Magnesium in PDB 3hrz: 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: 3hrz 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)	33.49 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	128.890, 283.390, 134.400, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 22.6

The structure of Cobra Venom Factor (Cvf) in Complex with Human Factor B also contains other interesting chemical elements:

Potassium

(K)

1 atom

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

Magnesium binding site 1 out of 2 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:27.6 occ:1.00 O A:HOH631 2.1 39.4 1.0 O A:HOH633 2.1 36.5 1.0 O A:VAL518 2.1 26.4 1.0 O A:PRO494 2.1 29.5 1.0 OD1 A:ASP520 2.1 37.4 1.0 OD1 A:ASP517 2.1 35.1 1.0 CG A:ASP520 3.1 36.1 1.0 C A:PRO494 3.2 28.1 1.0 C A:VAL518 3.3 31.1 1.0 CG A:ASP517 3.3 31.6 1.0 N A:VAL518 3.5 27.1 1.0 OD2 A:ASP520 3.6 40.1 1.0 CA A:PRO494 3.7 25.7 1.0 CB A:PRO494 3.8 25.1 1.0 OD2 A:ASP517 3.8 38.4 1.0 CA A:VAL518 4.0 25.3 1.0 N A:ASP520 4.0 33.8 1.0 O A:HOH661 4.2 31.3 1.0 CB A:ASP520 4.3 35.5 1.0 N A:LYS519 4.3 27.6 1.0 N A:SER495 4.4 31.8 1.0 C A:LYS519 4.4 31.0 1.0 CA A:ASP520 4.4 36.9 1.0 C A:ASP517 4.4 27.8 1.0 CB A:ASP517 4.5 24.9 1.0 OE2 A:GLU581 4.5 50.3 1.0 CA A:LYS519 4.6 28.8 1.0 CA A:ASP517 4.6 23.9 1.0 CB A:VAL518 4.7 30.6 1.0 CB A:SER495 4.8 22.5 1.0 O A:HOH779 4.8 45.6 1.0 CA A:SER495 4.8 24.9 1.0

Magnesium binding site 2 out of 2 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:29.6 occ:1.00 O D:HOH746 2.1 27.1 1.0 OG1 D:THR328 2.1 25.3 1.0 OXT C:THR1620 2.1 38.6 1.0 OG D:SER255 2.1 32.1 1.0 O D:HOH747 2.1 26.9 1.0 OG D:SER253 2.1 29.6 1.0 CB D:SER253 3.0 25.5 1.0 C C:THR1620 3.1 36.9 1.0 CB D:SER255 3.1 31.1 1.0 CB D:THR328 3.3 25.7 1.0 O C:THR1620 3.4 35.2 1.0 CG2 D:THR328 3.6 23.4 1.0 N D:SER255 3.8 30.7 1.0 CA D:SER255 4.1 32.3 1.0 OD1 D:ASP251 4.1 31.2 1.0 O D:LEU366 4.2 27.3 1.0 OD2 D:ASP364 4.2 34.5 1.0 OD2 D:ASP251 4.3 29.6 1.0 OD1 D:ASP364 4.3 26.3 1.0 CA D:SER253 4.3 27.8 1.0 O C:HOH410 4.4 32.9 1.0 CA C:THR1620 4.4 37.4 1.0 CA D:THR328 4.5 30.9 1.0 C D:SER253 4.5 27.3 1.0 N D:GLY254 4.6 28.6 1.0 CG D:ASP251 4.7 28.8 1.0 CG D:ASP364 4.7 32.9 1.0 CB C:THR1620 4.8 45.3 1.0 N D:THR328 4.8 29.2 1.0 N D:ILE256 4.8 34.0 1.0 C D:SER255 4.9 33.8 1.0 O D:GLY327 4.9 26.3 1.0 ND2 D:ASN368 5.0 28.9 1.0 CB D:LEU366 5.0 25.6 1.0 C D:GLY327 5.0 27.8 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