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Copper in PDB 2xjn: Crystal Structure of Streptococcus Suis Dpr with Copper

Protein crystallography data

The structure of Crystal Structure of Streptococcus Suis Dpr with Copper, PDB code: 2xjn 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) 24.76 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.840, 137.710, 142.120, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 21.1

Copper Binding Sites:

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

Copper binding site 1 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1173

b:10.3
occ:0.70
OE2 A:GLU78 1.7 34.3 1.0
NE2 C:HIS47 1.9 25.1 1.0
OD1 A:ASP74 2.0 35.4 1.0
OD2 A:ASP74 2.6 33.8 1.0
CG A:ASP74 2.6 33.6 1.0
CD A:GLU78 2.8 31.9 1.0
CD2 C:HIS47 2.8 25.5 1.0
O C:HOH2017 2.9 17.4 1.0
CE1 C:HIS47 3.1 26.9 1.0
OE1 A:GLU78 3.3 30.1 1.0
O C:HOH2019 3.6 15.8 1.0
CG A:GLU78 4.0 26.2 1.0
CG C:HIS47 4.0 24.8 1.0
CB A:ASP74 4.0 29.9 1.0
CE1 C:HIS59 4.1 28.3 1.0
ND1 C:HIS47 4.1 25.9 1.0
NE2 C:HIS59 4.2 29.6 1.0
OD1 C:ASP63 4.2 35.4 1.0
NE1 C:TRP48 4.2 26.6 1.0
CD1 C:TRP48 4.6 25.9 1.0
OD2 C:ASP63 4.6 38.5 1.0
CG C:ASP63 4.9 31.4 1.0
CE1 C:HIS44 4.9 28.7 1.0
CA A:ASP74 5.0 28.2 1.0

Copper binding site 2 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1174

b:16.7
occ:0.70
OE2 B:GLU78 1.7 12.7 0.5
NE2 D:HIS47 2.1 22.3 1.0
OD1 B:ASP74 2.1 22.1 1.0
OD2 B:ASP74 2.6 24.9 1.0
CG B:ASP74 2.7 23.7 1.0
CD B:GLU78 2.8 14.1 0.5
O B:HOH2053 2.9 15.0 1.0
CD2 D:HIS47 2.9 19.6 1.0
OE2 B:GLU78 3.0 25.9 0.5
CE1 D:HIS47 3.1 20.8 1.0
OE1 B:GLU78 3.3 15.0 0.5
CD B:GLU78 3.9 23.3 0.5
CG B:GLU78 4.0 16.8 0.5
CE1 D:HIS59 4.1 27.2 1.0
NE2 D:HIS59 4.1 29.0 1.0
CG B:GLU78 4.1 22.0 0.5
CG D:HIS47 4.1 18.9 1.0
ND1 D:HIS47 4.2 20.0 1.0
OD2 D:ASP63 4.2 31.1 1.0
CB B:ASP74 4.2 22.1 1.0
NE1 D:TRP48 4.3 21.0 1.0
O B:HOH2047 4.3 23.6 1.0
OD1 D:ASP63 4.4 32.8 1.0
CD1 D:TRP48 4.6 21.2 1.0
CG D:ASP63 4.7 28.8 1.0
CE1 D:HIS44 4.8 21.8 1.0
O B:ASP74 5.0 22.1 1.0

