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Terbium in PDB 2v15: Terbium Binding in Streptococcus Suis Dpr Protein

Protein crystallography data

The structure of Terbium Binding in Streptococcus Suis Dpr Protein, PDB code: 2v15 was solved by H.Havukainen, A.C.Papageorgiou, A.Kauko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.485, 137.715, 142.438, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.4

Other elements in 2v15:

The structure of Terbium Binding in Streptococcus Suis Dpr Protein also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms
Calcium (Ca) 4 atoms

Terbium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Terbium atom in the Terbium Binding in Streptococcus Suis Dpr Protein (pdb code 2v15). This binding sites where shown within 5.0 Angstroms radius around Terbium atom.
In total 12 binding sites of Terbium where determined in the Terbium Binding in Streptococcus Suis Dpr Protein, PDB code: 2v15:
Jump to Terbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Terbium binding site 1 out of 12 in 2v15

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Terbium binding site 1 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 1 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tb1174

b:33.9
occ:1.00
 OD2 A:ASP74 2.1 34.0 1.0
O C:HOH2014 2.4 33.7 1.0
OE2 A:GLU78 2.4 19.8 1.0
CL C:CL1173 2.5 46.9 1.0
NE2 C:HIS46 2.5 26.0 1.0
OE1 A:GLU78 2.5 23.7 1.0
O C:HOH2013 2.5 28.4 1.0
O A:HOH2018 2.6 34.0 1.0
OD1 A:ASP74 2.6 32.6 1.0
CG A:ASP74 2.7 34.7 1.0
CD A:GLU78 2.8 22.8 1.0
CE1 C:HIS46 3.4 31.8 1.0
CD2 C:HIS46 3.5 28.0 1.0
CE1 C:HIS58 4.2 30.8 1.0
CB A:ASP74 4.2 34.9 1.0
NE2 C:HIS58 4.3 34.2 1.0
CG A:GLU78 4.3 27.6 1.0
ND1 C:HIS46 4.6 28.4 1.0
OD1 C:ASP62 4.6 38.4 1.0
OD2 C:ASP62 4.6 37.9 1.0
CG C:HIS46 4.6 27.7 1.0
O A:HOH2020 4.7 34.8 1.0
NE1 C:TRP47 5.0 29.9 1.0

Terbium binding site 2 out of 12 in 2v15

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Terbium binding site 2 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 2 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Tb1174

b:30.6
occ:1.00
 OD2 B:ASP74 2.2 31.8 1.0
OE2 B:GLU78 2.4 21.8 1.0
O B:HOH2021 2.4 27.3 1.0
O D:HOH2020 2.4 31.1 1.0
OE1 B:GLU78 2.4 24.7 1.0
CL D:CL1175 2.4 49.1 1.0
OD1 B:ASP74 2.6 32.3 1.0
O B:HOH2020 2.6 29.1 1.0
NE2 D:HIS47 2.7 23.5 1.0
CG B:ASP74 2.7 32.5 1.0
CD B:GLU78 2.7 25.2 1.0
CD2 D:HIS47 3.6 23.2 1.0
CE1 D:HIS47 3.6 24.6 1.0
CB B:ASP74 4.2 32.3 1.0
CG B:GLU78 4.3 23.6 1.0
CE1 D:HIS59 4.4 26.4 1.0
OD2 D:ASP63 4.4 37.3 1.0
OD1 D:ASP63 4.6 33.9 1.0
NE2 D:HIS59 4.6 28.8 1.0
ND1 D:HIS47 4.8 23.9 1.0
CG D:HIS47 4.8 25.4 1.0
NE1 D:TRP48 4.9 20.1 1.0
CG D:ASP63 4.9 33.0 1.0

