Sodium in PDB 2bdg: Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine

The structure of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine, PDB code: 2bdg was solved by M.Debela, W.Bode, P.Goettig, Structural Proteomics In Europe (Spine), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 1.95
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	95.680, 95.680, 38.800, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 22.5

The structure of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine (pdb code 2bdg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine, PDB code: 2bdg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:17.9 occ:1.00 O A:LEU99 2.8 17.9 1.0 O A:HOH412 2.8 13.6 1.0 OG A:SER214 2.9 13.3 1.0 CG A:MET180 3.5 12.5 1.0 CB A:ASP102 3.6 13.2 1.0 CB A:SER214 3.7 13.1 1.0 CE2 A:PHE215 3.8 15.3 1.0 CE A:MET180 3.8 11.6 1.0 C A:LEU99 3.9 12.3 1.0 CD2 A:PHE215 4.0 18.8 1.0 SD A:MET180 4.3 13.7 1.0 CA A:ALA100 4.3 12.9 1.0 OD2 A:ASP102 4.4 15.4 1.0 N A:ASP102 4.4 13.6 1.0 CB A:MET180 4.5 12.1 1.0 CG1 A:VAL227 4.5 15.6 1.0 CG A:ASP102 4.5 15.2 1.0 N A:ALA100 4.6 13.9 1.0 C A:ALA100 4.7 12.7 1.0 OG1 A:THR229 4.7 14.2 1.0 CA A:ASP102 4.7 14.7 1.0 N A:ASN101 4.7 11.3 1.0 O A:SER179 4.8 12.8 1.0 CB A:LEU99 4.9 15.9 1.0 CA A:THR229 5.0 13.1 1.0 CA A:LEU99 5.0 15.5 1.0

Sodium binding site 2 out of 2 in the Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Kallikrein 4 Complex with Nickel and P-Aminobenzamidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:17.6 occ:1.00 OD1 A:ASN230 2.6 16.0 1.0 N A:CYS232 2.9 14.3 1.0 O A:GLN210 2.9 11.2 1.0 OE1 A:GLN210 2.9 16.8 1.0 N A:LEU231 3.2 11.5 1.0 SG A:CYS232 3.3 18.8 1.0 CB A:CYS232 3.3 16.9 1.0 C A:ASN230 3.5 12.7 1.0 CD A:PRO129 3.6 20.5 1.0 CG A:PRO129 3.6 18.4 1.0 CA A:CYS232 3.7 15.6 1.0 CG A:ASN230 3.7 13.2 1.0 CD A:GLN210 3.8 15.6 1.0 CA A:ASN230 3.8 11.9 1.0 C A:LEU231 3.8 13.3 1.0 CG A:GLN210 3.9 14.3 1.0 CA A:LEU231 3.9 13.0 1.0 C A:GLN210 3.9 12.0 1.0 O A:ASN230 4.2 12.2 1.0 CE2 A:PHE181 4.3 13.2 1.0 CB A:ASN230 4.4 11.7 1.0 CA A:GLN210 4.4 12.3 1.0 CB A:LEU231 4.4 11.7 1.0 N A:PRO129 4.5 19.0 1.0 CD2 A:PHE181 4.5 11.4 1.0 CA A:CYS128 4.6 19.2 1.0 O A:GLN127 4.6 16.5 1.0 CB A:GLN210 4.7 13.2 1.0 ND2 A:ASN230 4.8 12.7 1.0 C A:CYS232 4.8 15.9 1.0 O A:THR229 4.8 10.1 1.0 N A:LYS233 4.9 15.0 1.0 O A:LEU231 5.0 14.7 1.0

M.Debela, V.Magdolen, V.Grimminger, C.Sommerhoff, A.Messerschmidt, R.Huber, R.Friedrich, W.Bode, P.Goettig. Crystal Structures of Human Tissue Kallikrein 4: Activity Modulation By A Specific Zinc Binding Site. J.Mol.Biol. V. 362 1094 2006.
ISSN: ISSN 0022-2836
PubMed: 16950394
DOI: 10.1016/J.JMB.2006.08.003