Copper binding site 3 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1173

b:16.0
occ:0.70
OE2 C:GLU78 1.9 20.4 0.5
NE2 A:HIS47 2.0 23.4 1.0
OD1 C:ASP74 2.0 26.0 1.0
OE2 C:GLU78 2.4 28.4 0.5
CG C:ASP74 2.7 25.6 1.0
OD2 C:ASP74 2.7 24.8 1.0
CD C:GLU78 2.9 21.5 0.5
CD2 A:HIS47 3.0 24.2 1.0
CE1 A:HIS47 3.0 22.1 1.0
O C:HOH2041 3.2 14.7 1.0
OE1 C:GLU78 3.4 23.8 0.5
CD C:GLU78 3.5 27.7 0.5
CG C:GLU78 4.0 25.3 0.5
NE2 A:HIS59 4.0 24.5 1.0
CG C:GLU78 4.0 22.0 0.5
CE1 A:HIS59 4.1 26.2 1.0
ND1 A:HIS47 4.1 21.9 1.0
CG A:HIS47 4.1 22.8 1.0
CB C:ASP74 4.2 24.5 1.0
NE1 A:TRP48 4.2 23.1 1.0
O C:HOH2042 4.3 14.5 1.0
OD2 A:ASP63 4.4 40.8 1.0
OE1 C:GLU78 4.5 27.1 0.5
OD1 A:ASP63 4.5 38.1 1.0
CD1 A:TRP48 4.5 24.2 1.0
CE1 A:HIS44 4.8 26.4 1.0
CG A:ASP63 4.9 35.8 1.0

Copper binding site 4 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1173

b:16.5
occ:0.70
OE2 D:GLU78 1.8 20.3 0.5
NE2 B:HIS47 2.0 17.6 1.0
OD1 D:ASP74 2.1 29.0 1.0
O B:HOH2031 2.3 26.8 1.0
CD D:GLU78 2.6 19.6 0.5
CG D:ASP74 2.8 27.4 1.0
O D:HOH2054 2.8 14.1 1.0
OD2 D:ASP74 2.9 29.1 1.0
OE1 D:GLU78 2.9 18.5 0.5
CD2 B:HIS47 3.0 15.7 1.0
CE1 B:HIS47 3.0 18.9 1.0
O B:HOH2030 3.4 28.1 1.0
OE2 D:GLU78 3.4 27.5 0.5
CG D:GLU78 4.0 19.0 0.5
CD D:GLU78 4.0 26.0 0.5
NE2 B:HIS59 4.0 20.2 1.0
CE1 B:HIS59 4.1 19.9 1.0
ND1 B:HIS47 4.1 18.5 1.0
CG D:GLU78 4.1 23.5 0.5
CG B:HIS47 4.1 17.2 1.0
O D:HOH2053 4.2 13.2 1.0
OD1 B:ASP63 4.2 27.8 1.0
CB D:ASP74 4.2 24.8 1.0
NE1 B:TRP48 4.3 22.1 1.0
OD2 B:ASP63 4.4 30.2 1.0
CD1 B:TRP48 4.6 19.8 1.0
CG B:ASP63 4.7 26.5 1.0
CE1 B:HIS44 4.9 24.1 1.0
OE1 D:GLU78 5.0 20.9 0.5

Copper binding site 5 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu1174

b:16.7
occ:0.70
OE2 E:GLU78 1.8 22.0 0.5
OD1 E:ASP74 2.0 34.4 1.0
O E:HOH2033 2.0 21.6 1.0
NE2 G:HIS47 2.1 27.5 1.0
CG E:ASP74 2.7 33.3 1.0
OD2 E:ASP74 2.8 34.9 1.0
CD E:GLU78 2.8 23.7 0.5
OE2 E:GLU78 2.9 30.2 0.5
CD2 G:HIS47 2.9 23.0 1.0
O E:HOH2037 3.2 14.8 1.0
CE1 G:HIS47 3.2 24.8 1.0
O G:HOH2027 3.3 11.7 0.5
OE1 E:GLU78 3.3 22.0 0.5
CD E:GLU78 3.8 29.5 0.5
CG E:GLU78 4.0 24.4 0.5
CG G:HIS47 4.1 24.1 1.0
NE2 G:HIS59 4.1 26.9 1.0
CG E:GLU78 4.1 28.6 0.5
CE1 G:HIS59 4.2 27.7 1.0
CB E:ASP74 4.2 31.3 1.0
ND1 G:HIS47 4.2 26.4 1.0
NE1 G:TRP48 4.3 26.6 1.0
OD1 G:ASP63 4.4 41.4 1.0
OD2 G:ASP63 4.4 41.6 1.0
O E:HOH2036 4.4 19.4 1.0
CD1 G:TRP48 4.5 27.0 1.0
CE1 G:HIS44 4.7 27.3 1.0
CG G:ASP63 4.8 37.2 1.0
OE1 E:GLU78 4.9 31.5 0.5
O E:HOH2011 4.9 8.2 0.5
O E:ASP74 5.0 31.4 1.0