Terbium binding site 3 out of 12 in 2v15

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Terbium binding site 3 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 3 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Tb1172

b:34.3
occ:1.00
 OD2 C:ASP73 2.1 28.2 1.0
O A:HOH2015 2.4 28.4 1.0
OE1 C:GLU77 2.5 28.4 1.0
O A:HOH2016 2.5 27.9 1.0
OE2 C:GLU77 2.5 19.0 1.0
CL A:CL1173 2.5 49.0 1.0
OD1 C:ASP73 2.6 37.5 1.0
O C:HOH2015 2.6 27.9 1.0
NE2 A:HIS47 2.6 28.3 1.0
CG C:ASP73 2.7 34.2 1.0
CD C:GLU77 2.8 26.7 1.0
CD2 A:HIS47 3.5 26.1 1.0
CE1 A:HIS47 3.7 27.6 1.0
CB C:ASP73 4.2 35.1 1.0
NE2 A:HIS59 4.2 28.3 1.0
OD2 A:ASP63 4.3 35.7 1.0
CG C:GLU77 4.3 28.2 1.0
OD1 A:ASP63 4.4 34.0 1.0
O C:HOH2016 4.5 38.6 1.0
CE1 A:HIS59 4.5 29.0 1.0
CG A:HIS47 4.7 27.8 1.0
ND1 A:HIS47 4.7 27.0 1.0
CG A:ASP63 4.8 34.5 1.0
NE1 A:TRP48 5.0 27.9 1.0

Terbium binding site 4 out of 12 in 2v15

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Terbium binding site 4 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 4 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Tb1173

b:31.9
occ:1.00
 OD2 D:ASP74 2.3 34.7 1.0
O B:HOH2017 2.3 25.0 1.0
OE2 D:GLU78 2.4 24.2 1.0
O B:HOH2016 2.5 21.4 1.0
OE1 D:GLU78 2.5 22.3 1.0
CL D:CL1174 2.5 47.8 1.0
O D:HOH2025 2.6 30.4 1.0
NE2 B:HIS47 2.6 21.0 1.0
OD1 D:ASP74 2.7 34.3 1.0
CD D:GLU78 2.8 24.0 1.0
CG D:ASP74 2.8 33.3 1.0
CD2 B:HIS47 3.6 20.4 1.0
CE1 B:HIS47 3.6 26.2 1.0
NE2 B:HIS59 4.3 22.5 1.0
CG D:GLU78 4.3 24.2 1.0
CB D:ASP74 4.3 32.4 1.0
OD1 B:ASP63 4.5 34.9 1.0
OD2 B:ASP63 4.6 34.2 1.0
CE1 B:HIS59 4.6 21.1 1.0
O D:HOH2029 4.6 28.9 1.0
ND1 B:HIS47 4.7 26.4 1.0
CG B:HIS47 4.7 24.8 1.0
NE1 B:TRP48 4.9 19.7 1.0
CG B:ASP63 5.0 33.2 1.0

Terbium binding site 5 out of 12 in 2v15

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Terbium binding site 5 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 5 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Tb1175

b:37.1
occ:1.00
 O G:HOH2011 2.1 37.0 1.0
OD2 E:ASP74 2.4 36.1 1.0
OE2 E:GLU78 2.4 39.9 1.0
OD1 E:ASP74 2.4 31.6 1.0
O G:HOH2019 2.4 36.4 1.0
NE2 G:HIS47 2.5 23.5 1.0
O G:HOH2020 2.5 20.4 1.0
OE1 E:GLU78 2.5 37.5 1.0
CL E:CL1176 2.6 47.3 1.0
CG E:ASP74 2.7 35.4 1.0
CD E:GLU78 2.8 38.0 1.0
CD2 G:HIS47 3.4 21.9 1.0
CE1 G:HIS47 3.5 26.8 1.0
NE2 G:HIS59 4.2 26.0 1.0
CB E:ASP74 4.3 34.6 1.0
CG E:GLU78 4.3 35.1 1.0
OD2 G:ASP63 4.4 35.9 1.0
OD1 G:ASP63 4.6 38.6 1.0
CG G:HIS47 4.6 25.0 1.0
ND1 G:HIS47 4.6 24.9 1.0
CE1 G:HIS59 4.6 25.6 1.0
O E:HOH2017 4.7 37.4 1.0
CG G:ASP63 4.9 33.9 1.0

