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

Protein crystallography data

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

Other elements in 2o6e:

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

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

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 2o6e

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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 2o6e

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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 2o6e

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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 2o6e

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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 2o6e

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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 2o6e

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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 2o6e

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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 2o6e

Go back to Zinc Binding Sites List in 2o6e
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

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 03:45:29 2020

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