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Cadmium in PDB 3kls: Structure of Complement C5 in Complex with SSL7

Protein crystallography data

The structure of Structure of Complement C5 in Complex with SSL7, PDB code: 3kls was solved by N.S.Laursen, N.Gordon, S.Hermans, N.Lorenz, N.Jackson, B.Wines, E.Spillner, J.B.Christensen, M.Jensen, F.Fredslund, M.Bjerre, L.Sottrup-Jensen, J.D.Fraser, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.05 / 3.60
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 143.875, 143.875, 241.240, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 26.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Complement C5 in Complex with SSL7 (pdb code 3kls). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Structure of Complement C5 in Complex with SSL7, PDB code: 3kls:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3kls

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Cadmium binding site 1 out of 9 in the Structure of Complement C5 in Complex with SSL7


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1677

b:0.2
occ:0.50
OE2 B:GLU247 2.3 72.3 1.0
OE2 A:GLU247 2.4 77.7 1.0
CD A:GLU247 2.7 84.1 1.0
CD B:GLU247 3.0 88.1 1.0
CG B:GLU247 3.3 0.6 1.0
OE1 A:GLU247 3.3 79.9 1.0
CG A:GLU247 3.5 0.6 1.0
NE2 B:GLN298 3.8 0.6 1.0
OE1 B:GLN298 3.9 1.0 1.0
OE1 A:GLN298 3.9 0.4 1.0
OE1 B:GLU247 4.0 80.6 1.0
NE2 A:GLN298 4.1 0.3 1.0
CB B:GLU247 4.2 0.9 1.0
CD B:GLN298 4.3 0.7 1.0
CB A:GLU247 4.4 0.3 1.0
CD A:GLN298 4.4 0.4 1.0

Cadmium binding site 2 out of 9 in 3kls

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Cadmium binding site 2 out of 9 in the Structure of Complement C5 in Complex with SSL7


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1678

b:0.1
occ:1.00
OE2 A:GLU480 2.4 0.9 1.0
OD2 A:ASP471 2.4 0.0 1.0
OD1 A:ASP471 2.4 0.1 1.0
OE1 A:GLU480 2.4 0.9 1.0
CD A:GLU480 2.7 0.7 1.0
CG A:ASP471 2.7 0.7 1.0
ND1 A:HIS473 3.2 0.7 1.0
CE1 A:HIS473 3.3 0.0 1.0
CG A:HIS473 3.9 1.0 1.0
NE2 A:HIS473 4.0 0.1 1.0
CB A:ASP471 4.3 0.5 1.0
CG A:GLU480 4.3 0.7 1.0
CD2 A:HIS473 4.3 0.0 1.0
O A:ALA475 4.4 0.2 1.0
CB A:HIS473 4.7 0.4 1.0
N A:LEU477 4.9 0.6 1.0
CA A:LEU476 4.9 0.4 1.0
CD1 A:LEU477 4.9 0.3 1.0

Cadmium binding site 3 out of 9 in 3kls

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Cadmium binding site 3 out of 9 in the Structure of Complement C5 in Complex with SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1679

b:0.9
occ:1.00
ND1 A:HIS753 2.4 0.8 1.0
OD2 A:ASP264 2.4 0.8 1.0
CE1 A:HIS753 3.1 0.8 1.0
CG A:HIS753 3.5 0.2 1.0
CG A:ASP264 3.6 0.9 1.0
O A:HIS753 3.8 0.7 1.0
N A:HIS753 3.9 0.2 1.0
CB A:HIS753 3.9 0.3 1.0
OD1 A:ASP264 4.1 0.6 1.0
NE2 A:HIS753 4.3 0.0 1.0
CA A:HIS753 4.3 0.2 1.0
C A:HIS753 4.5 0.4 1.0
CD2 A:HIS753 4.5 0.5 1.0
C A:LEU752 4.7 0.6 1.0
OH A:TYR266 4.7 0.3 1.0
CB A:ASP264 4.7 0.5 1.0
CA A:LEU752 4.8 0.4 1.0

Cadmium binding site 4 out of 9 in 3kls

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Cadmium binding site 4 out of 9 in the Structure of Complement C5 in Complex with SSL7


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1680

b:0.2
occ:1.00
OE2 A:GLU764 2.2 0.7 1.0
OE1 A:GLU764 2.4 0.6 1.0
OE1 A:GLU339 2.4 0.9 1.0
CD A:GLU764 2.6 0.9 1.0
OE2 A:GLU339 3.0 0.8 1.0
CD A:GLU339 3.1 0.5 1.0
NH2 A:ARG766 4.0 0.8 1.0
CG A:GLU764 4.1 0.3 1.0
CG A:GLU339 4.6 0.9 1.0
CB A:GLU764 4.9 0.2 1.0
CB A:PRO759 4.9 0.6 1.0

Cadmium binding site 5 out of 9 in 3kls

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Cadmium binding site 5 out of 9 in the Structure of Complement C5 in Complex with SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1681

b:0.8
occ:1.00
OE2 A:GLU1589 2.4 0.5 1.0
OE1 A:GLU1589 2.4 0.1 1.0
OE1 A:GLN886 2.4 0.8 1.0
NE2 A:HIS894 2.6 0.0 1.0
CD A:GLU1589 2.7 0.7 1.0
CE1 A:HIS894 2.8 0.1 1.0
CD2 A:HIS894 3.2 0.9 1.0
CD A:GLN886 3.3 0.2 1.0
ND1 A:HIS894 3.4 0.2 1.0
CG A:HIS894 3.6 0.8 1.0
CG A:GLN886 3.6 0.3 1.0
CG A:GLU1589 4.2 0.8 1.0
CB A:ALA1558 4.4 0.9 1.0
NE2 A:GLN886 4.5 0.2 1.0
CB A:HIS894 4.8 0.8 1.0

