Calcium in PDB 8a7e: Papp-A Dimer in Complex with Its Inhibitor STC2

All present enzymatic activity of Papp-A Dimer in Complex with Its Inhibitor STC2:
3.4.24.79;

The structure of Papp-A Dimer in Complex with Its Inhibitor STC2 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Papp-A Dimer in Complex with Its Inhibitor STC2 (pdb code 8a7e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Papp-A Dimer in Complex with Its Inhibitor STC2, PDB code: 8a7e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1702 b:311.7 occ:1.00 OD1 C:ASP421 2.3 280.0 1.0 OD2 C:ASP425 2.5 321.0 1.0 OD2 C:ASP436 2.6 318.3 1.0 N C:ILE419 2.6 280.8 1.0 OD2 C:ASP439 2.7 314.2 1.0 CG C:ASP421 2.7 280.0 1.0 CA C:ILE419 2.8 280.8 1.0 OD1 C:ASP436 2.8 318.3 1.0 CG C:ASP436 3.0 318.3 1.0 OD2 C:ASP421 3.0 280.0 1.0 C C:ILE419 3.3 280.8 1.0 N C:GLY420 3.3 277.1 1.0 N C:ASP421 3.5 280.0 1.0 CG C:ASP425 3.5 321.0 1.0 C C:LYS418 3.8 256.9 1.0 CB C:ASP421 3.8 280.0 1.0 O C:ASN423 3.8 300.5 1.0 CG C:ASP439 3.9 314.2 1.0 O C:ASP436 4.0 318.3 1.0 O C:ILE419 4.2 280.8 1.0 CB C:ILE419 4.2 280.8 1.0 CA C:ASP421 4.2 280.0 1.0 OD1 C:ASP425 4.2 321.0 1.0 CB C:LYS418 4.3 256.9 1.0 CB C:ASP436 4.4 318.3 1.0 CA C:LYS418 4.4 256.9 1.0 CA C:GLY420 4.4 277.1 1.0 C C:GLY420 4.4 277.1 1.0 CG1 C:ILE419 4.5 280.8 1.0 CB C:ASP425 4.5 321.0 1.0 CB C:ASP439 4.6 314.2 1.0 O C:LYS418 4.8 256.9 1.0 NZ C:LYS418 4.8 256.9 1.0 C C:ASP436 4.8 318.3 1.0 OD1 C:ASP439 4.9 314.2 1.0 C C:ASP421 4.9 280.0 1.0 CE C:LYS418 4.9 256.9 1.0 CA C:ASP436 5.0 318.3 1.0

Calcium binding site 2 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1703 b:268.6 occ:1.00 O C:TYR1566 2.3 255.8 1.0 OD1 C:ASP1579 2.3 272.3 1.0 O C:PHE1561 2.3 267.6 1.0 OD1 C:ASP1564 2.4 252.8 1.0 OD2 C:ASP1582 2.7 260.3 1.0 OD2 C:ASP1579 2.7 272.3 1.0 CG C:ASP1579 2.9 272.3 1.0 OD1 C:ASP1568 3.2 291.6 1.0 C C:PHE1561 3.3 267.6 1.0 CG C:ASP1564 3.3 252.8 1.0 C C:TYR1566 3.4 255.8 1.0 CB C:PHE1561 3.6 267.6 1.0 ND2 C:ASN1571 3.7 285.7 1.0 CG C:ASP1582 3.7 260.3 1.0 OD2 C:ASP1564 3.7 252.8 1.0 CG C:ASP1568 3.8 291.6 1.0 CB C:ASP1582 4.0 260.3 1.0 N C:MET1562 4.1 272.5 1.0 N C:TYR1566 4.1 255.8 1.0 CA C:PHE1561 4.1 267.6 1.0 OD2 C:ASP1568 4.1 291.6 1.0 CA C:MET1562 4.1 272.5 1.0 CA C:TYR1566 4.2 255.8 1.0 N C:ASP1568 4.3 291.6 1.0 CB C:TYR1566 4.3 255.8 1.0 N C:ASP1564 4.3 252.8 1.0 O C:ASP1579 4.4 272.3 1.0 CB C:ASP1579 4.4 272.3 1.0 N C:CYS1567 4.4 279.3 1.0 N C:GLY1563 4.5 261.1 1.0 CB C:ASP1564 4.5 252.8 1.0 C C:MET1562 4.6 272.5 1.0 CA C:CYS1567 4.7 279.3 1.0 CG C:ASN1571 4.7 285.7 1.0 CB C:ASN1571 4.7 285.7 1.0 OD1 C:ASP1582 4.8 260.3 1.0 CG C:PHE1561 4.8 267.6 1.0 CA C:ASP1564 4.8 252.8 1.0 N C:ASN1565 4.8 261.1 1.0 CB C:ASP1568 4.9 291.6 1.0 C C:ASP1564 5.0 252.8 1.0

