Calcium in PDB 9clp: Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11

The structure of Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11 (pdb code 9clp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11, PDB code: 9clp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:90.4 occ:1.00 O A:VAL407 2.3 84.8 1.0 O A:ILE412 2.4 80.3 1.0 OE2 A:GLU417 2.4 93.6 1.0 OD2 A:ASP420 2.5 94.6 1.0 OD1 A:ASN410 2.5 81.7 1.0 OE1 A:GLU414 2.5 84.8 1.0 CG A:ASP420 2.9 94.6 1.0 CD A:GLU417 3.2 93.6 1.0 OE1 A:GLU417 3.3 93.6 1.0 OD1 A:ASP420 3.4 94.6 1.0 C A:VAL407 3.5 84.8 1.0 CD A:GLU414 3.5 84.8 1.0 CG A:ASN410 3.5 81.7 1.0 C A:ILE412 3.6 80.3 1.0 CB A:ASP420 3.8 94.6 1.0 OE2 A:GLU414 3.8 84.8 1.0 ND2 A:ASN410 4.0 81.7 1.0 N A:ILE412 4.2 80.3 1.0 N A:VAL407 4.2 84.8 1.0 CA A:CYS408 4.2 94.0 1.0 N A:CYS408 4.3 94.0 1.0 CA A:ILE412 4.3 80.3 1.0 N A:GLY409 4.5 88.5 1.0 N A:ASN410 4.5 81.7 1.0 CA A:VAL407 4.5 84.8 1.0 N A:GLU414 4.5 84.8 1.0 N A:TRP413 4.6 86.4 1.0 CB A:ILE412 4.6 80.3 1.0 CG A:GLU417 4.6 93.6 1.0 C A:CYS408 4.7 94.0 1.0 CG1 A:VAL407 4.7 84.8 1.0 CA A:TRP413 4.8 86.4 1.0 CB A:ASN410 4.8 81.7 1.0 CG A:GLU414 4.9 84.8 1.0 N A:GLU411 5.0 84.4 1.0

Calcium binding site 2 out of 3 in the Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:82.0 occ:1.00 OD1 A:ASN486 2.5 90.7 1.0 O A:VAL472 2.5 93.0 1.0 OD1 A:ASP471 2.6 93.3 1.0 O A:GLU487 3.4 87.9 1.0 C A:VAL472 3.6 93.0 1.0 CG A:ASN486 3.7 90.7 1.0 CD A:ARG464 3.7 90.3 1.0 CG A:ASP471 3.7 93.3 1.0 CG A:ARG464 4.0 90.3 1.0 CA A:ALA473 4.2 96.0 1.0 N A:GLU487 4.2 87.9 1.0 N A:ALA473 4.3 96.0 1.0 OD2 A:ASP471 4.3 93.3 1.0 ND2 A:ASN486 4.4 90.7 1.0 C A:ASP471 4.4 93.3 1.0 N A:VAL472 4.4 93.0 1.0 C A:ALA473 4.4 96.0 1.0 O A:ARG464 4.5 90.3 1.0 C A:GLU487 4.5 87.9 1.0 N A:GLU474 4.6 102.0 1.0 O A:ASP471 4.6 93.3 1.0 CG A:GLU474 4.6 102.0 1.0 CA A:VAL472 4.7 93.0 1.0 CB A:ARG464 4.7 90.3 1.0 CA A:ASN486 4.7 90.7 1.0 CB A:ASN486 4.7 90.7 1.0 O A:PRO465 4.9 90.4 1.0 CB A:ASP471 4.9 93.3 1.0 CA A:ASP471 4.9 93.3 1.0 NE A:ARG464 4.9 90.3 1.0 C A:ASN486 5.0 90.7 1.0 CB A:GLU474 5.0 102.0 1.0

Calcium binding site 3 out of 3 in the Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Ecarin From the Venom of Kenyan Saw-Scaled Viper in Complex with the Fab of Neutralizing Antibody H11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:49.0 occ:1.00 OE2 A:GLU204 2.4 56.7 1.0 O A:CYS392 2.4 60.5 1.0 OD2 A:ASP288 2.6 55.2 1.0 OD1 A:ASP288 3.1 55.2 1.0 CG A:ASP288 3.2 55.2 1.0 CD A:GLU204 3.6 56.7 1.0 C A:CYS392 3.6 60.5 1.0 O A:ASP395 3.9 71.3 1.0 CA A:ILE393 4.2 54.3 1.0 CG A:GLU204 4.3 56.7 1.0 N A:ILE393 4.4 54.3 1.0 OE1 A:GLU204 4.5 56.7 1.0 CA A:CYS392 4.7 60.5 1.0 CB A:ASP288 4.7 55.2 1.0 O A:PHE202 4.7 52.9 1.0 C A:ILE393 4.9 54.3 1.0 C A:ASP395 5.0 71.3 1.0

L.E.Misson Mindrebo, J.T.Mindrebo, Q.Tran, M.C.Wilkinson, J.M.Smith, M.Verma, N.R.Casewell, G.C.Lander, J.G.Jardine. Importance of the Cysteine-Rich Domain of Snake Venom Prothrombin Activators: Insights Gained From Synthetic Neutralizing Antibodies. Toxins V. 16 2024.
ISSN: ESSN 2072-6651
PubMed: 39195771
DOI: 10.3390/TOXINS16080361