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Nickel in PDB 2xjo: Crystal Structure of Streptococcus Suis Dpr with Nickel

Protein crystallography data

The structure of Crystal Structure of Streptococcus Suis Dpr with Nickel, PDB code: 2xjo was solved by T.Haikarainen, A.Thanassoulas, P.Stavros, G.Nounesis, S.Haataja, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.856, 137.459, 141.729, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 22.2

Other elements in 2xjo:

The structure of Crystal Structure of Streptococcus Suis Dpr with Nickel also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Calcium (Ca) 7 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Streptococcus Suis Dpr with Nickel (pdb code 2xjo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Crystal Structure of Streptococcus Suis Dpr with Nickel, PDB code: 2xjo:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12;

Nickel binding site 1 out of 12 in 2xjo

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Nickel binding site 1 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1173

b:12.9
occ:1.00
O C:HOH2011 1.9 17.6 1.0
OE2 A:GLU78 2.0 37.6 0.6
OD1 A:ASP74 2.1 55.0 1.0
O A:HOH2025 2.2 5.0 1.0
NE2 C:HIS47 2.3 42.3 1.0
OD2 A:ASP74 2.5 55.6 1.0
CG A:ASP74 2.6 52.5 1.0
CD A:GLU78 2.8 36.6 0.6
OE1 A:GLU78 3.0 36.6 0.6
OE2 A:GLU78 3.1 38.1 0.4
CD2 C:HIS47 3.2 41.8 1.0
CE1 C:HIS47 3.3 42.1 1.0
CE1 C:HIS59 4.0 45.6 1.0
NE2 C:HIS59 4.1 44.6 1.0
CD A:GLU78 4.1 36.9 0.4
CB A:ASP74 4.1 48.6 1.0
CG A:GLU78 4.2 37.3 0.6
CG A:GLU78 4.2 36.5 0.4
OD2 C:ASP63 4.3 55.6 1.0
CG C:HIS47 4.4 40.4 1.0
ND1 C:HIS47 4.4 41.4 1.0
OD1 C:ASP63 4.5 52.7 1.0
NE1 C:TRP48 4.7 41.5 1.0
CG C:ASP63 4.8 47.8 1.0
O A:ASP74 5.0 46.8 1.0
CA A:ASP74 5.0 47.3 1.0
CD1 C:TRP48 5.0 39.5 1.0

Nickel binding site 2 out of 12 in 2xjo

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Nickel binding site 2 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni1174

b:4.5
occ:1.00
OE2 B:GLU78 1.9 41.1 1.0
O D:HOH2024 2.1 6.5 1.0
NE2 D:HIS47 2.1 32.7 1.0
OD1 B:ASP74 2.2 48.5 1.0
O B:HOH2033 2.2 2.0 1.0
OD2 B:ASP74 2.6 47.9 1.0
CG B:ASP74 2.7 47.7 1.0
CD B:GLU78 2.9 39.0 1.0
CD2 D:HIS47 3.1 31.7 1.0
CE1 D:HIS47 3.2 34.4 1.0
OE1 B:GLU78 3.3 39.1 1.0
NE2 D:HIS59 4.0 39.8 1.0
OD2 D:ASP63 4.1 48.4 1.0
CE1 D:HIS59 4.2 36.4 1.0
CB B:ASP74 4.2 41.9 1.0
CG D:HIS47 4.2 31.9 1.0
CG B:GLU78 4.3 35.7 1.0
ND1 D:HIS47 4.3 32.6 1.0
OD1 D:ASP63 4.5 49.9 1.0
CG D:ASP63 4.7 43.5 1.0
NE1 D:TRP48 4.7 33.8 1.0
CD1 D:TRP48 5.0 32.4 1.0

