Zinc in PDB 2zwr: Crystal Structure of TTHA1623 From Thermus Thermophilus HB8

The structure of Crystal Structure of TTHA1623 From Thermus Thermophilus HB8, PDB code: 2zwr was solved by A.Yamamura, A.Okada, Y.Kameda, J.Ohtsuka, N.Nakagawa, A.Ebihara, S.Yokoyama, S.Kuramitsu, K.Nagata, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.46 / 2.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	79.136, 114.122, 114.711, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8 (pdb code 2zwr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8, PDB code: 2zwr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


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 TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:12.0 occ:1.00 O A:HOH216 1.9 14.0 1.0 NE2 A:HIS184 2.0 8.2 1.0 NE2 A:HIS59 2.1 7.8 1.0 OD2 A:ASP144 2.1 9.8 1.0 OD2 A:ASP58 2.3 8.4 1.0 CD2 A:HIS59 2.9 7.6 1.0 CE1 A:HIS184 2.9 9.6 1.0 CD2 A:HIS184 3.0 9.0 1.0 CG A:ASP144 3.1 11.0 1.0 CG A:ASP58 3.3 9.3 1.0 CE1 A:HIS59 3.3 7.0 1.0 ZN A:ZN209 3.3 11.1 1.0 OD1 A:ASP144 3.3 8.9 1.0 OD1 A:ASP58 3.5 9.9 1.0 ND1 A:HIS184 4.0 9.5 1.0 CG A:HIS59 4.1 7.6 1.0 CG A:HIS184 4.1 10.1 1.0 NE2 A:HIS54 4.2 7.4 1.0 ND1 A:HIS59 4.2 7.1 1.0 CE1 A:HIS54 4.3 9.0 1.0 CB A:ASP144 4.5 10.6 1.0 CB A:ASP58 4.6 8.6 1.0 CG A:GLU13 4.7 12.2 1.0 NE2 A:HIS125 4.8 12.4 1.0 O A:GLY183 4.9 10.3 1.0

Zinc binding site 2 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


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 TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:11.1 occ:1.00 O A:HOH216 2.1 14.0 1.0 NE2 A:HIS125 2.1 12.4 1.0 ND1 A:HIS56 2.2 9.0 1.0 NE2 A:HIS54 2.2 7.4 1.0 OD2 A:ASP144 2.5 9.8 1.0 CD2 A:HIS125 2.9 12.0 1.0 CD2 A:HIS54 3.1 8.6 1.0 CE1 A:HIS56 3.1 7.7 1.0 CG A:HIS56 3.2 9.0 1.0 CE1 A:HIS54 3.2 9.0 1.0 CE1 A:HIS125 3.2 13.3 1.0 ZN A:ZN208 3.3 12.0 1.0 CB A:HIS56 3.5 8.4 1.0 CG A:ASP144 3.5 11.0 1.0 CB A:ASP144 4.0 10.6 1.0 NE2 A:HIS59 4.0 7.8 1.0 CD2 A:HIS59 4.1 7.6 1.0 CG A:HIS125 4.1 10.9 1.0 NE2 A:HIS56 4.2 9.8 1.0 ND1 A:HIS125 4.2 12.0 1.0 CG A:HIS54 4.3 8.5 1.0 ND1 A:HIS54 4.3 7.9 1.0 CD2 A:HIS56 4.3 6.7 1.0 OD1 A:ASP58 4.4 9.9 1.0 CD1 A:LEU156 4.5 28.3 1.0 OD1 A:ASP144 4.6 8.9 1.0 OD2 A:ASP58 4.8 8.4 1.0 CA A:HIS56 4.9 9.0 1.0

Zinc binding site 3 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


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 TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:19.9 occ:1.00 OD2 A:ASP71 2.0 15.6 1.0 CG A:ASP71 2.8 14.6 1.0 OD1 A:ASP71 3.0 16.7 1.0 O A:GLU68 3.9 15.0 1.0 CB A:ASP71 4.3 12.3 1.0 CA A:ASP71 4.8 12.4 1.0 N A:ASP71 4.8 11.3 1.0 O A:VAL67 4.8 13.9 1.0 C A:GLU68 4.9 14.9 1.0

Zinc binding site 4 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


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 TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn211 b:21.8 occ:1.00 ND1 A:HIS121 2.2 11.5 1.0 OE1 B:GLU109 2.3 13.4 1.0 CG A:HIS121 3.1 11.8 1.0 CE1 A:HIS121 3.2 10.1 1.0 CB A:HIS121 3.4 11.4 1.0 CD B:GLU109 3.4 15.7 1.0 O B:HOH250 3.6 20.1 1.0 OE2 B:GLU109 4.0 12.9 1.0 O A:HIS121 4.1 11.4 1.0 NE2 A:HIS121 4.3 11.5 1.0 CD2 A:HIS121 4.3 12.4 1.0 CA A:HIS121 4.6 11.5 1.0 C A:HIS121 4.6 11.7 1.0 CG B:GLU109 4.6 14.7 1.0 CB A:GLU110 4.7 15.1 1.0 OE1 A:GLU110 4.7 18.4 1.0 CB B:GLU109 4.7 14.6 1.0

Zinc binding site 5 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


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 TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn212 b:36.0 occ:1.00 O A:HOH244 2.1 18.9 1.0 OD1 A:ASP31 2.1 17.4 1.0 CG A:ASP31 2.9 13.8 1.0 OD2 A:ASP31 3.0 18.7 1.0 O A:ALA97 4.1 13.9 1.0 N A:GLU32 4.3 12.8 1.0 CB A:ASP31 4.4 12.6 1.0 O A:HOH227 4.4 23.7 1.0 CG2 A:ILE98 4.7 12.7 1.0 CA A:ASP31 4.9 11.8 1.0

