Zinc in PDB 2o6e: Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals

The structure of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals, PDB code: 2o6e was solved by M.Machius, C.A.Brautigam, R.K.Deka, D.R.Tomchick, S.B.Lumpkins, M.V.Norgard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.60 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.451, 65.921, 151.744, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.3

The structure of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals (pdb code 2o6e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals, PDB code: 2o6e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.9 occ:1.00 NE2 B:HIS155 2.0 9.4 1.0 OE2 A:GLU72 2.1 20.9 1.0 NE2 A:HIS70 2.1 18.0 1.0 NE2 A:HIS124 2.1 19.3 1.0 CE1 B:HIS155 2.7 10.6 1.0 CE1 A:HIS124 3.0 19.2 1.0 CD A:GLU72 3.0 20.9 1.0 CD2 A:HIS70 3.0 14.9 1.0 SD A:MET117 3.0 19.4 1.0 CE1 A:HIS70 3.1 16.2 1.0 CD2 B:HIS155 3.2 11.0 1.0 CD2 A:HIS124 3.2 18.9 1.0 CG A:GLU72 3.3 18.7 1.0 CG A:MET117 3.8 19.4 1.0 ND1 B:HIS155 4.0 14.4 1.0 OE1 A:GLU72 4.1 25.1 1.0 ND1 A:HIS124 4.1 19.5 1.0 CG A:HIS70 4.2 19.4 1.0 ND1 A:HIS70 4.2 16.6 1.0 CG B:HIS155 4.2 12.7 1.0 CG A:HIS124 4.3 18.2 1.0 CE A:MET117 4.5 17.6 1.0 CB A:ALA119 4.7 20.7 1.0 CB A:GLU72 4.7 19.9 1.0 CZ A:PHE49 4.8 17.9 1.0 CA A:GLY126 4.9 18.1 1.0 CG2 A:VAL52 4.9 18.6 1.0

Zinc binding site 2 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:0.0 occ:1.00 OD1 A:ASP74 2.2 22.8 0.5 ND1 A:HIS76 2.5 34.2 1.0 CE1 A:HIS76 2.7 37.2 1.0 CG A:ASP74 2.9 23.4 0.5 OD2 A:ASP74 3.0 26.7 0.5 O A:HOH596 3.2 35.1 1.0 O A:HOH535 3.5 25.8 1.0 CG A:HIS76 3.8 29.0 1.0 NE2 A:HIS76 4.0 35.3 1.0 CB A:ASP74 4.2 23.7 0.5 CB A:ASP74 4.4 22.5 0.5 CD2 A:HIS76 4.6 32.2 1.0 CB A:HIS76 4.6 25.4 1.0 O A:HOH610 4.6 32.9 1.0 C A:ASP74 4.7 22.6 0.5 CA A:ASP74 4.7 23.2 0.5 O A:ILE75 4.7 23.6 1.0 N A:ILE75 4.7 21.8 1.0 CA A:ASP74 4.8 22.5 0.5 C A:ASP74 4.9 22.2 0.5 C A:ILE75 4.9 23.2 1.0

Zinc binding site 3 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:0.2 occ:1.00 OD2 A:ASP121 2.7 38.2 1.0 OE2 A:GLU30 2.7 37.4 1.0 O A:HOH572 2.7 22.5 1.0 OE1 A:GLU30 3.0 37.0 1.0 CD A:GLU30 3.2 30.8 1.0 OE1 A:GLU72 3.2 25.1 1.0 O A:HOH544 3.3 40.3 1.0 OD1 A:ASP74 3.4 31.2 0.5 CG A:ASP121 3.6 32.8 1.0 OD2 A:ASP74 3.7 29.6 0.5 OD1 A:ASP121 3.8 33.8 1.0 CG A:ASP74 3.8 26.7 0.5 CG2 A:VAL47 4.3 24.0 1.0 CD A:GLU72 4.5 20.9 1.0 CG A:GLU30 4.6 29.1 1.0 O A:HOH596 4.9 35.1 1.0 CB A:ASP121 5.0 29.4 1.0