Copper binding site 6 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu1173

b:7.5
occ:0.70
OE2 F:GLU78 1.8 20.4 0.5
OD1 F:ASP74 1.9 34.5 1.0
NE2 H:HIS47 2.0 23.5 1.0
O F:HOH2043 2.0 16.5 1.0
CG F:ASP74 2.6 32.1 1.0
OD2 F:ASP74 2.7 34.1 1.0
CD F:GLU78 2.7 19.8 0.5
CD2 H:HIS47 2.9 18.4 1.0
O F:HOH2048 3.0 14.5 1.0
OE2 F:GLU78 3.1 22.0 0.5
OE1 F:GLU78 3.1 16.9 0.5
CE1 H:HIS47 3.1 21.1 1.0
CG F:GLU78 4.0 18.8 0.5
CD F:GLU78 4.0 21.5 0.5
CG H:HIS47 4.1 22.2 1.0
CB F:ASP74 4.1 27.8 1.0
NE2 H:HIS59 4.1 21.6 1.0
CE1 H:HIS59 4.1 23.0 1.0
ND1 H:HIS47 4.2 21.3 1.0
CG F:GLU78 4.2 20.9 0.5
NE1 H:TRP48 4.2 25.3 1.0
OD2 H:ASP63 4.3 33.5 1.0
OD1 H:ASP63 4.3 31.7 1.0
O F:HOH2047 4.5 14.9 1.0
CD1 H:TRP48 4.6 24.3 1.0
O F:HOH2017 4.6 22.1 1.0
CE1 H:HIS44 4.7 25.7 1.0
CG H:ASP63 4.8 29.8 1.0
O F:ASP74 4.9 27.9 1.0
CA F:ASP74 5.0 26.8 1.0

Copper binding site 7 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu1173

b:18.1
occ:0.70
OE2 G:GLU78 1.7 41.7 1.0
NE2 E:HIS47 1.9 26.4 1.0
OD1 G:ASP74 2.0 35.9 1.0
CD G:GLU78 2.8 38.3 1.0
CG G:ASP74 2.8 34.0 1.0
CD2 E:HIS47 2.9 26.8 1.0
CE1 E:HIS47 2.9 25.1 1.0
OD2 G:ASP74 3.0 33.7 1.0
O E:HOH2019 3.1 15.3 1.0
OE1 G:GLU78 3.3 38.3 1.0
CG G:GLU78 4.0 35.5 1.0
ND1 E:HIS47 4.0 25.3 1.0
CG E:HIS47 4.1 26.0 1.0
NE2 E:HIS59 4.1 29.6 1.0
CE1 E:HIS59 4.2 29.6 1.0
CB G:ASP74 4.2 32.2 1.0
O G:HOH2040 4.3 19.4 1.0
OD1 E:ASP63 4.3 32.8 1.0
NE1 E:TRP48 4.3 29.2 1.0
CD1 E:TRP48 4.6 28.4 1.0
OD2 E:ASP63 4.6 35.7 1.0
CE1 E:HIS44 4.9 31.2 1.0
CG E:ASP63 4.9 31.8 1.0
O G:ASP74 5.0 30.3 1.0

