Magnesium in PDB 6cxo: Complement Component-9

Protein crystallography data

The structure of Complement Component-9, PDB code: 6cxo was solved by R.H.P.Law, B.A.Spicer, T.T.Caradoc-Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.74 / 2.20
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 52.588, 149.213, 165.827, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.1

Other elements in 6cxo:

The structure of Complement Component-9 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complement Component-9 (pdb code 6cxo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complement Component-9, PDB code: 6cxo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6cxo

Go back to Magnesium Binding Sites List in 6cxo
Magnesium binding site 1 out of 2 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complement Component-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:71.2
occ:1.00
O A:ASN212 1.9 71.0 1.0
O A:SER209 2.3 73.0 1.0
O A:HOH770 2.3 55.3 1.0
O A:HOH743 2.6 55.7 1.0
O A:ASP214 2.6 66.8 1.0
C A:ASN212 3.1 71.6 1.0
C A:SER209 3.4 72.5 1.0
C A:ASP214 3.7 68.5 1.0
CA A:ASN212 4.0 67.3 1.0
CB A:ASN212 4.0 66.1 1.0
C A:ALA213 4.0 73.4 1.0
O A:ALA213 4.1 74.5 1.0
O A:ALA216 4.1 52.1 1.0
N A:ALA213 4.2 69.4 1.0
N A:ASN212 4.2 67.7 1.0
ND2 A:ASN204 4.2 83.2 1.0
N A:ALA216 4.3 53.3 1.0
CA A:SER209 4.3 68.2 1.0
OD1 A:ASN204 4.3 86.6 1.0
N A:ASP214 4.3 67.4 1.0
CB A:SER209 4.4 70.9 1.0
N A:ASN210 4.4 68.8 1.0
ND2 A:ASN212 4.4 52.2 1.0
CA A:ALA213 4.5 69.7 1.0
N A:PHE215 4.5 63.8 1.0
CA A:PHE215 4.5 62.8 1.0
CA A:ASN210 4.5 68.3 1.0
CG A:ASN212 4.6 75.4 1.0
CA A:ASP214 4.6 66.6 1.0
CG A:ASN204 4.8 92.9 1.0
C A:ASN210 4.8 71.6 1.0
O A:ILE140 4.8 54.1 1.0
O A:ASN210 4.9 70.8 1.0
C A:PHE215 5.0 59.6 1.0
C A:ALA216 5.0 54.4 1.0

Magnesium binding site 2 out of 2 in 6cxo

Go back to Magnesium Binding Sites List in 6cxo
Magnesium binding site 2 out of 2 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complement Component-9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:94.4
occ:1.00
ND2 B:ASN204 2.8 72.2 0.5
OD1 B:ASN204 3.0 85.5 0.5
CG B:ASN204 3.3 86.9 0.5
O B:ASP214 3.4 66.8 0.5
CD1 B:PHE215 4.1 75.4 1.0
CA B:PHE215 4.2 64.4 1.0
O B:ALA216 4.3 51.4 1.0
N B:ALA216 4.4 54.4 1.0
C B:ASP214 4.4 67.6 0.5
CE1 B:PHE215 4.5 76.9 1.0
CD2 B:LEU217 4.5 57.5 1.0
C B:PHE215 4.6 62.6 1.0
N B:PHE215 4.8 64.5 1.0
CB B:ASN204 4.8 70.2 1.0
CG B:LEU217 4.8 52.7 1.0
CG B:PHE215 4.9 71.0 1.0

Reference:

B.A.Spicer, R.H.P.Law, T.T.Caradoc-Davies, S.M.Ekkel, C.Bayly-Jones, S.S.Pang, P.J.Conroy, G.Ramm, M.Radjainia, H.Venugopal, J.C.Whisstock, M.A.Dunstone. The First Transmembrane Region of Complement Component-9 Acts As A Brake on Its Self-Assembly. Nat Commun V. 9 3266 2018.
ISSN: ESSN 2041-1723
PubMed: 30111885
DOI: 10.1038/S41467-018-05717-0
Page generated: Mon Dec 14 22:32:55 2020

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