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Zinc in PDB 3pjn: The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5

Protein crystallography data

The structure of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5, PDB code: 3pjn 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) 32.90 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.573, 65.397, 152.359, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 (pdb code 3pjn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5, PDB code: 3pjn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 3pjn

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Zinc binding site 1 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn186

b:17.5
occ:1.00
NE2 A:HIS124 2.0 17.0 1.0
NE2 B:HIS155 2.0 14.5 1.0
NE2 A:HIS70 2.1 14.1 1.0
OE1 A:GLU72 2.2 17.7 1.0
CE1 B:HIS155 2.8 19.8 1.0
CE1 A:HIS124 2.9 19.8 1.0
CD2 A:HIS70 3.0 14.4 1.0
CD A:GLU72 3.0 21.2 1.0
CE1 A:HIS70 3.1 14.3 1.0
SD A:MET117 3.1 19.7 1.0
CD2 A:HIS124 3.1 16.1 1.0
CD2 B:HIS155 3.2 18.9 1.0
CG A:GLU72 3.4 17.6 1.0
CG A:MET117 3.9 19.4 1.0
ND1 A:HIS124 4.0 17.1 1.0
ND1 B:HIS155 4.0 19.7 1.0
OE2 A:GLU72 4.1 20.2 1.0
CG A:HIS124 4.1 15.3 1.0
ND1 A:HIS70 4.1 13.8 1.0
CG A:HIS70 4.1 13.3 1.0
CG B:HIS155 4.2 20.1 1.0
CE A:MET117 4.6 24.6 1.0
CB A:GLU72 4.7 15.5 1.0
CA A:GLY126 4.8 17.5 1.0
CB A:ALA119 4.9 18.2 1.0
CZ A:PHE49 4.9 17.5 1.0

Zinc binding site 2 out of 15 in 3pjn

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Zinc binding site 2 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn187

b:40.1
occ:1.00
NE2 B:HIS149 1.9 30.7 1.0
NE2 A:HIS55 2.0 32.1 1.0
O B:HOH262 2.3 44.2 1.0
O A:HOH271 2.4 32.5 1.0
CE1 B:HIS149 2.8 36.0 1.0
CE1 A:HIS55 2.9 36.0 1.0
CD2 B:HIS149 2.9 33.5 1.0
CD2 A:HIS55 3.1 31.0 1.0
ND1 B:HIS149 3.9 36.6 1.0
CG B:HIS149 4.0 32.9 1.0
ND1 A:HIS55 4.0 36.7 1.0
CG A:HIS55 4.2 31.2 1.0
O B:HOH194 4.5 23.2 1.0
O A:HOH220 4.9 23.9 1.0

Zinc binding site 3 out of 15 in 3pjn

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Zinc binding site 3 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn188

b:30.7
occ:1.00
NE2 A:HIS149 2.0 21.4 1.0
O A:HOH273 2.0 26.3 1.0
NE2 B:HIS55 2.1 25.7 1.0
O A:HOH272 2.3 12.6 1.0
CE1 A:HIS149 2.9 32.0 1.0
CD2 A:HIS149 3.0 27.1 1.0
CD2 B:HIS55 3.1 26.6 1.0
CE1 B:HIS55 3.1 30.2 1.0
ND1 A:HIS149 4.1 30.6 1.0
CG A:HIS149 4.1 26.6 1.0
ND1 B:HIS55 4.2 26.5 1.0
CG B:HIS55 4.2 25.1 1.0
O A:HOH203 4.3 18.3 1.0
O A:HOH293 4.3 43.0 1.0
O B:HOH195 4.8 19.4 1.0

Zinc binding site 4 out of 15 in 3pjn

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Zinc binding site 4 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn189

b:37.5
occ:1.00
OE2 A:GLU30 2.0 34.3 1.0
OD2 A:ASP121 2.0 30.8 1.0
O A:HOH270 2.2 29.3 1.0
O A:HOH274 2.3 38.5 1.0
CD A:GLU30 2.7 27.0 1.0
O A:HOH275 2.8 43.8 1.0
OE1 A:GLU30 2.9 35.1 1.0
CG A:ASP121 3.0 30.5 1.0
OD1 A:ASP121 3.3 25.9 1.0
OE2 A:GLU72 3.6 20.2 1.0
O A:HOH302 3.7 40.5 1.0
CG A:GLU30 4.2 22.1 1.0
OD2 A:ASP74 4.3 26.3 0.5
CB A:ASP121 4.3 27.6 1.0
CZ A:PHE28 4.4 26.5 1.0
CE2 A:PHE28 4.4 23.8 1.0
OD1 A:ASP74 4.5 27.4 0.5
O A:HOH315 4.5 42.6 1.0
CG2 A:VAL47 4.8 20.0 1.0
CD A:GLU72 4.8 21.2 1.0
CG A:ASP74 4.8 21.5 0.5

Zinc binding site 5 out of 15 in 3pjn

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Zinc binding site 5 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn190

b:0.2
occ:1.00
OD2 A:ASP36 2.2 37.9 1.0
NE2 A:HIS43 2.3 29.2 1.0
CD2 A:HIS43 3.2 27.2 1.0
CE1 A:HIS43 3.2 24.4 1.0
CG A:ASP36 3.3 28.1 1.0
O A:HOH310 3.8 49.9 1.0
CB A:ASP36 3.9 21.3 1.0
OD1 A:ASP36 4.2 28.4 1.0
ND1 A:HIS43 4.3 30.1 1.0
CG A:HIS43 4.3 24.2 1.0
CE1 A:HIS76 4.9 23.8 0.4
ZN A:ZN192 5.0 60.0 1.0

