Cobalt in PDB 3pjl: The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5

The structure of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5, PDB code: 3pjl was solved by C.A.Brautigam, R.K.Deka, D.R.Tomchick, M.Machius, M.V.Norgard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.88 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.406, 65.984, 152.374, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.1

The binding sites of Cobalt atom in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 (pdb code 3pjl). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5, PDB code: 3pjl:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co186 b:19.6 occ:1.00 NE2 B:HIS155 2.1 16.6 1.0 NE2 A:HIS124 2.1 16.1 1.0 NE2 A:HIS70 2.2 14.9 1.0 OE2 A:GLU72 2.3 21.1 1.0 OE1 A:GLU72 2.4 23.9 1.0 SD A:MET117 2.6 17.4 1.0 CD A:GLU72 2.7 21.3 1.0 CE1 B:HIS155 2.9 18.5 1.0 CE1 A:HIS124 3.0 20.0 1.0 CD2 A:HIS70 3.0 17.0 1.0 CD2 A:HIS124 3.2 18.9 1.0 CE1 A:HIS70 3.2 17.6 1.0 CD2 B:HIS155 3.3 19.5 1.0 CG A:MET117 3.5 17.0 1.0 CE A:MET117 3.7 19.7 1.0 ND1 B:HIS155 4.1 20.4 1.0 CG A:GLU72 4.1 25.2 1.0 ND1 A:HIS124 4.2 19.2 1.0 CG A:HIS70 4.2 15.3 1.0 CG A:HIS124 4.3 16.2 1.0 ND1 A:HIS70 4.3 15.7 1.0 CG B:HIS155 4.3 21.5 1.0 O A:HOH270 4.5 37.3 1.0 CA A:GLY126 4.6 17.6 1.0 CB A:MET117 4.9 15.3 1.0 CB A:GLU72 4.9 18.6 1.0

Cobalt binding site 2 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co187 b:34.4 occ:0.47 NE2 B:HIS149 2.0 61.0 1.0 O A:HOH304 2.0 38.4 1.0 O A:HOH305 2.1 50.5 1.0 NE2 A:HIS55 2.4 33.0 1.0 CE1 B:HIS149 2.9 66.1 1.0 CD2 B:HIS149 3.0 62.0 1.0 CE1 A:HIS55 3.4 39.2 1.0 CD2 A:HIS55 3.4 32.2 1.0 O B:HOH198 4.0 22.4 1.0 ND1 B:HIS149 4.0 66.8 1.0 CG B:HIS149 4.1 61.1 1.0 O A:HOH221 4.3 22.8 1.0 ND1 A:HIS55 4.5 37.5 1.0 CG A:HIS55 4.5 30.7 1.0 O B:HOH265 4.6 36.4 1.0 O B:HOH249 4.8 40.0 1.0

Cobalt binding site 3 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co186 b:24.8 occ:0.56 NE2 B:HIS124 1.9 15.2 0.4 NE2 A:HIS155 2.2 19.6 1.0 NE2 B:HIS70 2.2 21.6 1.0 CD2 B:HIS124 2.9 20.9 0.4 CE1 B:HIS124 2.9 20.1 0.4 CE1 A:HIS155 2.9 20.8 1.0 SD B:MET117 3.0 21.5 1.0 CD2 B:HIS70 3.2 27.0 1.0 CE1 B:HIS70 3.2 22.6 1.0 OE1 B:GLU72 3.3 51.7 1.0 CD2 A:HIS155 3.4 21.3 1.0 CG B:MET117 3.6 19.5 1.0 ND1 B:HIS124 4.0 24.0 0.4 CG B:HIS124 4.0 22.0 0.4 ND1 A:HIS155 4.1 21.8 1.0 CA B:GLY126 4.2 25.3 1.0 ND1 B:HIS70 4.3 18.9 1.0 CG B:HIS70 4.3 22.3 1.0 CG A:HIS155 4.4 18.8 1.0 CE B:MET117 4.4 24.8 1.0 O B:HOH271 4.5 45.4 1.0 CD B:GLU72 4.5 47.6 1.0 CB B:GLU72 4.5 33.7 1.0 CB B:HIS124 4.5 24.1 0.6 N B:GLY126 4.8 21.9 1.0 ND1 B:HIS124 4.9 31.4 0.6 C B:GLY126 4.9 22.1 1.0 CB B:MET117 5.0 18.3 1.0 CG B:HIS124 5.0 26.5 0.6