Copper binding site 8 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cu1173

b:16.7
occ:0.70
OE2 H:GLU78 1.9 17.1 0.5
NE2 F:HIS47 2.0 20.0 1.0
OD1 H:ASP74 2.0 29.7 1.0
OE2 H:GLU78 2.4 24.2 0.5
OD2 H:ASP74 2.5 28.0 1.0
CG H:ASP74 2.6 29.3 1.0
CD H:GLU78 2.8 18.3 0.5
CD2 F:HIS47 2.9 21.9 1.0
CE1 F:HIS47 3.0 17.7 1.0
O H:HOH2039 3.1 17.3 1.0
OE1 H:GLU78 3.3 18.7 0.5
CD H:GLU78 3.5 24.2 0.5
CG H:GLU78 4.0 24.0 0.5
CG H:GLU78 4.0 21.6 0.5
CE1 F:HIS59 4.1 24.5 1.0
CG F:HIS47 4.1 20.8 1.0
ND1 F:HIS47 4.1 19.2 1.0
CB H:ASP74 4.1 28.0 1.0
NE2 F:HIS59 4.2 24.4 1.0
NE1 F:TRP48 4.3 23.5 1.0
OD1 F:ASP63 4.3 35.4 1.0
O H:HOH2038 4.4 18.0 1.0
OD2 F:ASP63 4.4 38.3 1.0
OE1 H:GLU78 4.5 25.2 0.5
CD1 F:TRP48 4.5 22.0 1.0
CG F:ASP63 4.8 33.2 1.0
NE2 F:HIS44 4.9 28.1 1.0

Copper binding site 9 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu1174

b:17.9
occ:0.70
OE2 I:GLU78 1.7 14.6 0.5
OD1 I:ASP74 2.0 24.2 1.0
NE2 K:HIS47 2.1 20.7 1.0
OE2 I:GLU78 2.6 25.7 0.5
CG I:ASP74 2.7 25.4 1.0
OD2 I:ASP74 2.7 26.3 1.0
CD I:GLU78 2.7 17.4 0.5
CD2 K:HIS47 2.9 20.8 1.0
O I:HOH2048 3.1 11.9 1.0
CE1 K:HIS47 3.2 18.8 1.0
OE1 I:GLU78 3.2 20.4 0.5
CD I:GLU78 3.6 25.4 0.5
CG I:GLU78 3.9 19.7 0.5
CG I:GLU78 4.0 23.8 0.5
O I:HOH2047 4.1 18.9 1.0
CG K:HIS47 4.1 21.8 1.0
OD1 K:ASP63 4.1 36.3 1.0
CB I:ASP74 4.2 24.1 1.0
CE1 K:HIS59 4.2 22.5 1.0
NE2 K:HIS59 4.2 21.8 1.0
ND1 K:HIS47 4.2 21.6 1.0
NE1 K:TRP48 4.3 22.2 1.0
OD2 K:ASP63 4.4 34.0 1.0
CD1 K:TRP48 4.5 21.3 1.0
OE1 I:GLU78 4.7 24.7 0.5
CG K:ASP63 4.7 31.0 1.0
CE1 K:HIS44 4.8 22.1 1.0
O I:ASP74 5.0 24.3 1.0

Copper binding site 10 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cu1173

b:13.1
occ:0.70
OE2 J:GLU78 1.8 36.8 1.0
OD1 J:ASP74 2.0 33.3 1.0
NE2 L:HIS47 2.0 27.3 1.0
OD2 J:ASP74 2.6 32.2 1.0
CG J:ASP74 2.6 32.5 1.0
CD J:GLU78 2.8 33.8 1.0
CD2 L:HIS47 2.8 24.7 1.0
CE1 L:HIS47 3.1 28.3 1.0
OE1 J:GLU78 3.4 32.6 1.0
CG J:GLU78 3.9 30.2 1.0
CG L:HIS47 4.0 26.3 1.0
O J:HOH2037 4.1 10.4 1.0
NE2 L:HIS59 4.1 27.7 1.0
CB J:ASP74 4.1 30.4 1.0
ND1 L:HIS47 4.1 27.9 1.0
NE1 L:TRP48 4.2 25.5 1.0
CE1 L:HIS59 4.2 26.0 1.0
OD1 L:ASP63 4.2 42.5 1.0
CD1 L:TRP48 4.5 25.4 1.0
CE1 L:HIS44 4.8 27.9 1.0
OD2 L:ASP63 4.9 44.0 1.0
O J:ASP74 4.9 30.1 1.0
CG L:ASP63 5.0 37.9 1.0
CA J:ASP74 5.0 30.1 1.0

