Magnesium in PDB 3hs0: Cobra Venom Factor (Cvf) in Complex with Human Factor B

All present enzymatic activity of Cobra Venom Factor (Cvf) in Complex with Human Factor B:
3.4.21.47;

The structure of Cobra Venom Factor (Cvf) in Complex with Human Factor B, PDB code: 3hs0 was solved by B.J.C.Janssen, L.Gomes, R.I.Koning, D.I.Svergun, A.J.Koster, D.C.Fritzinger, C.-W.Vogel, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	134.026, 136.975, 283.740, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24.3

The binding sites of Magnesium atom in the Cobra Venom Factor (Cvf) in Complex with Human Factor B (pdb code 3hs0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cobra Venom Factor (Cvf) in Complex with Human Factor B, PDB code: 3hs0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cobra Venom Factor (Cvf) in Complex with Human Factor B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cobra Venom Factor (Cvf) in Complex with Human Factor B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg628 b:0.5 occ:1.00 O A:VAL518 2.1 45.9 1.0 O A:HOH630 2.1 45.0 1.0 O A:HOH629 2.1 46.9 1.0 OD1 A:ASP517 2.1 71.0 1.0 OD1 A:ASP520 2.1 67.9 1.0 O A:PRO494 2.1 55.8 1.0 CG A:ASP520 3.1 62.3 1.0 C A:PRO494 3.2 47.7 1.0 CG A:ASP517 3.2 68.9 1.0 C A:VAL518 3.2 47.5 1.0 N A:VAL518 3.5 40.1 1.0 OD2 A:ASP520 3.6 66.2 1.0 CA A:PRO494 3.7 50.3 1.0 OD2 A:ASP517 3.8 72.3 1.0 CB A:PRO494 3.9 47.0 1.0 CA A:VAL518 3.9 44.1 1.0 N A:ASP520 4.1 64.3 1.0 N A:LYS519 4.3 48.3 1.0 N A:SER495 4.3 39.9 1.0 C A:ASP517 4.4 46.5 1.0 CB A:ASP520 4.4 46.6 1.0 CB A:ASP517 4.4 58.2 1.0 CA A:ASP517 4.5 48.9 1.0 C A:LYS519 4.5 61.9 1.0 OE2 A:GLU581 4.6 86.3 1.0 CA A:LYS519 4.6 55.6 1.0 CA A:ASP520 4.6 55.3 1.0 CB A:VAL518 4.6 41.7 1.0 CB A:SER495 4.6 53.9 1.0 CA A:SER495 4.8 49.6 1.0

Magnesium binding site 2 out of 4 in the Cobra Venom Factor (Cvf) in Complex with Human Factor B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cobra Venom Factor (Cvf) in Complex with Human Factor B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg742 b:0.6 occ:1.00 OXT C:THR1620 2.1 80.2 1.0 OG1 D:THR328 2.1 55.6 1.0 OG D:SER255 2.1 56.8 1.0 O D:HOH743 2.1 62.2 1.0 O C:HOH32 2.1 62.4 1.0 OG D:SER253 2.1 96.1 1.0 CB D:SER253 2.9 91.6 1.0 C C:THR1620 3.1 91.8 1.0 CB D:SER255 3.1 66.9 1.0 CB D:THR328 3.3 57.4 1.0 O C:THR1620 3.4 92.1 1.0 CG2 D:THR328 3.6 48.1 1.0 N D:SER255 4.0 77.8 1.0 OD2 D:ASP364 4.1 69.8 1.0 CA D:SER255 4.1 72.8 1.0 CA D:SER253 4.2 84.3 1.0 O D:LEU366 4.4 69.7 1.0 OD2 D:ASP251 4.4 75.4 1.0 OD1 D:ASP364 4.4 74.1 1.0 CA C:THR1620 4.4 0.3 1.0 CA D:THR328 4.4 62.6 1.0 OD1 D:ASP251 4.4 91.0 1.0 C D:SER253 4.5 82.2 1.0 N D:GLY254 4.7 84.6 1.0 CG D:ASP364 4.7 73.9 1.0 N D:THR328 4.7 73.2 1.0 CB C:THR1620 4.8 1.0 1.0 O D:GLY327 4.8 84.7 1.0 N D:SER253 4.9 82.6 1.0 CG D:ASP251 4.9 81.7 1.0 C D:GLY327 4.9 84.7 1.0 C D:SER255 4.9 75.3 1.0 CB D:LEU366 4.9 60.6 1.0 O D:SER253 5.0 75.3 1.0