Terbium binding site 6 out of 12 in 2v15

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Terbium binding site 6 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 6 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Tb1173

b:32.6
occ:1.00
 O F:HOH2018 2.0 27.5 1.0
O H:HOH2013 2.3 27.8 1.0
O F:HOH2017 2.4 20.6 1.0
O H:HOH2012 2.4 23.9 1.0
OD2 F:ASP74 2.4 31.4 1.0
OE2 F:GLU78 2.4 34.5 1.0
NE2 H:HIS47 2.5 19.7 1.0
OE1 F:GLU78 2.5 31.6 1.0
OD1 F:ASP74 2.5 32.1 1.0
CD F:GLU78 2.8 34.8 1.0
CG F:ASP74 2.8 33.5 1.0
CE1 H:HIS47 3.4 22.4 1.0
CD2 H:HIS47 3.5 21.6 1.0
NE2 H:HIS59 4.2 30.1 1.0
CG F:GLU78 4.3 30.0 1.0
CB F:ASP74 4.4 33.1 1.0
OD2 H:ASP63 4.5 31.5 1.0
ND1 H:HIS47 4.5 21.7 1.0
O F:HOH2020 4.6 35.9 1.0
CE1 H:HIS59 4.6 33.6 1.0
CG H:HIS47 4.6 23.9 1.0
OD1 H:ASP63 4.7 32.2 1.0

Terbium binding site 7 out of 12 in 2v15

Go back to Terbium Binding Sites List in 2v15
Terbium binding site 7 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 7 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Tb1173

b:36.2
occ:1.00
 O E:HOH2007 2.1 25.7 1.0
OD2 G:ASP74 2.3 39.9 1.0
CL E:CL1174 2.4 55.3 1.0
OE1 G:GLU78 2.4 32.0 1.0
OE2 G:GLU78 2.4 33.4 1.0
O G:HOH2024 2.4 22.4 1.0
O E:HOH2013 2.5 20.8 1.0
OD1 G:ASP74 2.5 35.0 1.0
NE2 E:HIS47 2.6 27.7 1.0
CD G:GLU78 2.8 35.1 1.0
CG G:ASP74 2.8 38.3 1.0
CD2 E:HIS47 3.4 28.9 1.0
CE1 E:HIS47 3.7 33.5 1.0
NE2 E:HIS59 4.2 24.1 1.0
CG G:GLU78 4.3 33.1 1.0
CB G:ASP74 4.3 36.2 1.0
O E:HOH2006 4.3 52.0 1.0
OD2 E:ASP63 4.5 42.6 1.0
O L:HOH2040 4.6 34.9 1.0
OD1 E:ASP63 4.6 39.4 1.0
CE1 E:HIS59 4.6 28.8 1.0
CG E:HIS47 4.6 27.2 1.0
ND1 E:HIS47 4.8 31.8 1.0

Terbium binding site 8 out of 12 in 2v15

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Terbium binding site 8 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 8 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Tb1173

b:34.5
occ:1.00
 O H:HOH2019 2.0 23.1 1.0
O F:HOH2015 2.2 26.6 1.0
OD2 H:ASP74 2.4 36.7 1.0
OE2 H:GLU78 2.4 24.9 1.0
O H:HOH2018 2.5 20.2 1.0
OE1 H:GLU78 2.5 30.4 1.0
O F:HOH2014 2.6 25.1 1.0
OD1 H:ASP74 2.6 33.5 1.0
NE2 F:HIS47 2.7 21.8 1.0
CD H:GLU78 2.8 29.7 1.0
CG H:ASP74 2.8 35.7 1.0
CE1 F:HIS47 3.6 26.2 1.0
CD2 F:HIS47 3.6 22.8 1.0
CG H:GLU78 4.2 29.2 1.0
OD2 F:ASP63 4.3 38.8 1.0
CB H:ASP74 4.3 35.1 1.0
CE1 F:HIS59 4.3 29.8 1.0
OD1 F:ASP63 4.5 37.4 1.0
NE2 F:HIS59 4.6 31.5 1.0
ND1 F:HIS47 4.7 22.2 1.0
CG F:HIS47 4.8 21.0 1.0
CG F:ASP63 4.9 35.4 1.0