Nickel binding site 3 out of 12 in 2xjo

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Nickel binding site 3 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni1173

b:22.3
occ:1.00
NE2 A:HIS47 2.0 37.9 1.0
O A:HOH2017 2.1 19.2 1.0
OE2 C:GLU78 2.2 50.5 1.0
OD1 C:ASP74 2.2 54.5 1.0
O A:HOH2014 2.3 16.3 1.0
OD2 C:ASP74 2.7 57.8 1.0
CG C:ASP74 2.8 54.8 1.0
CE1 A:HIS47 2.9 38.4 1.0
CD2 A:HIS47 3.1 39.1 1.0
CD C:GLU78 3.1 50.1 1.0
OE1 C:GLU78 3.5 47.9 1.0
NE2 A:HIS59 3.9 39.6 1.0
CE1 A:HIS59 4.0 39.9 1.0
O A:HOH2016 4.0 30.7 1.0
ND1 A:HIS47 4.1 39.7 1.0
OD1 A:ASP63 4.1 51.6 1.0
CG A:HIS47 4.2 38.9 1.0
CB C:ASP74 4.3 49.5 1.0
CG C:GLU78 4.5 46.5 1.0
OD2 A:ASP63 4.6 53.0 1.0
NE1 A:TRP48 4.8 40.9 1.0
CG A:ASP63 4.8 47.7 1.0
CD1 A:TRP48 5.0 40.1 1.0

Nickel binding site 4 out of 12 in 2xjo

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Nickel binding site 4 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1173

b:9.5
occ:1.00
OE2 D:GLU78 2.0 22.9 0.5
O D:HOH2037 2.0 10.9 1.0
OD1 D:ASP74 2.1 47.8 0.8
NE2 B:HIS47 2.2 29.1 1.0
O D:HOH2042 2.2 8.0 1.0
OD2 D:ASP74 2.6 44.0 0.8
CG D:ASP74 2.7 43.6 0.8
OE2 D:GLU78 2.9 35.1 0.5
CD D:GLU78 2.9 23.0 0.5
CD2 B:HIS47 3.0 28.8 1.0
OE1 D:GLU78 3.2 22.7 0.5
CE1 B:HIS47 3.2 30.6 1.0
O B:HOH2018 3.6 17.4 1.0
CD D:GLU78 3.9 30.8 0.5
NE2 B:HIS59 4.0 33.0 1.0
CB D:ASP74 4.0 36.5 0.2
CE1 B:HIS59 4.1 29.6 1.0
CB D:ASP74 4.2 38.4 0.8
CG B:HIS47 4.2 29.0 1.0
CG D:GLU78 4.2 30.6 0.5
ND1 B:HIS47 4.3 30.2 1.0
CG D:GLU78 4.3 23.4 0.5
OD2 B:ASP63 4.3 47.0 1.0
OD1 B:ASP63 4.5 47.2 1.0
NE1 B:TRP48 4.6 30.9 1.0
O D:ASP74 4.6 36.8 0.2
CG D:ASP74 4.6 35.5 0.2
CG B:ASP63 4.8 41.8 1.0
CD1 B:TRP48 4.9 31.8 1.0
OD2 D:ASP74 5.0 34.4 0.2
CA D:ASP74 5.0 35.6 0.2
OE1 D:GLU78 5.0 28.9 0.5

Nickel binding site 5 out of 12 in 2xjo

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Nickel binding site 5 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni1173

b:19.8
occ:1.00
OD1 E:ASP74 2.1 61.0 1.0
O G:HOH2011 2.1 20.1 1.0
NE2 G:HIS47 2.1 42.0 1.0
OE2 E:GLU78 2.2 36.7 0.5
O G:HOH2008 2.5 15.8 1.0
CG E:ASP74 2.9 56.5 1.0
OD2 E:ASP74 3.0 59.3 1.0
CD2 G:HIS47 3.1 38.7 1.0
CD E:GLU78 3.1 37.5 0.5
CE1 G:HIS47 3.1 40.3 1.0
OE2 E:GLU78 3.2 40.9 0.5
OE1 E:GLU78 3.4 35.5 0.5
NE2 G:HIS59 3.9 44.3 1.0
OD1 G:ASP63 4.0 47.5 0.7
OD2 G:ASP63 4.1 45.6 0.7
CD E:GLU78 4.2 39.9 0.5
CG G:HIS47 4.2 40.8 1.0
ND1 G:HIS47 4.2 41.8 1.0
CE1 G:HIS59 4.2 43.7 1.0
CB E:ASP74 4.3 50.9 1.0
CG E:GLU78 4.5 38.7 0.5
CG G:ASP63 4.5 43.4 0.7
CG E:GLU78 4.6 39.8 0.5
NE1 G:TRP48 4.9 45.7 1.0

