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Zinc in PDB 2o6d: Structure of Native RTP34 From Treponema Pallidum

Protein crystallography data

The structure of Structure of Native RTP34 From Treponema Pallidum, PDB code: 2o6d 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) 27.54 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.071, 65.881, 150.605, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 23.5

Other elements in 2o6d:

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

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Native RTP34 From Treponema Pallidum (pdb code 2o6d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Native RTP34 From Treponema Pallidum, PDB code: 2o6d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2o6d

Go back to Zinc Binding Sites List in 2o6d
Zinc binding site 1 out of 2 in the Structure of Native RTP34 From Treponema Pallidum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:71.7
occ:1.00
NE2 A:HIS124 2.0 26.3 0.5
CE1 A:HIS124 2.2 31.6 0.5
NE2 A:HIS70 2.2 24.7 1.0
NE2 B:HIS155 2.2 26.5 1.0
CE1 A:HIS124 2.2 28.1 0.5
SD A:MET117 2.8 31.4 1.0
CE1 B:HIS155 2.8 27.4 1.0
ND1 A:HIS124 3.0 29.1 0.5
CE1 A:HIS70 3.0 26.0 1.0
CD2 A:HIS70 3.1 24.7 1.0
NE2 A:HIS124 3.2 30.3 0.5
CD2 A:HIS124 3.3 26.0 0.5
CG A:MET117 3.5 29.0 1.0
CD2 B:HIS155 3.5 25.4 1.0
ND1 A:HIS124 3.5 25.2 0.5
CG A:HIS124 4.0 26.9 0.5
ND1 A:HIS70 4.1 23.3 1.0
ND1 B:HIS155 4.1 27.1 1.0
CG A:HIS70 4.2 23.7 1.0
CG A:HIS124 4.2 28.7 0.5
CD2 A:HIS124 4.3 30.5 0.5
CG B:HIS155 4.4 25.5 1.0
CE A:MET117 4.4 26.2 1.0
CA A:GLY126 4.4 24.4 1.0
OE1 A:GLU72 4.7 35.2 1.0
CB A:MET117 4.7 24.9 1.0
CZ A:PHE49 4.8 29.2 1.0
N A:GLY126 4.8 24.3 1.0
CB A:GLU72 4.9 29.1 1.0
C A:GLY126 4.9 24.0 1.0

Zinc binding site 2 out of 2 in 2o6d

Go back to Zinc Binding Sites List in 2o6d
Zinc binding site 2 out of 2 in the Structure of Native RTP34 From Treponema Pallidum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:50.7
occ:1.00
NE2 B:HIS124 1.8 25.0 0.5
NE2 B:HIS70 2.2 28.1 1.0
NE2 A:HIS155 2.3 18.7 1.0
CE1 B:HIS124 2.7 26.3 0.5
SD B:MET117 2.8 29.6 1.0
CD2 B:HIS124 2.9 26.0 0.5
CE1 A:HIS155 3.1 19.8 1.0
CE1 B:HIS70 3.1 26.5 1.0
CD2 B:HIS70 3.2 29.3 1.0
CG B:MET117 3.3 26.4 1.0
OE2 B:GLU72 3.4 44.2 1.0
CD2 A:HIS155 3.5 20.6 1.0
CG B:GLU72 3.8 37.2 1.0
ND1 B:HIS124 3.9 28.5 0.5
CG B:HIS124 3.9 25.6 0.5
CA B:GLY126 4.0 27.3 1.0
CD B:GLU72 4.1 37.5 1.0
CE B:MET117 4.2 30.5 1.0
ND1 B:HIS70 4.2 23.8 1.0
CG B:HIS70 4.3 27.6 1.0
ND1 A:HIS155 4.3 18.7 1.0
CG A:HIS155 4.5 19.9 1.0
N B:GLY126 4.6 27.5 1.0
CD2 B:HIS124 4.6 31.5 0.5
C B:GLY126 4.7 27.1 1.0
CB B:HIS124 4.7 29.1 0.5
CB B:MET117 4.8 24.1 1.0
N B:ALA127 4.9 26.8 1.0
CG B:HIS124 4.9 29.9 0.5

Reference:

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
Page generated: Wed Dec 16 03:45:25 2020

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