Terbium binding site 9 out of 12 in 2v15

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Terbium binding site 9 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 9 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Tb1174

b:33.4
occ:1.00
 O I:HOH2019 2.1 22.8 1.0
O I:HOH2018 2.4 29.4 1.0
OD2 I:ASP74 2.4 24.7 1.0
OE2 I:GLU78 2.5 29.3 1.0
O K:HOH2015 2.5 30.4 1.0
NE2 K:HIS47 2.5 24.4 1.0
OE1 I:GLU78 2.6 27.7 1.0
CL I:CL1175 2.6 52.5 1.0
OD1 I:ASP74 2.7 30.5 1.0
CD I:GLU78 2.9 30.2 1.0
CG I:ASP74 2.9 31.6 1.0
CD2 K:HIS47 3.4 22.8 1.0
CE1 K:HIS47 3.6 24.5 1.0
CG I:GLU78 4.4 29.5 1.0
NE2 K:HIS59 4.4 26.9 1.0
CB I:ASP74 4.4 32.8 1.0
OD2 K:ASP63 4.5 34.5 1.0
OD1 K:ASP63 4.5 35.6 1.0
CG K:HIS47 4.6 23.9 1.0
ND1 K:HIS47 4.7 24.9 1.0
CE1 K:HIS59 4.8 31.5 1.0
O I:HOH2021 4.8 32.6 1.0
CG K:ASP63 4.9 31.6 1.0

Terbium binding site 10 out of 12 in 2v15

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Terbium binding site 10 out of 12 in the Terbium Binding in Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Terbium with other atoms in the Tb binding site number 10 of Terbium Binding in Streptococcus Suis Dpr Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Tb1174

b:36.2
occ:1.00
 OD2 J:ASP74 2.3 31.5 1.0
O L:HOH2006 2.3 29.4 1.0
O J:HOH2018 2.4 27.1 1.0
O L:HOH2012 2.4 29.2 1.0
NE2 L:HIS47 2.5 24.6 1.0
OE2 J:GLU78 2.5 31.0 1.0
OE1 J:GLU78 2.5 29.8 1.0
OD1 J:ASP74 2.7 32.7 1.0
O L:HOH2011 2.8 34.8 1.0
CG J:ASP74 2.8 34.7 1.0
CD J:GLU78 2.8 30.8 1.0
CD2 L:HIS47 3.4 30.0 1.0
CE1 L:HIS47 3.5 25.8 1.0
NE2 L:HIS59 4.3 29.5 1.0
CG J:GLU78 4.3 31.0 1.0
CB J:ASP74 4.4 34.9 1.0
OD2 L:ASP63 4.4 40.8 1.0
CE1 L:HIS59 4.5 25.8 1.0
ND1 L:HIS47 4.6 26.9 1.0
CG L:HIS47 4.6 27.6 1.0
OD1 L:ASP63 4.7 37.4 1.0
NE1 L:TRP48 4.9 25.2 1.0
O J:ASP74 4.9 35.2 1.0

Reference:

H.Havukainen, S.Haataja, A.Kauko, A.T.Pulliainen, A.Salminen, T.Haikarainen, J.Finne, A.C.Papageorgiou. Structural Basis of the Zinc- and Terbium-Mediated Inhibition of Ferroxidase Activity in Dps Ferritin-Like Proteins. Protein Sci. V. 17 1513 2008.
ISSN: ESSN 1469-896X
PubMed: 18552126
DOI: 10.1110/PS.036236.108
Page generated: Fri Oct 11 08:12:23 2024

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