Nickel binding site 6 out of 12 in 2xjo

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Nickel binding site 6 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni1173

b:5.0
occ:1.00
OE2 F:GLU78 1.9 28.9 0.5
O H:HOH2014 2.0 6.8 1.0
OD1 F:ASP74 2.1 50.4 1.0
NE2 H:HIS47 2.2 32.1 1.0
O F:HOH2031 2.4 5.5 1.0
OD2 F:ASP74 2.5 51.2 1.0
CG F:ASP74 2.6 48.5 1.0
CD F:GLU78 2.8 29.7 0.5
OE2 F:GLU78 2.9 33.4 0.5
CD2 H:HIS47 3.0 29.6 1.0
OE1 F:GLU78 3.1 30.7 0.5
CE1 H:HIS47 3.3 30.3 1.0
CD F:GLU78 3.9 31.7 0.5
NE2 H:HIS59 4.0 37.2 1.0
OD2 H:ASP63 4.0 50.2 1.0
CB F:ASP74 4.2 42.3 1.0
CE1 H:HIS59 4.2 37.9 1.0
CG F:GLU78 4.2 31.7 0.5
O H:HOH2016 4.2 31.4 1.0
CG H:HIS47 4.2 32.3 1.0
CG F:GLU78 4.3 34.5 0.5
ND1 H:HIS47 4.3 30.5 1.0
OD1 H:ASP63 4.5 50.0 1.0
NE1 H:TRP48 4.7 37.0 1.0
CG H:ASP63 4.7 45.2 1.0
CD1 H:TRP48 4.9 35.0 1.0

Nickel binding site 7 out of 12 in 2xjo

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Nickel binding site 7 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni1174

b:27.0
occ:1.00
OE2 G:GLU78 2.0 34.3 0.5
O G:HOH2016 2.0 28.8 1.0
OD1 G:ASP74 2.1 58.4 1.0
NE2 E:HIS47 2.2 38.2 1.0
O G:HOH2018 2.4 20.9 1.0
CG G:ASP74 2.8 54.5 1.0
OD2 G:ASP74 2.9 58.5 1.0
CD G:GLU78 2.9 36.2 0.5
OE2 G:GLU78 2.9 43.0 0.5
CD2 E:HIS47 3.1 36.8 1.0
OE1 G:GLU78 3.1 37.4 0.5
CE1 E:HIS47 3.2 39.7 1.0
CD G:GLU78 3.8 42.8 0.5
NE2 E:HIS59 4.0 44.5 1.0
CE1 E:HIS59 4.1 41.0 1.0
CG G:GLU78 4.2 41.0 0.5
CG E:HIS47 4.3 38.0 1.0
CG G:GLU78 4.3 38.7 0.5
CB G:ASP74 4.3 49.6 1.0
ND1 E:HIS47 4.3 37.1 1.0
OD2 E:ASP63 4.5 54.6 1.0
NE1 E:TRP48 4.6 41.0 1.0
OD1 E:ASP63 4.7 52.0 1.0
OE1 G:GLU78 4.8 41.8 0.5
CD1 E:TRP48 4.9 41.8 1.0