Zinc binding site 6 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


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 TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn213 b:69.5 occ:1.00 O A:HOH243 2.3 19.7 1.0 OE1 A:GLU22 2.4 29.3 1.0 OE2 A:GLU22 2.5 29.6 1.0 CD A:GLU22 2.7 27.1 1.0 O A:HOH271 3.7 22.6 1.0 N A:PHE115 4.0 16.0 1.0 CG A:GLU22 4.2 25.1 1.0 CA A:LEU114 4.4 16.1 1.0 N A:GLY116 4.6 17.0 1.0 C A:LEU114 4.6 16.1 1.0 O A:ARG113 4.7 16.5 1.0 CA A:PHE115 4.7 16.4 1.0 N A:LEU114 4.9 16.0 1.0 C A:ARG113 5.0 16.8 1.0

Zinc binding site 7 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn214 b:77.3 occ:1.00 O A:MET1 2.4 27.9 1.0 N A:MET1 2.6 28.7 1.0 CA A:MET1 3.1 28.5 1.0 C A:MET1 3.1 27.6 1.0 CB A:MET1 3.4 28.3 1.0 NE2 A:GLN139 4.1 21.1 1.0 CG A:MET1 4.3 28.8 1.0 N A:ARG2 4.4 26.4 1.0

Zinc binding site 8 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn215 b:65.5 occ:1.00 OD2 A:ASP160 2.1 25.7 1.0 CG A:ASP160 3.2 23.8 1.0 OD1 A:ASP160 3.7 25.6 1.0 CB A:ASP160 4.5 21.8 1.0 O A:HOH266 4.5 18.1 1.0 CB A:ALA163 4.9 17.1 1.0

Zinc binding site 9 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn208 b:11.4 occ:1.00 O B:HOH214 1.9 8.4 1.0 OD2 B:ASP144 2.1 7.2 1.0 NE2 B:HIS184 2.1 8.9 1.0 NE2 B:HIS59 2.2 8.7 1.0 OD2 B:ASP58 2.3 11.8 1.0 CD2 B:HIS59 2.9 9.3 1.0 CD2 B:HIS184 3.0 10.5 1.0 CG B:ASP144 3.0 9.2 1.0 CE1 B:HIS184 3.1 10.2 1.0 ZN B:ZN209 3.2 13.2 1.0 OD1 B:ASP144 3.3 8.2 1.0 CE1 B:HIS59 3.3 10.9 1.0 CG B:ASP58 3.4 11.4 1.0 OD1 B:ASP58 3.8 11.8 1.0 NE2 B:HIS54 4.1 9.1 1.0 CG B:HIS184 4.1 11.7 1.0 CG B:HIS59 4.2 9.5 1.0 ND1 B:HIS184 4.2 9.9 1.0 CE1 B:HIS54 4.2 10.0 1.0 ND1 B:HIS59 4.3 10.0 1.0 CB B:ASP144 4.4 10.3 1.0 CB B:ASP58 4.6 10.8 1.0 NE2 B:HIS125 4.7 9.3 1.0 CG B:GLU13 4.8 14.0 1.0 O B:GLY183 4.8 12.0 1.0

Zinc binding site 10 out of 14 in the Crystal Structure of TTHA1623 From Thermus Thermophilus HB8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of TTHA1623 From Thermus Thermophilus HB8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn209 b:13.2 occ:1.00 NE2 B:HIS125 2.0 9.3 1.0 O B:HOH214 2.1 8.4 1.0 NE2 B:HIS54 2.2 9.1 1.0 ND1 B:HIS56 2.3 13.1 1.0 OD2 B:ASP144 2.4 7.2 1.0 CD2 B:HIS125 3.0 9.4 1.0 CE1 B:HIS125 3.1 9.0 1.0 CD2 B:HIS54 3.1 9.7 1.0 ZN B:ZN208 3.2 11.4 1.0 CE1 B:HIS54 3.2 10.0 1.0 CG B:HIS56 3.3 12.6 1.0 CE1 B:HIS56 3.3 14.6 1.0 CG B:ASP144 3.4 9.2 1.0 CB B:HIS56 3.5 11.8 1.0 CB B:ASP144 3.9 10.3 1.0 NE2 B:HIS59 4.0 8.7 1.0 CD2 B:HIS59 4.1 9.3 1.0 CG B:HIS125 4.2 10.5 1.0 ND1 B:HIS125 4.2 8.5 1.0 CG B:HIS54 4.3 9.8 1.0 ND1 B:HIS54 4.3 9.3 1.0 OD1 B:ASP58 4.4 11.8 1.0 CD2 B:HIS56 4.4 13.3 1.0 NE2 B:HIS56 4.4 14.5 1.0 OD1 B:ASP144 4.5 8.2 1.0 OD2 B:ASP58 4.5 11.8 1.0 CG B:ASP58 4.9 11.4 1.0 CA B:HIS56 4.9 11.8 1.0 CE1 B:HIS59 4.9 10.9 1.0

A.Yamamura, A.Okada, Y.Kameda, J.Ohtsuka, N.Nakagawa, A.Ebihara, K.Nagata, M.Tanokura. Structure of TTHA1623, A Novel Metallo-Beta-Lactamase Superfamily Protein From Thermus Thermophilus HB8 Acta Crystallogr.,Sect.F V. 65 455 2009.
ISSN: ESSN 1744-3091
PubMed: 19407375
DOI: 10.1107/S174430910901361X