Calcium binding site 3 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1704 b:341.3 occ:1.00 O C:THR603 2.3 306.0 1.0 OE2 C:GLU589 2.3 324.0 1.0 O C:CYS600 2.3 308.1 1.0 OG1 C:THR603 2.4 306.0 1.0 OD1 C:ASP598 2.4 306.6 1.0 OD2 C:ASP598 2.8 306.6 1.0 CG C:ASP598 3.0 306.6 1.0 CD C:GLU589 3.2 324.0 1.0 C C:THR603 3.3 306.0 1.0 CA C:PRO592 3.4 343.4 1.0 CB C:THR603 3.4 306.0 1.0 C C:CYS600 3.5 308.1 1.0 CB C:PRO592 3.5 343.4 1.0 CA C:THR603 3.7 306.0 1.0 N C:THR603 3.7 306.0 1.0 OE1 C:GLU589 3.7 324.0 1.0 N C:SER593 3.8 318.8 1.0 C C:PRO592 4.0 343.4 1.0 N C:CYS600 4.1 308.1 1.0 O C:SER593 4.2 318.8 1.0 CA C:CYS600 4.2 308.1 1.0 CG C:GLU589 4.2 324.0 1.0 CB C:CYS600 4.4 308.1 1.0 CB C:ASP598 4.4 306.6 1.0 N C:ASN604 4.5 320.2 1.0 CG C:PRO592 4.5 343.4 1.0 N C:ASN601 4.5 303.5 1.0 N C:PRO592 4.6 343.4 1.0 CG2 C:THR603 4.7 306.0 1.0 CA C:ASN601 4.8 303.5 1.0 C C:ASN601 4.8 303.5 1.0 O C:THR596 4.9 306.6 1.0 N C:ASP602 4.9 284.9 1.0 C C:ASN604 4.9 320.2 1.0 C C:SER593 5.0 318.8 1.0 CA C:SER593 5.0 318.8 1.0 C C:ASP602 5.0 284.9 1.0

