kuramitsu, K.Fukui. In Vivo, in Vitro, and X-Ray Crystallographic Analyses Suggest the Involvement of An Uncharacterized Triose-Phosphate Isomerase (Tim) Barrel Protein in Protection Against Oxidative Stress J.Biol.Chem. V. 286 41636 2011.
ISSN: ISSN 0021-9258
PubMed: 21984829
DOI: 10.1074/JBC.M111.293886