Copper binding site 11 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 11 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu1174

b:15.9
occ:0.70
OE2 K:GLU78 1.8 16.9 0.5
NE2 I:HIS47 1.9 19.7 1.0
OD1 K:ASP74 2.0 23.2 1.0
O I:HOH2032 2.3 23.9 1.0
CG K:ASP74 2.7 23.3 1.0
OD2 K:ASP74 2.7 24.8 1.0
CD K:GLU78 2.7 16.3 0.5
OE2 K:GLU78 2.8 21.4 0.5
CD2 I:HIS47 2.8 15.8 1.0
CE1 I:HIS47 3.0 20.7 1.0
O K:HOH2058 3.2 22.1 1.0
OE1 K:GLU78 3.2 17.4 0.5
CD K:GLU78 3.8 21.4 0.5
CG K:GLU78 3.9 16.0 0.5
CG I:HIS47 4.0 17.8 1.0
CE1 I:HIS59 4.0 20.1 1.0
ND1 I:HIS47 4.1 18.9 1.0
NE2 I:HIS59 4.1 18.5 1.0
CB K:ASP74 4.2 22.2 1.0
CG K:GLU78 4.2 19.2 0.5
NE1 I:TRP48 4.2 18.4 1.0
OD1 I:ASP63 4.2 35.8 1.0
OD2 I:ASP63 4.3 36.8 1.0
O K:HOH2057 4.3 15.1 1.0
O I:HOH2030 4.4 22.7 1.0
CD1 I:TRP48 4.5 17.6 1.0
CG I:ASP63 4.7 31.1 1.0
OE1 K:GLU78 4.9 21.7 0.5
CE1 I:HIS44 4.9 21.6 1.0
O K:ASP74 4.9 21.4 1.0

Copper binding site 12 out of 12 in 2xjn

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 12 of Crystal Structure of Streptococcus Suis Dpr with Copper within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cu1173

b:16.1
occ:0.70
OE2 L:GLU78 1.8 17.9 0.5
NE2 J:HIS47 1.9 24.2 1.0
OD1 L:ASP74 2.0 25.1 1.0
O L:HOH2033 2.3 18.0 1.0
OE2 L:GLU78 2.4 22.7 0.5
CG L:ASP74 2.7 24.8 1.0
CD L:GLU78 2.8 19.6 0.5
OD2 L:ASP74 2.8 23.8 1.0
CD2 J:HIS47 2.8 20.9 1.0
CE1 J:HIS47 3.0 22.1 1.0
O L:HOH2036 3.2 15.3 1.0
OE1 L:GLU78 3.3 20.2 0.5
CD L:GLU78 3.4 22.3 0.5
CG L:GLU78 3.9 21.5 0.5
CG L:GLU78 4.0 20.2 0.5
CG J:HIS47 4.0 20.7 1.0
ND1 J:HIS47 4.1 20.7 1.0
CE1 J:HIS59 4.1 23.8 1.0
NE2 J:HIS59 4.1 22.0 1.0
CB L:ASP74 4.2 23.6 1.0
NE1 J:TRP48 4.2 24.6 1.0
OD2 J:ASP63 4.2 30.2 1.0
O L:HOH2037 4.3 17.7 1.0
OE1 L:GLU78 4.5 20.7 0.5
OD1 J:ASP63 4.5 34.6 1.0
CD1 J:TRP48 4.5 24.9 1.0
CE1 J:HIS44 4.7 27.0 1.0
CG J:ASP63 4.8 28.8 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 Sep 3 16:54:19 2020
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