Nickel binding site 8 out of 12 in 2xjo

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Nickel binding site 8 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni1173

b:16.1
occ:1.00
OE2 H:GLU78 2.1 30.4 0.5
OD1 H:ASP74 2.1 52.1 1.0
NE2 F:HIS47 2.2 31.5 1.0
O F:HOH2020 2.4 29.7 1.0
O H:HOH2022 2.4 10.0 1.0
OD2 H:ASP74 2.7 51.2 1.0
OE1 H:GLU78 2.7 36.8 0.5
CG H:ASP74 2.7 49.8 1.0
CD H:GLU78 2.8 28.2 0.5
OE1 H:GLU78 2.9 26.8 0.5
CE1 F:HIS47 3.1 29.1 1.0
CD2 F:HIS47 3.2 31.2 1.0
CD H:GLU78 3.7 37.0 0.5
NE2 F:HIS59 4.0 34.0 1.0
CE1 F:HIS59 4.1 33.0 1.0
CB H:ASP74 4.2 45.6 1.0
CG H:GLU78 4.2 35.9 0.5
ND1 F:HIS47 4.3 30.9 1.0
CG H:GLU78 4.3 30.5 0.5
CG F:HIS47 4.3 31.0 1.0
OD1 F:ASP63 4.5 44.9 1.0
OD2 F:ASP63 4.5 47.3 1.0
NE1 F:TRP48 4.6 32.4 1.0
OE2 H:GLU78 4.7 36.9 0.5
CD1 F:TRP48 4.9 32.0 1.0
CG F:ASP63 4.9 40.4 1.0

Nickel binding site 9 out of 12 in 2xjo

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Nickel binding site 9 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni1173

b:12.4
occ:1.00
OE2 I:GLU78 2.0 47.0 1.0
O I:HOH2023 2.1 23.8 1.0
NE2 K:HIS47 2.2 34.7 1.0
O K:HOH2014 2.3 17.4 1.0
OD2 I:ASP74 2.4 50.0 1.0
OD1 I:ASP74 2.4 51.4 1.0
CG I:ASP74 2.7 50.9 1.0
CD I:GLU78 3.0 45.6 1.0
CD2 K:HIS47 3.2 33.6 1.0
CE1 K:HIS47 3.2 33.4 1.0
OE1 I:GLU78 3.4 45.4 1.0
NE2 K:HIS59 4.0 39.2 1.0
CE1 K:HIS59 4.2 38.2 1.0
OD2 K:ASP63 4.2 52.8 1.0
CB I:ASP74 4.3 45.8 1.0
OD1 K:ASP63 4.3 53.0 1.0
ND1 K:HIS47 4.3 34.3 1.0
CG I:GLU78 4.3 42.6 1.0
CG K:HIS47 4.3 35.2 1.0
CG K:ASP63 4.7 46.5 1.0
NE1 K:TRP48 4.7 35.4 1.0
CD1 K:TRP48 5.0 34.7 1.0

Nickel binding site 10 out of 12 in 2xjo

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Nickel binding site 10 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni1173

b:10.3
occ:1.00
OD1 J:ASP74 2.0 54.8 1.0
OE2 J:GLU78 2.1 51.0 1.0
NE2 L:HIS47 2.2 38.2 1.0
O L:HOH2014 2.2 14.7 1.0
O L:HOH2012 2.3 7.0 1.0
CG J:ASP74 2.7 52.4 1.0
OD2 J:ASP74 2.7 55.3 1.0
CD J:GLU78 3.0 47.5 1.0
CD2 L:HIS47 3.1 39.5 1.0
CE1 L:HIS47 3.2 36.3 1.0
OE1 J:GLU78 3.3 47.6 1.0
NE2 L:HIS59 3.9 37.7 1.0
CE1 L:HIS59 4.1 38.4 1.0
CB J:ASP74 4.2 47.1 1.0
OD1 L:ASP63 4.2 53.0 1.0
ND1 L:HIS47 4.3 35.2 1.0
CG L:HIS47 4.3 37.4 1.0
CG J:GLU78 4.3 44.8 1.0
OD2 L:ASP63 4.4 52.7 1.0
NE1 L:TRP48 4.7 37.9 1.0
CG L:ASP63 4.8 46.2 1.0
CD1 L:TRP48 4.9 36.5 1.0
CD2 L:HIS59 5.0 39.2 1.0

