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Cadmium in PDB 3cu7: Human Complement Component 5

Protein crystallography data

The structure of Human Complement Component 5, PDB code: 3cu7 was solved by F.Fredslund, G.R.Andersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 3.11
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 144.260, 144.260, 241.000, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 28.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Human Complement Component 5 (pdb code 3cu7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Human Complement Component 5, PDB code: 3cu7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 3cu7

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Cadmium binding site 1 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2004

b:0.8
occ:0.50
OE1 B:GLU247 2.3 0.7 1.0
OE1 A:GLU247 2.3 0.5 1.0
OE2 B:GLU247 2.3 0.7 1.0
OE2 A:GLU247 2.3 0.8 1.0
CD B:GLU247 2.5 0.1 1.0
CD A:GLU247 2.5 0.3 1.0
CG B:GLU247 3.9 0.6 1.0
CG A:GLU247 3.9 0.1 1.0
OE1 A:GLN298 4.2 0.4 1.0
OE1 B:GLN298 4.2 0.5 1.0
NE2 A:GLN298 4.5 1.0 1.0
NE2 B:GLN298 4.6 0.5 1.0
CB B:GLU247 4.8 0.3 1.0
CB A:GLU247 4.8 0.4 1.0
CD A:GLN298 4.8 0.8 1.0
CD B:GLN298 4.8 0.3 1.0

Cadmium binding site 2 out of 9 in 3cu7

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Cadmium binding site 2 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2005

b:0.8
occ:1.00
OD1 A:ASP471 2.3 0.3 1.0
OE1 A:GLU480 2.3 0.6 1.0
OE2 A:GLU480 2.3 0.6 1.0
NE2 A:HIS473 2.4 0.4 1.0
OD2 A:ASP471 2.4 0.2 1.0
CD A:GLU480 2.6 0.3 1.0
CG A:ASP471 2.7 0.3 1.0
CD2 A:HIS473 2.9 0.4 1.0
CE1 A:HIS473 3.5 0.8 1.0
CG A:GLU480 4.0 0.4 1.0
CB A:ASP471 4.2 0.1 1.0
CG A:HIS473 4.2 0.3 1.0
OD1 A:ASN472 4.4 0.6 1.0
ND1 A:HIS473 4.5 0.2 1.0
CB A:GLU480 4.8 0.6 1.0
CA A:ASP471 4.9 0.5 1.0

Cadmium binding site 3 out of 9 in 3cu7

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Cadmium binding site 3 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2006

b:0.9
occ:1.00
OD2 A:ASP264 2.3 0.5 1.0
ND1 A:HIS753 2.4 0.9 1.0
CE1 A:HIS753 3.1 0.6 1.0
CG A:ASP264 3.3 0.8 1.0
CG A:HIS753 3.5 0.2 1.0
N A:HIS753 3.7 0.1 1.0
OD1 A:ASP264 4.0 1.0 1.0
CB A:HIS753 4.0 0.3 1.0
CA A:LEU752 4.2 0.2 1.0
CD1 A:LEU752 4.2 0.1 1.0
C A:LEU752 4.3 0.2 1.0
NE2 A:HIS753 4.3 0.0 1.0
CB A:ASP264 4.3 0.4 1.0
CA A:HIS753 4.4 0.1 1.0
O A:HIS753 4.5 0.7 1.0
CD2 A:HIS753 4.5 0.7 1.0
OH A:TYR266 4.7 0.9 1.0
N A:LEU752 4.8 0.1 1.0
O A:ARG751 4.8 0.8 1.0
C A:HIS753 4.9 0.3 1.0

Cadmium binding site 4 out of 9 in 3cu7

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Cadmium binding site 4 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2007

b:0.4
occ:1.00
OE1 A:GLU339 2.3 0.5 1.0
OE1 A:GLU764 2.4 1.0 1.0
OE2 A:GLU764 2.9 0.5 1.0
CD A:GLU764 3.0 0.1 1.0
CD A:GLU339 3.3 0.4 1.0
OE2 A:GLU339 3.6 0.7 1.0
NH2 A:ARG766 4.1 0.6 1.0
CG A:GLU764 4.5 0.0 1.0
O A:PRO759 4.6 0.0 1.0
CG A:GLU339 4.7 0.6 1.0
CA A:PRO759 4.8 0.9 1.0
CB A:PRO759 4.9 0.7 1.0

Cadmium binding site 5 out of 9 in 3cu7

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Cadmium binding site 5 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2008

b:0.4
occ:1.00
NE2 A:HIS894 2.3 0.3 1.0
OE2 A:GLU1589 2.3 0.7 1.0
OE1 A:GLU1589 2.4 1.0 1.0
OE1 A:GLN886 2.4 0.8 1.0
CD A:GLU1589 2.7 0.0 1.0
CD2 A:HIS894 3.0 0.5 1.0
CD A:GLN886 3.4 0.3 1.0
CE1 A:HIS894 3.5 0.1 1.0
CB A:ALA1558 3.5 0.3 1.0
CG A:GLN886 4.1 0.8 1.0
CG A:GLU1589 4.2 1.0 1.0
CG A:HIS894 4.3 0.3 1.0
CA A:ALA1558 4.4 0.7 1.0
ND1 A:HIS894 4.5 0.7 1.0
NE2 A:GLN886 4.5 0.0 1.0
CD A:LYS1622 5.0 0.9 1.0

