Calcium in PDB 3k7n: Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins

The structure of Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins, PDB code: 3k7n was solved by H.H.Guan, Y.W.Huang, W.G.Wu, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.999, 62.999, 273.265, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 24.1

The structure of Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins (pdb code 3k7n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins, PDB code: 3k7n:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:40.8 occ:1.00 O A:CYS395 2.2 44.4 1.0 O A:HOH23 2.3 36.5 1.0 OE1 A:GLU208 2.3 40.9 1.0 O A:HOH16 2.4 41.2 1.0 OD1 A:ASP292 2.5 37.9 1.0 ND2 A:ASN398 2.5 33.9 1.0 OD2 A:ASP292 2.5 36.3 1.0 CG A:ASP292 2.9 37.4 1.0 CD A:GLU208 3.4 41.2 1.0 C A:CYS395 3.4 45.5 1.0 CG A:ASN398 3.6 44.5 1.0 CG A:GLU208 3.8 38.6 1.0 OD1 A:ASN398 3.9 44.7 1.0 CA A:CYS395 4.1 49.7 1.0 CB A:CYS395 4.2 57.0 1.0 CB A:GLU208 4.3 38.0 1.0 N A:ILE396 4.4 43.4 1.0 CB A:ASP292 4.4 35.4 1.0 O A:TYR206 4.4 42.5 1.0 OE2 A:GLU208 4.5 47.9 1.0 CA A:ILE396 4.5 43.2 1.0 O A:ASN398 4.6 45.9 1.0 SG A:CYS395 4.6 65.5 1.0 N A:GLU208 4.6 37.0 1.0 O A:HOH26 4.8 60.9 1.0 CB A:ASN398 4.9 45.0 1.0 N A:ASN398 5.0 42.7 1.0

Calcium binding site 2 out of 3 in the Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:37.8 occ:1.00 O A:PHE415 2.3 40.2 1.0 OD2 A:ASP423 2.3 41.6 1.0 OE1 A:GLU420 2.4 35.2 1.0 OE1 A:GLU417 2.4 36.9 1.0 O A:ILE410 2.5 45.1 1.0 ND2 A:ASN413 2.5 35.4 1.0 OE2 A:GLU420 2.6 37.1 1.0 CD A:GLU420 2.9 34.6 1.0 CD A:GLU417 3.4 40.1 1.0 C A:ILE410 3.4 45.6 1.0 CG A:ASP423 3.4 43.6 1.0 C A:PHE415 3.5 41.4 1.0 CG A:ASN413 3.5 40.3 1.0 CB A:ASP423 3.9 44.8 1.0 N A:ILE410 4.0 42.5 1.0 OD1 A:ASN413 4.1 40.5 1.0 CG A:GLU417 4.1 36.3 1.0 N A:PHE415 4.2 41.8 1.0 CA A:CYS411 4.2 47.6 1.0 N A:GLU417 4.2 34.4 1.0 N A:CYS411 4.2 46.0 1.0 OE2 A:GLU417 4.3 38.5 1.0 CB A:GLU417 4.3 34.5 1.0 CA A:ILE410 4.3 42.8 1.0 N A:ASN413 4.3 41.1 1.0 N A:GLY412 4.3 43.5 1.0 CG A:GLU420 4.4 37.5 1.0 CA A:PHE415 4.4 40.8 1.0 N A:VAL416 4.5 39.9 1.0 OD1 A:ASP423 4.5 37.6 1.0 CA A:VAL416 4.5 39.0 1.0 CB A:ASN413 4.6 39.2 1.0 C A:VAL416 4.7 38.5 1.0 C A:CYS411 4.7 46.5 1.0 N A:TYR414 4.8 40.2 1.0 CA A:ASN413 4.8 40.0 1.0 CB A:PHE415 4.9 40.9 1.0 CB A:ILE410 4.9 41.7 1.0 C A:ASN413 4.9 40.7 1.0 CA A:GLU417 4.9 35.7 1.0

Calcium binding site 3 out of 3 in the Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:46.1 occ:1.00 OD1 A:ASP472 2.2 43.7 1.0 O A:LEU458 2.2 48.6 1.0 O A:SER473 2.4 40.0 1.0 OD2 A:ASP457 2.6 47.2 1.0 OE2 A:GLU460 2.7 47.7 1.0 OE1 A:GLU460 2.7 47.7 1.0 CD A:GLU460 3.1 46.3 1.0 C A:LEU458 3.4 48.3 1.0 CG A:ASP472 3.4 43.2 1.0 C A:SER473 3.6 42.1 1.0 CG A:ASP457 3.6 49.8 1.0 N A:SER473 3.7 43.7 1.0 N A:LEU458 3.8 48.5 1.0 CA A:ASP472 4.0 48.0 1.0 CA A:LEU458 4.0 48.4 1.0 OD1 A:ASP457 4.1 45.4 1.0 C A:ASP472 4.1 48.5 1.0 OD2 A:ASP472 4.2 42.6 1.0 CA A:SER473 4.3 43.0 1.0 CB A:ASP472 4.3 41.7 1.0 O A:HOH72 4.3 43.9 1.0 N A:PRO459 4.5 50.7 1.0 CB A:LEU458 4.5 52.1 1.0 N A:GLU460 4.5 40.6 1.0 CD A:ARG450 4.6 42.0 1.0 C A:PRO459 4.6 47.1 1.0 CG A:GLU460 4.6 45.3 1.0 CA A:PRO459 4.6 49.3 1.0 N A:LEU474 4.7 41.9 1.0 C A:ASP457 4.8 49.8 1.0 CB A:SER473 4.9 51.1 1.0 CB A:ASP457 4.9 47.3 1.0 CA A:LEU474 5.0 41.5 1.0 CD2 A:LEU474 5.0 39.3 1.0 O A:ASP472 5.0 49.4 1.0

H.H.Guan, K.S.Goh, F.Davamani, P.L.Wu, Y.W.Huang, J.Jeyakanthan, W.G.Wu, C.J.Chen. Structures of Two Elapid Snake Venom Metalloproteases with Distinct Activities Highlight the Disulfide Patterns in the D Domain of Adamalysin Family Proteins J.Struct.Biol. V. 169 294 2010.
ISSN: ISSN 1047-8477
PubMed: 19932752
DOI: 10.1016/J.JSB.2009.11.009