Cadmium binding site 6 out of 9 in 3kls

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Cadmium binding site 6 out of 9 in the Structure of Complement C5 in Complex with SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1677

b:0.6
occ:1.00
OE1 B:GLU480 2.4 0.6 1.0
OD2 B:ASP471 2.4 0.9 1.0
OE2 B:GLU480 2.4 0.2 1.0
OD1 B:ASP471 2.4 0.2 1.0
CD B:GLU480 2.7 0.2 1.0
CG B:ASP471 2.7 0.8 1.0
CE1 B:HIS473 3.0 0.9 1.0
ND1 B:HIS473 3.1 0.4 1.0
NE2 B:HIS473 3.6 0.6 1.0
CG B:HIS473 3.8 0.9 1.0
CD2 B:HIS473 4.1 0.9 1.0
CG B:GLU480 4.2 0.3 1.0
CB B:ASP471 4.3 0.3 1.0
O B:ALA475 4.5 0.1 1.0
CB B:HIS473 4.8 0.7 1.0
N B:LEU477 5.0 0.7 1.0
CD1 B:LEU477 5.0 0.9 1.0

Cadmium binding site 7 out of 9 in 3kls

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Cadmium binding site 7 out of 9 in the Structure of Complement C5 in Complex with SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1678

b:0.7
occ:1.00
OD2 B:ASP264 2.4 0.9 1.0
ND1 B:HIS753 2.4 0.2 1.0
CE1 B:HIS753 3.2 0.6 1.0
CG B:HIS753 3.5 0.5 1.0
CG B:ASP264 3.6 0.5 1.0
O B:HIS753 3.8 0.2 1.0
N B:HIS753 3.9 0.6 1.0
CB B:HIS753 3.9 0.9 1.0
OD1 B:ASP264 4.1 0.1 1.0
CA B:HIS753 4.3 0.2 1.0
NE2 B:HIS753 4.4 0.5 1.0
C B:HIS753 4.4 0.1 1.0
CD2 B:HIS753 4.5 0.3 1.0
OH B:TYR266 4.6 0.3 1.0
C B:LEU752 4.7 0.3 1.0
CB B:ASP264 4.8 0.1 1.0
CA B:LEU752 4.8 0.3 1.0

Cadmium binding site 8 out of 9 in 3kls

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Cadmium binding site 8 out of 9 in the Structure of Complement C5 in Complex with SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1679

b:0.5
occ:1.00
OE2 B:GLU764 2.2 0.8 1.0
OE1 B:GLU339 2.4 0.1 1.0
OE1 B:GLU764 2.4 0.9 1.0
CD B:GLU764 2.6 0.7 1.0
OE2 B:GLU339 2.9 0.6 1.0
CD B:GLU339 3.0 0.6 1.0
NH2 B:ARG766 4.0 0.1 1.0
CG B:GLU764 4.1 0.8 1.0
CG B:GLU339 4.5 0.4 1.0
CB B:GLU764 4.9 0.4 1.0
CB B:PRO759 4.9 0.7 1.0

Cadmium binding site 9 out of 9 in 3kls

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Cadmium binding site 9 out of 9 in the Structure of Complement C5 in Complex with SSL7


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Complement C5 in Complex with SSL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1680

b:0.8
occ:1.00
OE2 A:GLU1666 2.3 0.4 1.0
OE1 A:GLU1666 2.4 0.9 1.0
OE1 B:GLN886 2.4 0.8 1.0
CD A:GLU1666 2.6 0.4 1.0
NE2 B:HIS894 2.7 0.3 1.0
CE1 B:HIS894 2.8 0.6 1.0
CD2 B:HIS894 3.3 0.7 1.0
CD B:GLN886 3.3 0.9 1.0
ND1 B:HIS894 3.4 0.8 1.0
CG B:GLN886 3.5 0.7 1.0
CG B:HIS894 3.6 0.1 1.0
CG A:GLU1666 4.1 0.3 1.0
NE2 B:GLN886 4.5 0.8 1.0
CB A:GLU1666 4.7 0.6 1.0
CB B:HIS894 4.8 0.8 1.0
CA A:GLU1666 4.9 0.7 1.0
CB B:GLN886 5.0 0.1 1.0

Reference:

N.S.Laursen, N.Gordon, S.Hermans, N.Lorenz, N.Jackson, B.Wines, E.Spillner, J.B.Christensen, M.Jensen, F.Fredslund, M.Bjerre, L.Sottrup-Jensen, J.D.Fraser, G.R.Andersen. Structural Basis For Inhibition of Complement C5 By the SSL7 Protein From Staphylococcus Aureus Proc.Natl.Acad.Sci.Usa V. 107 3681 2010.
ISSN: ISSN 0027-8424
PubMed: 20133685
DOI: 10.1073/PNAS.0910565107
Page generated: Fri Aug 28 13:46:23 2020
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