Zinc binding site 6 out of 15 in 3pjn

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Zinc binding site 6 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn191

b:0.5
occ:1.00
OD1 A:ASP38 2.5 29.6 1.0
OD2 A:ASP38 2.5 38.9 1.0
ND1 A:HIS43 2.6 30.1 1.0
CG A:ASP38 2.8 31.7 1.0
O A:HOH296 3.2 37.5 1.0
CE1 A:HIS43 3.4 24.4 1.0
CG A:HIS43 3.5 24.2 1.0
CB A:HIS43 3.9 21.8 1.0
ZN A:ZN192 3.9 60.0 1.0
CB A:ASP38 4.3 28.3 1.0
CB A:ASN78 4.3 24.8 1.0
NE2 A:HIS43 4.5 29.2 1.0
O A:HOH226 4.6 28.1 1.0
CD2 A:HIS43 4.6 27.2 1.0
CA A:HIS43 4.8 16.5 1.0
O A:HOH321 4.8 49.0 1.0
ND2 A:ASN78 5.0 23.7 1.0

Zinc binding site 7 out of 15 in 3pjn

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Zinc binding site 7 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn192

b:60.0
occ:1.00
NE2 A:HIS76 2.2 25.9 0.4
O A:HOH296 2.3 37.5 1.0
CD2 A:HIS76 3.1 24.9 0.4
CE1 A:HIS76 3.3 23.8 0.4
CG A:HIS43 3.3 24.2 1.0
CB A:HIS43 3.6 21.8 1.0
CD2 A:HIS43 3.7 27.2 1.0
ND1 A:HIS43 3.7 30.1 1.0
ZN A:ZN191 3.9 0.5 1.0
CE1 A:HIS43 4.1 24.4 1.0
NE2 A:HIS43 4.1 29.2 1.0
CG A:HIS76 4.3 21.4 0.4
ND1 A:HIS76 4.4 24.1 0.4
O A:ALA77 5.0 19.1 1.0
ZN A:ZN190 5.0 0.2 1.0

Zinc binding site 8 out of 15 in 3pjn

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Zinc binding site 8 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn193

b:74.0
occ:1.00
ND1 A:HIS104 2.3 29.8 1.0
CG A:HIS104 3.2 28.4 1.0
CE1 A:HIS104 3.3 25.6 1.0
O A:HOH298 3.3 38.2 1.0
CB A:HIS104 3.4 25.6 1.0
CD2 A:HIS104 4.4 26.6 1.0
NE2 A:HIS104 4.4 25.5 1.0
CB A:THR137 4.6 21.6 1.0
OD1 A:ASP177 4.7 40.5 1.0
CG2 A:THR137 4.8 18.7 1.0
OG1 A:THR137 4.8 19.8 1.0
O A:HOH297 4.9 40.8 1.0
CA A:HIS104 4.9 25.0 1.0

Zinc binding site 9 out of 15 in 3pjn

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Zinc binding site 9 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn194

b:28.9
occ:1.00
OD1 A:ASP74 2.2 28.8 0.5
NE2 A:HIS76 2.3 25.0 0.6
CE1 A:HIS76 2.7 24.8 0.6
O A:HOH210 3.2 24.0 1.0
CG A:ASP74 3.2 21.2 0.5
OD2 A:ASP74 3.5 32.3 0.5
CD2 A:HIS76 3.6 24.0 0.6
ND1 A:HIS76 4.0 25.0 0.6
O A:PRO123 4.1 19.2 1.0
OD1 A:ASP74 4.2 27.4 0.5
O A:HOH302 4.3 40.5 1.0
CG A:HIS76 4.4 21.6 0.6
CB A:ASP74 4.5 20.2 0.5
CG A:ASP74 4.6 21.5 0.5
CB A:ASP74 4.6 19.8 0.5
O A:ASP121 4.9 28.3 1.0

Zinc binding site 10 out of 15 in 3pjn

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Zinc binding site 10 out of 15 in the The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Crystal Structure of TP34 Bound to Zn(II) Ion at pH 7.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn186

b:23.6
occ:1.00
NE2 B:HIS124 2.0 17.5 1.0
NE2 A:HIS155 2.0 18.4 1.0
NE2 B:HIS70 2.1 16.6 1.0
OE2 B:GLU72 2.2 24.3 1.0
CE1 A:HIS155 2.8 20.8 1.0
CE1 B:HIS124 2.9 21.9 1.0
CD2 B:HIS70 3.0 20.2 1.0
SD B:MET117 3.0 21.2 1.0
CD2 B:HIS124 3.1 17.9 1.0
CE1 B:HIS70 3.1 18.9 1.0
CD B:GLU72 3.1 23.8 1.0
CD2 A:HIS155 3.2 21.1 1.0
CG B:GLU72 3.4 20.3 1.0
CG B:MET117 3.8 21.0 1.0
ND1 A:HIS155 4.0 21.6 1.0
ND1 B:HIS124 4.0 23.8 1.0
CG B:HIS124 4.1 19.9 1.0
CG B:HIS70 4.1 17.4 1.0
ND1 B:HIS70 4.1 17.6 1.0
OE1 B:GLU72 4.2 26.5 1.0
CG A:HIS155 4.2 20.1 1.0
CE B:MET117 4.4 21.9 1.0
CA B:GLY126 4.6 21.3 1.0
CB B:GLU72 4.7 19.9 1.0
CB B:ALA119 4.8 22.5 1.0
CZ B:PHE49 4.9 23.1 1.0
CG2 B:VAL52 4.9 20.7 1.0

Reference:

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.
Page generated: Wed Dec 16 04:43:12 2020

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