Nickel binding site 11 out of 12 in 2xjo

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Nickel binding site 11 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 11 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ni1174

b:17.3
occ:1.00
OE2 K:GLU78 2.0 25.3 0.5
OD1 K:ASP74 2.0 52.9 1.0
NE2 I:HIS47 2.1 36.6 1.0
O I:HOH2017 2.1 16.5 1.0
O I:HOH2015 2.3 16.2 1.0
CG K:ASP74 2.7 51.0 1.0
CD K:GLU78 2.8 25.7 0.5
OD2 K:ASP74 2.8 53.9 1.0
OE1 K:GLU78 2.9 24.3 0.5
CD2 I:HIS47 3.1 32.4 1.0
CE1 I:HIS47 3.1 36.3 1.0
OE1 K:GLU78 3.3 38.7 0.5
NE2 I:HIS59 4.0 34.9 1.0
CE1 I:HIS59 4.0 34.4 1.0
OD2 I:ASP63 4.1 52.5 1.0
CD K:GLU78 4.2 35.2 0.5
CG K:GLU78 4.2 25.9 0.5
CB K:ASP74 4.2 44.6 1.0
ND1 I:HIS47 4.2 33.4 1.0
CG I:HIS47 4.2 33.2 1.0
CG K:GLU78 4.3 31.9 0.5
OD1 I:ASP63 4.4 53.2 1.0
CG I:ASP63 4.7 46.5 1.0
NE1 I:TRP48 4.7 34.2 1.0
CD1 I:TRP48 4.9 32.1 1.0

Nickel binding site 12 out of 12 in 2xjo

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Nickel binding site 12 out of 12 in the Crystal Structure of Streptococcus Suis Dpr with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 12 of Crystal Structure of Streptococcus Suis Dpr with Nickel within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ni1174

b:17.4
occ:1.00
OD1 L:ASP74 2.0 56.9 1.0
NE2 J:HIS47 2.1 32.6 1.0
OE2 L:GLU78 2.1 24.9 0.5
O J:HOH2015 2.1 13.7 1.0
O L:HOH2024 2.5 17.3 1.0
CG L:ASP74 2.7 51.0 1.0
OD2 L:ASP74 2.7 54.9 1.0
CD L:GLU78 3.0 25.1 0.5
CE1 J:HIS47 3.0 34.0 1.0
OE1 L:GLU78 3.1 37.8 0.5
OE1 L:GLU78 3.1 25.3 0.5
CD2 J:HIS47 3.2 29.3 1.0
O J:HOH2016 3.9 28.3 1.0
NE2 J:HIS59 4.0 36.1 1.0
CD L:GLU78 4.1 33.9 0.5
ND1 J:HIS47 4.1 29.5 1.0
CB L:ASP74 4.2 45.1 1.0
CE1 J:HIS59 4.2 36.1 1.0
OD1 J:ASP63 4.2 49.3 1.0
OD2 J:ASP63 4.2 45.9 1.0
CG J:HIS47 4.3 30.6 1.0
CG L:GLU78 4.3 27.8 0.5
CG L:GLU78 4.4 32.5 0.5
CG J:ASP63 4.7 43.3 1.0
O L:HOH2025 4.7 20.8 1.0
NE1 J:TRP48 4.7 33.1 1.0
CD1 J:TRP48 5.0 30.5 1.0

Reference:

T.Haikarainen, A.Thanassoulas, P.Stavros, G.Nounesis, S.Haataja, A.C.Papageorgiou. Structural and Thermodynamic Characterization of Metal Ion Binding in Streptococcus Suis Dpr. J.Mol.Biol. V. 405 448 2011.
ISSN: ISSN 0022-2836
PubMed: 21056572
DOI: 10.1016/J.JMB.2010.10.058
Page generated: Thu Oct 29 06:18:37 2020
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