Cadmium binding site 6 out of 9 in 3cu7

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Cadmium binding site 6 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2004

b:0.3
occ:1.00
NE2 B:HIS473 2.3 0.5 1.0
OE1 B:GLU480 2.3 0.3 1.0
OD1 B:ASP471 2.3 1.0 1.0
OE2 B:GLU480 2.3 1.0 1.0
OD2 B:ASP471 2.4 0.2 1.0
CD B:GLU480 2.6 0.4 1.0
CG B:ASP471 2.7 0.1 1.0
CD2 B:HIS473 2.9 0.7 1.0
CE1 B:HIS473 3.5 0.6 1.0
CG B:GLU480 4.0 0.3 1.0
CB B:ASP471 4.2 0.1 1.0
CG B:HIS473 4.2 0.3 1.0
OD1 B:ASN472 4.4 0.9 1.0
ND1 B:HIS473 4.5 0.0 1.0
CB B:GLU480 4.8 0.1 1.0
CA B:ASP471 4.9 0.3 1.0

Cadmium binding site 7 out of 9 in 3cu7

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Cadmium binding site 7 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2005

b:0.8
occ:1.00
OD2 B:ASP264 2.3 0.1 1.0
ND1 B:HIS753 2.4 0.6 1.0
CE1 B:HIS753 3.2 0.9 1.0
CG B:ASP264 3.3 0.1 1.0
CG B:HIS753 3.4 0.7 1.0
CB B:HIS753 3.8 0.7 1.0
N B:HIS753 3.9 0.7 1.0
OD1 B:ASP264 3.9 0.0 1.0
CB B:ASP264 4.2 1.0 1.0
CA B:HIS753 4.3 0.2 1.0
O B:HIS753 4.3 0.7 1.0
NE2 B:HIS753 4.4 0.4 1.0
CD2 B:HIS753 4.5 0.0 1.0
C B:LEU752 4.6 0.5 1.0
CA B:LEU752 4.7 0.9 1.0
C B:HIS753 4.8 0.7 1.0
OH B:TYR266 4.9 0.9 1.0

Cadmium binding site 8 out of 9 in 3cu7

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Cadmium binding site 8 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2006

b:0.2
occ:1.00
OE1 B:GLU339 2.3 0.8 1.0
OE1 B:GLU764 2.4 0.1 1.0
OE2 B:GLU764 2.9 0.7 1.0
CD B:GLU764 3.0 0.7 1.0
CD B:GLU339 3.4 0.7 1.0
OE2 B:GLU339 3.7 0.5 1.0
NH2 B:ARG766 4.0 0.7 1.0
CG B:GLU764 4.5 0.2 1.0
O B:PRO759 4.6 0.7 1.0
CG B:GLU339 4.7 0.0 1.0
CB B:PRO759 4.8 0.2 1.0
CA B:PRO759 4.8 0.1 1.0
CE B:LYS1440 5.0 0.2 1.0

Cadmium binding site 9 out of 9 in 3cu7

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Cadmium binding site 9 out of 9 in the Human Complement Component 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Human Complement Component 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd2007

b:0.4
occ:1.00
NE2 B:HIS894 2.3 0.8 1.0
OE2 A:GLU1666 2.3 0.8 1.0
OE1 A:GLU1666 2.3 0.3 1.0
OE1 B:GLN886 2.4 0.5 1.0
CD2 B:HIS894 2.6 0.4 1.0
CD A:GLU1666 2.7 0.5 1.0
CD B:GLN886 3.2 0.8 1.0
CG B:GLN886 3.6 0.5 1.0
CE1 B:HIS894 3.6 0.8 1.0
CG B:HIS894 3.8 0.7 1.0
CG A:GLU1666 4.2 0.5 1.0
ND1 B:HIS894 4.3 0.9 1.0
NE2 B:GLN886 4.4 0.1 1.0
CB B:GLN886 4.9 0.9 1.0
CB A:GLU1666 5.0 0.7 1.0

Reference:

F.Fredslund, N.S.Laursen, P.Roversi, L.Jenner, C.L.P.Oliveira, J.S.Pedersen, M.A.Nunn, S.M.Lea, R.Discipio, L.Sottrup-Jensen, G.R.Andersen. Structure of and Influence of A Tick Complement Inhibitor on Human Complement Component 5 Nat.Immunol. V. 9 753 2008.
ISSN: ISSN 1529-2908
PubMed: 18536718
DOI: 10.1038/NI.1625
Page generated: Fri Aug 28 13:32:21 2020
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