Zinc in PDB 4d9q: Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D

The structure of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D, PDB code: 4d9q was solved by J.M.Murray, C.Wiesmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.38 / 2.28
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	182.330, 80.760, 142.630, 90.00, 107.19, 90.00
R / Rfree (%)	18.9 / 23

The binding sites of Zinc atom in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D (pdb code 4d9q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D, PDB code: 4d9q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:0.4 occ:1.00 OD1 A:ASP61 2.5 89.7 1.0 NE2 A:HIS57 2.6 66.0 1.0 CD2 A:HIS57 3.3 65.7 1.0 CE1 A:HIS57 3.4 65.4 1.0 CG A:ASP61 3.5 82.0 1.0 OD2 A:ASP61 3.7 81.4 1.0 CG A:HIS57 4.3 61.9 1.0 ND1 A:HIS57 4.3 64.9 1.0 CB A:ASP61 4.8 70.0 1.0

Zinc binding site 2 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:36.1 occ:1.00 OE2 B:GLU131 2.1 26.1 1.0 CD B:GLU131 2.7 35.2 1.0 OE1 B:GLU131 2.7 23.8 1.0 CG B:GLU131 4.2 34.5 1.0 O B:HOH428 4.2 35.7 1.0 O B:HOH412 4.6 69.5 1.0 O B:HOH439 4.7 63.4 1.0

Zinc binding site 3 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn303 b:33.4 occ:1.00 O D:ASP1 2.3 26.8 1.0 CB D:ASP1 2.4 29.5 1.0 CA D:ASP1 2.8 26.4 1.0 C D:ASP1 2.9 28.2 1.0 N D:ASP1 2.9 25.5 1.0 CG D:ASP1 3.5 48.7 1.0 OD2 D:ASP1 3.6 58.2 1.0 O E:HOH461 4.2 44.8 1.0 N D:ILE2 4.2 26.9 1.0 O D:HOH528 4.4 45.3 1.0 O D:HOH491 4.4 43.1 1.0 OD1 D:ASP1 4.7 56.1 1.0

Zinc binding site 4 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn304 b:83.2 occ:1.00 NE2 E:HIS172 2.1 46.5 1.0 OD1 D:ASN138 2.5 62.4 1.0 ND2 D:ASN138 2.7 74.5 1.0 CE1 E:HIS172 3.0 45.9 1.0 CG D:ASN138 3.0 72.1 1.0 CD2 E:HIS172 3.3 46.8 1.0 O D:HOH445 3.8 54.7 1.0 O D:HOH418 3.8 38.8 1.0 O E:HOH433 4.1 55.2 1.0 ND1 E:HIS172 4.2 46.2 1.0 CG E:HIS172 4.3 44.1 1.0 ND2 D:ASN137 4.3 60.6 1.0 OD1 D:ASP167 4.4 51.0 1.0 CB D:ASN138 4.5 41.6 1.0 OD2 D:ASP170 4.6 67.0 1.0 OG D:SER174 4.7 37.2 1.0 OD1 D:ASN137 4.7 65.9 1.0 CA E:GLY170 4.8 44.6 1.0 CG D:ASN137 4.8 69.2 1.0 CG D:ASP167 4.9 43.9 1.0 O E:GLY170 4.9 49.7 1.0

Zinc binding site 5 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:73.2 occ:1.00 NE2 H:HIS172 2.2 47.4 1.0 OD1 L:ASN138 2.4 53.5 1.0 ND2 L:ASN138 2.4 65.2 1.0 CG L:ASN138 2.7 63.7 1.0 CE1 H:HIS172 3.0 46.8 1.0 CD2 H:HIS172 3.4 48.1 1.0 O L:HOH500 4.0 39.2 1.0 OD2 L:ASP170 4.2 58.1 1.0 CB L:ASN138 4.2 42.8 1.0 ND1 H:HIS172 4.2 47.5 1.0 O L:HOH429 4.2 50.4 1.0 CG H:HIS172 4.4 46.2 1.0 ND2 L:ASN137 4.4 51.0 1.0 OG1 L:THR172 4.7 43.8 1.0 O H:HOH402 4.8 55.4 1.0 OG L:SER174 4.8 44.3 1.0 OD1 L:ASP167 4.8 46.6 1.0 OD1 L:ASP170 4.8 48.8 1.0 CG L:ASP170 4.9 49.0 1.0 OD1 L:ASN137 4.9 57.4 1.0 CA L:ASN138 4.9 41.6 1.0 CG L:ASN137 5.0 60.8 1.0

Zinc binding site 6 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn301 b:41.7 occ:1.00 OD2 L:ASP28 2.0 30.1 1.0 CG L:ASP28 3.0 25.9 1.0 OD1 L:ASP28 3.3 29.8 1.0 O L:HOH478 4.0 37.1 1.0 O L:HOH513 4.3 45.5 1.0 CB L:ASP28 4.3 18.2 1.0 O L:HOH443 4.4 42.1 1.0 OD1 L:ASP30 4.4 44.8 1.0

Zinc binding site 7 out of 7 in the Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Inhibiting Alternative Pathway Complement Activation By Targeting the Exosite on Factor D within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn302 b:96.4 occ:1.00 OD1 L:ASP32 2.6 36.0 1.0 OD1 L:ASP31 3.0 50.9 1.0 O2 A:GOL302 3.3 78.5 1.0 CG L:ASP32 3.6 37.0 1.0 CG L:ASP31 3.8 48.8 1.0 OD2 L:ASP32 4.0 37.2 1.0 C3 A:GOL302 4.0 78.0 1.0 OD2 L:ASP31 4.0 59.1 1.0 C2 A:GOL302 4.1 79.2 1.0 NZ A:LYS224 4.2 33.1 1.0 O3 A:GOL302 4.2 77.1 1.0 O A:THR170B 4.3 31.9 1.0 O L:HOH438 4.4 24.6 1.0 CA L:GLY50 4.7 30.6 1.0 O L:ASP31 4.7 30.9 1.0 C L:ASP31 4.8 32.0 1.0 CB L:ASP32 4.8 30.5 1.0 N L:ASP32 4.8 28.4 1.0 CA L:ASP32 4.8 27.3 1.0 C L:GLY50 4.9 38.3 1.0

K.J.Katschke, P.Wu, R.Ganesan, R.F.Kelley, M.A.Mathieu, P.E.Hass, J.Murray, D.Kirchhofer, C.Wiesmann, M.Van Lookeren Campagne. Inhibiting Alternative Pathway Complement Activation By Targeting the Factor D Exosite. J.Biol.Chem. V. 287 12886 2012.
ISSN: ISSN 0021-9258
PubMed: 22362762
DOI: 10.1074/JBC.M112.345082