Cobalt binding site 4 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co187 b:69.0 occ:0.35 OD2 B:ASP38 2.3 45.0 1.0 OD1 B:ASP38 2.5 56.0 1.0 ND1 B:HIS43 2.6 39.3 0.7 CG B:ASP38 2.7 50.4 1.0 CD2 B:HIS43 2.8 39.8 0.3 CE1 B:HIS43 3.4 41.7 0.7 CG B:HIS43 3.5 36.8 0.7 CG B:HIS43 3.5 37.0 0.3 CB B:HIS43 3.7 33.6 0.3 CB B:HIS43 3.8 33.8 0.7 CB B:ASN78 3.8 36.5 1.0 NE2 B:HIS43 3.9 41.1 0.3 CB B:ASP38 4.2 43.5 1.0 NE2 B:HIS43 4.4 39.6 0.7 CD2 B:HIS43 4.5 39.0 0.7 CA B:HIS43 4.6 28.7 0.7 ND2 B:ASN78 4.6 33.5 1.0 CA B:HIS43 4.6 29.3 0.3 ND1 B:HIS43 4.7 38.1 0.3 CG B:ASN78 4.8 36.6 1.0 CE1 B:HIS43 4.9 39.4 0.3 CA B:ASN78 4.9 33.3 1.0

Cobalt binding site 5 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co188 b:28.8 occ:0.38 O A:HOH192 2.2 55.6 1.0 O B:HOH236 2.2 49.6 1.0 NE2 B:HIS55 2.7 33.5 1.0 CD2 B:HIS55 3.4 33.3 1.0 CE1 B:HIS55 3.8 35.2 1.0 O A:HOH202 4.0 20.8 1.0 O B:HOH200 4.2 23.6 1.0 O A:HOH239 4.2 27.9 1.0 ND1 A:HIS149 4.3 65.5 1.0 CE1 A:HIS149 4.6 66.3 1.0 CG B:HIS55 4.6 29.8 1.0 CG B:PRO56 4.7 34.6 1.0 O A:HOH283 4.7 41.3 1.0 ND1 B:HIS55 4.8 36.3 1.0 CD B:PRO56 4.9 30.5 1.0 O A:HOH282 4.9 31.2 1.0

Cobalt binding site 6 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co189 b:73.4 occ:0.44 NE2 B:HIS43 2.4 39.6 0.7 OD2 B:ASP36 2.4 40.1 1.0 CE1 B:HIS43 2.5 39.4 0.3 NE2 B:HIS43 2.6 41.1 0.3 CE1 B:HIS43 3.1 41.7 0.7 CD2 B:HIS43 3.4 39.0 0.7 CG B:ASP36 3.4 40.9 1.0 ND1 B:HIS43 3.8 38.1 0.3 CB B:ASP36 3.8 37.6 1.0 CD2 B:HIS43 3.9 39.8 0.3 ND1 B:HIS43 4.3 39.3 0.7 O B:HOH215 4.4 51.0 1.0 CG B:HIS43 4.5 37.0 0.3 CG B:HIS43 4.5 36.8 0.7 OD1 B:ASP36 4.6 40.8 1.0

Cobalt binding site 7 out of 7 in the The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of The Crystal Structure of TP34 Bound to Co (II) Ion at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co190 b:53.0 occ:0.46 OD1 B:ASP74 2.3 60.0 1.0 NE2 B:HIS124 2.5 33.2 0.6 O B:HOH257 2.5 41.2 1.0 CG B:ASP74 2.9 53.2 1.0 CD2 B:HIS124 3.1 30.6 0.6 OD2 B:ASP74 3.3 61.4 1.0 CE1 B:HIS124 3.7 31.1 0.6 OD2 B:ASP121 4.0 58.5 1.0 OE2 B:GLU72 4.0 50.6 1.0 CB B:ASP74 4.0 38.1 1.0 O B:HOH270 4.3 56.1 1.0 CG B:HIS124 4.4 26.5 0.6 ND1 B:HIS124 4.6 31.4 0.6 O B:HOH224 4.7 29.6 1.0 CG B:ASP121 4.7 50.6 1.0 CD B:GLU72 5.0 47.6 1.0

C.A.Brautigam, R.K.Deka, Z.Ouyang, M.Goldberg, M.Machius, G.Knutsen, D.R.Tomchick, M.V.Norgard. Characterization of the TP34 Lipoprotein From Treponema Pallidum Suggests A Role in Transition Metal Homeostasis To Be Published.