Zinc in PDB 6cxo: Complement Component-9

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

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

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	2 atoms

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

Zinc binding site 1 out of 5 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:0.8 occ:1.00 ND1 A:HIS196 2.8 71.9 1.0 O A:ASP194 3.3 64.7 1.0 N A:HIS196 3.4 63.4 1.0 CE1 A:HIS196 3.6 71.6 1.0 CG A:HIS196 3.7 69.4 1.0 CB A:HIS196 3.9 65.8 1.0 CA A:GLU195 3.9 57.5 1.0 C A:GLU195 4.2 63.7 1.0 CA A:HIS196 4.3 63.9 1.0 C A:ASP194 4.3 62.1 1.0 O A:LYS270 4.4 70.0 1.0 O A:HOH801 4.5 66.9 1.0 N A:GLU195 4.6 57.5 1.0 O A:GLN267 4.6 90.6 1.0 CE1 A:PHE272 4.7 57.0 1.0 O A:SER268 4.7 85.7 1.0 NE2 A:HIS196 4.7 71.4 1.0 CD2 A:HIS196 4.8 71.0 1.0 CA A:SER268 4.8 86.6 1.0 CB A:GLU195 4.9 58.5 1.0

Zinc binding site 2 out of 5 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn606 b:0.3 occ:1.00 ND2 A:ASN362 3.2 0.8 1.0 ND1 A:HIS357 3.4 87.0 1.0 CE1 A:PHE361 3.7 1.0 1.0 CA A:HIS357 3.9 74.5 1.0 CB A:HIS357 4.1 77.6 1.0 CG A:HIS357 4.2 84.1 1.0 CD1 A:PHE361 4.3 0.0 1.0 CE1 A:HIS357 4.3 88.2 1.0 CG A:ASN362 4.4 0.7 1.0 CZ A:PHE361 4.7 0.3 1.0 N A:HIS357 4.8 71.4 1.0 O A:HIS357 4.8 76.7 1.0 C A:HIS357 4.9 78.0 1.0

Zinc binding site 3 out of 5 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:0.1 occ:1.00 O B:HOH733 2.5 60.8 1.0 ND1 B:HIS196 3.0 72.4 1.0 O B:HOH883 3.1 64.7 1.0 O B:ASP194 3.2 66.8 1.0 O B:HOH843 3.9 67.4 1.0 CE1 B:HIS196 3.9 72.0 1.0 N B:HIS196 3.9 65.2 1.0 CG B:HIS196 4.0 70.0 1.0 O B:LYS270 4.2 61.5 1.0 CB B:HIS196 4.2 66.5 1.0 C B:ASP194 4.4 64.2 1.0 O B:GLN267 4.5 70.3 1.0 CA B:GLU195 4.6 61.9 1.0 CE1 B:PHE272 4.7 50.0 1.0 CA B:HIS196 4.7 65.0 1.0 C B:GLU195 4.8 66.8 1.0 N B:LYS270 4.8 61.1 1.0 N B:GLU195 4.9 61.5 1.0 CB B:LYS270 5.0 60.0 1.0

Zinc binding site 4 out of 5 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn606 b:0.6 occ:1.00 ND1 B:HIS357 2.8 79.8 1.0 ND2 B:ASN362 3.1 0.8 1.0 CE1 B:HIS357 3.6 80.7 1.0 CG B:ASN362 3.8 0.0 1.0 CE1 B:PHE361 3.9 99.6 1.0 O B:HOH831 3.9 88.0 1.0 OD1 B:ASN362 3.9 0.1 1.0 CG B:HIS357 4.0 77.6 1.0 CB B:HIS357 4.3 72.1 1.0 CA B:HIS357 4.4 70.0 1.0 CD1 B:PHE361 4.6 98.3 1.0 CZ B:PHE361 4.7 98.1 1.0 NE2 B:HIS357 4.8 81.7 1.0

Zinc binding site 5 out of 5 in the Complement Component-9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complement Component-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn607 b:99.2 occ:1.00 ND1 B:HIS525 2.7 94.5 1.0 CG B:HIS525 3.2 92.4 1.0 CB B:HIS525 3.3 88.5 1.0 CE1 B:HIS525 3.7 93.8 1.0 O B:HOH867 3.9 67.6 1.0 CD2 B:HIS525 4.3 94.4 1.0 NE2 B:HIS525 4.6 94.1 1.0 CA B:HIS525 4.7 86.4 1.0 CE1 B:PHE517 4.9 83.0 1.0

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