Magnesium binding site 3 out of 4 in the Cobra Venom Factor (Cvf) in Complex with Human Factor B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cobra Venom Factor (Cvf) in Complex with Human Factor B within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg628 b:73.4 occ:1.00 O F:HOH630 2.1 44.8 1.0 O F:VAL518 2.1 70.6 1.0 O F:HOH629 2.1 99.3 1.0 OD1 F:ASP520 2.1 82.5 1.0 OD1 F:ASP517 2.1 93.7 1.0 O F:PRO494 2.1 69.0 1.0 CG F:ASP520 3.1 76.9 1.0 C F:PRO494 3.2 56.7 1.0 C F:VAL518 3.2 71.7 1.0 CG F:ASP517 3.2 85.7 1.0 N F:VAL518 3.4 64.5 1.0 OD2 F:ASP520 3.4 82.2 1.0 OD2 F:ASP517 3.7 81.1 1.0 CA F:PRO494 3.8 52.9 1.0 CA F:VAL518 3.9 68.5 1.0 N F:ASP520 4.0 70.8 1.0 CB F:PRO494 4.1 48.6 1.0 N F:LYS519 4.3 74.3 1.0 N F:SER495 4.3 53.0 1.0 CB F:ASP520 4.3 60.2 1.0 C F:ASP517 4.3 69.0 1.0 CB F:ASP517 4.5 81.3 1.0 CB F:VAL518 4.5 64.8 1.0 C F:LYS519 4.5 76.0 1.0 CA F:ASP520 4.5 61.2 1.0 CA F:ASP517 4.6 71.9 1.0 OE2 F:GLU581 4.6 95.3 1.0 CA F:LYS519 4.6 79.3 1.0 CB F:SER495 4.7 67.1 1.0 CA F:SER495 4.7 61.6 1.0

Magnesium binding site 4 out of 4 in the Cobra Venom Factor (Cvf) in Complex with Human Factor B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cobra Venom Factor (Cvf) in Complex with Human Factor B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg742 b:97.5 occ:1.00 OXT H:THR1620 2.1 84.8 1.0 O I:HOH743 2.1 48.0 1.0 O H:HOH32 2.1 55.6 1.0 OG I:SER255 2.1 63.9 1.0 OG I:SER253 2.1 83.8 1.0 OG1 I:THR328 2.1 56.2 1.0 CB I:SER253 2.9 82.0 1.0 C H:THR1620 3.1 87.3 1.0 CB I:SER255 3.1 72.7 1.0 CB I:THR328 3.3 58.4 1.0 O H:THR1620 3.4 85.2 1.0 CG2 I:THR328 3.6 39.9 1.0 N I:SER255 3.9 79.2 1.0 CA I:SER255 4.1 81.0 1.0 CA I:SER253 4.2 80.8 1.0 OD2 I:ASP364 4.3 71.7 1.0 O I:LEU366 4.3 60.9 1.0 CA H:THR1620 4.4 89.4 1.0 C I:SER253 4.4 81.1 1.0 CA I:THR328 4.4 61.8 1.0 OD2 I:ASP251 4.5 75.1 1.0 OD1 I:ASP251 4.5 89.4 1.0 N I:GLY254 4.5 76.8 1.0 OD1 I:ASP364 4.6 75.4 1.0 CB H:THR1620 4.8 92.2 1.0 N I:THR328 4.8 69.8 1.0 CG I:ASP364 4.8 75.2 1.0 N I:ILE256 4.8 87.8 1.0 N I:SER253 4.9 75.6 1.0 O I:GLY327 4.9 81.9 1.0 C I:SER255 4.9 88.7 1.0 O I:SER253 4.9 79.9 1.0 CG I:ASP251 5.0 84.0 1.0 CB I:LEU366 5.0 50.3 1.0 C I:GLY327 5.0 77.3 1.0

B.J.Janssen, L.Gomes, R.I.Koning, D.I.Svergun, A.J.Koster, D.C.Fritzinger, C.W.Vogel, P.Gros. Insights Into Complement Convertase Formation Based on the Structure of the Factor B-Cobra Venom Factor Complex Embo J. V. 28 2469 2009.
ISSN: ISSN 0261-4189
PubMed: 19574954
DOI: 10.1038/EMBOJ.2009.184