Zinc binding site 4 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:0.9 occ:1.00 NE2 A:HIS55 2.4 27.2 1.0 NE2 B:HIS149 2.7 43.1 1.0 CE1 B:HIS149 3.2 43.8 1.0 CD2 A:HIS55 3.3 27.1 1.0 CE1 A:HIS55 3.4 27.9 1.0 CD2 B:HIS149 4.0 42.0 1.0 O B:HOH514 4.3 24.5 1.0 ND1 A:HIS55 4.5 26.9 1.0 CG A:HIS55 4.5 25.6 1.0 ND1 B:HIS149 4.5 43.1 1.0 CG B:HIS149 4.9 39.5 1.0

Zinc binding site 5 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:0.1 occ:1.00 ND1 A:HIS104 2.3 23.8 1.0 CG A:HIS104 3.1 21.1 1.0 CB A:HIS104 3.3 21.6 1.0 CE1 A:HIS104 3.4 19.2 1.0 O A:HOH586 3.7 35.2 1.0 CD2 A:HIS104 4.3 21.0 1.0 NE2 A:HIS104 4.4 20.0 1.0 CA A:HIS104 4.7 21.1 1.0 CB A:THR137 4.7 18.3 1.0 OD1 A:ASP177 4.9 35.5 1.0 OG1 A:THR137 4.9 18.2 1.0 CG2 A:THR137 5.0 15.9 1.0

Zinc binding site 6 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:0.2 occ:1.00 O A:HOH599 3.2 45.2 1.0 CB A:ALA60 4.0 33.2 1.0 O A:ALA60 4.2 31.7 1.0 CA A:ALA60 4.4 33.3 1.0 C A:ALA60 4.6 31.6 1.0

Zinc binding site 7 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:30.3 occ:1.00 OE2 B:GLU72 2.0 22.1 1.0 NE2 A:HIS155 2.1 12.3 1.0 NE2 B:HIS124 2.1 19.4 1.0 NE2 B:HIS70 2.2 17.2 1.0 CE1 A:HIS155 2.8 10.6 1.0 CD B:GLU72 2.9 22.8 1.0 CD2 B:HIS70 2.9 17.0 1.0 CE1 B:HIS124 3.0 21.5 1.0 SD B:MET117 3.1 19.6 1.0 CD2 B:HIS124 3.1 19.1 1.0 CD2 A:HIS155 3.3 14.8 1.0 CE1 B:HIS70 3.3 16.9 1.0 CG B:GLU72 3.3 22.0 1.0 CG B:MET117 3.8 19.2 1.0 OE1 B:GLU72 4.0 19.6 1.0 ND1 A:HIS155 4.0 12.4 1.0 CG B:HIS70 4.1 16.6 1.0 ND1 B:HIS124 4.1 19.7 1.0 CG B:HIS124 4.2 20.0 1.0 ND1 B:HIS70 4.2 16.4 1.0 CG A:HIS155 4.3 13.0 1.0 CE B:MET117 4.5 19.6 1.0 CB B:GLU72 4.6 19.7 1.0 CA B:GLY126 4.7 18.8 1.0 CZ B:PHE49 4.8 20.2 1.0 CB B:ALA119 4.8 18.2 1.0 CG2 B:VAL52 4.9 17.8 1.0

Zinc binding site 8 out of 8 in the Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Native RTP34 From Treponema Pallidum From Zinc-Soaked Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:88.3 occ:1.00 NE2 B:HIS55 2.2 22.1 1.0 CE1 B:HIS55 3.0 24.8 1.0 NE2 A:HIS149 3.1 40.1 1.0 CD2 B:HIS55 3.3 23.0 1.0 CD2 A:HIS149 3.4 38.2 1.0 ND1 B:HIS55 4.2 23.3 1.0 CE1 A:HIS149 4.3 39.9 1.0 CG B:HIS55 4.3 23.0 1.0 CG B:PRO56 4.6 22.8 1.0 CG A:HIS149 4.8 35.2 1.0 O B:HOH504 5.0 24.9 1.0

R.K.Deka, C.A.Brautigam, F.L.Tomson, S.B.Lumpkins, D.R.Tomchick, M.Machius, M.V.Norgard. Crystal Structure of the TP34 (TP0971) Lipoprotein of Treponema Pallidum: Implications of Its Metal-Bound State and Affinity For Human Lactoferrin. J.Biol.Chem. V. 282 5944 2007.
ISSN: ISSN 0021-9258
PubMed: 17192261
DOI: 10.1074/JBC.M610215200