Calcium binding site 4 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1705 b:401.0 occ:1.00 OD2 C:ASP469 2.4 376.1 1.0 OD2 C:ASP458 2.4 399.3 1.0 OD1 C:ASN454 2.4 383.4 1.0 OD1 C:ASP469 2.5 376.1 1.0 O C:LYS451 2.6 381.9 1.0 CG C:ASP469 2.7 376.1 1.0 O C:VAL456 2.8 373.3 1.0 CG C:ASP458 3.2 399.3 1.0 CG C:ASN454 3.2 383.4 1.0 OE1 C:GLU472 3.4 377.8 1.0 CB C:ASP458 3.4 399.3 1.0 ND2 C:ASN454 3.4 383.4 1.0 C C:LYS451 3.6 381.9 1.0 SG C:CYS461 3.7 390.2 1.0 N C:ASP458 3.8 399.3 1.0 CB C:CYS461 3.9 390.2 1.0 C C:VAL456 4.0 373.3 1.0 CB C:ASP469 4.1 376.1 1.0 OD1 C:ASP458 4.2 399.3 1.0 CA C:ASP458 4.2 399.3 1.0 CA C:GLN452 4.2 378.1 1.0 CD C:GLU472 4.3 377.8 1.0 N C:GLN452 4.3 378.1 1.0 C C:CYS457 4.3 383.7 1.0 CB C:ASN454 4.5 383.4 1.0 CB C:LYS451 4.5 381.9 1.0 CA C:LYS451 4.6 381.9 1.0 OE2 C:GLU472 4.6 377.8 1.0 CA C:CYS457 4.6 383.7 1.0 N C:ASN454 4.7 383.4 1.0 N C:VAL456 4.7 373.3 1.0 C C:GLN452 4.8 378.1 1.0 N C:CYS457 4.8 383.7 1.0 N C:HIS453 4.9 378.2 1.0 CA C:ASP469 5.0 376.1 1.0 OE1 C:GLN452 5.0 378.1 1.0

Calcium binding site 5 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1706 b:118.0 occ:1.00 O C:ARG758 2.3 119.8 1.0 O C:GLU742 2.3 134.6 1.0 OD2 C:ASP748 2.4 107.2 1.0 OD1 C:ASP865 2.8 105.0 1.0 OD1 C:ASP748 3.0 107.2 1.0 CG C:ASP748 3.0 107.2 1.0 NZ C:LYS535 3.1 167.3 1.0 C C:GLU742 3.2 134.6 1.0 CA C:GLU742 3.4 134.6 1.0 C C:ARG758 3.5 119.8 1.0 O C:ASP865 3.6 105.0 1.0 CB C:GLU742 3.9 134.6 1.0 CB C:ARG758 3.9 119.8 1.0 CE C:LYS535 4.0 167.3 1.0 CG C:ASP865 4.0 105.0 1.0 CA C:ARG758 4.2 119.8 1.0 C C:ASP865 4.4 105.0 1.0 N C:ALA743 4.4 141.6 1.0 CB C:ASP748 4.4 107.2 1.0 CG C:GLU742 4.5 134.6 1.0 O C:GLU744 4.5 130.2 1.0 N C:THR759 4.5 121.7 1.0 CA C:ASP865 4.7 105.0 1.0 CA C:THR759 4.8 121.7 1.0 O C:ARG741 4.8 155.1 1.0 OD2 C:ASP865 4.8 105.0 1.0 O C:HIS746 4.8 121.6 1.0 N C:GLU742 4.8 134.6 1.0 N C:ASP748 4.9 107.2 1.0 CA C:ALA743 5.0 141.6 1.0 CB C:ASP865 5.0 105.0 1.0

Calcium binding site 6 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1707 b:214.7 occ:1.00 OD2 C:ASP961 2.2 195.8 1.0 OE1 C:GLN953 2.3 199.7 1.0 O C:TYR946 2.3 199.8 1.0 OE1 C:GLU958 2.3 196.8 1.0 OE2 C:GLU958 2.3 196.8 1.0 CD C:GLU958 2.6 196.8 1.0 C C:TYR946 2.7 199.8 1.0 CA C:CYS947 2.7 218.8 1.0 N C:CYS947 2.9 218.8 1.0 CD C:GLN953 3.1 199.7 1.0 OD1 C:ASP949 3.3 199.8 1.0 O C:ILE951 3.3 206.4 1.0 N C:GLY948 3.4 208.4 1.0 CG C:ASP961 3.5 195.8 1.0 C C:CYS947 3.5 218.8 1.0 NE2 C:GLN953 3.7 199.7 1.0 CA C:TYR946 3.9 199.8 1.0 CB C:CYS947 3.9 218.8 1.0 CG C:GLU958 3.9 196.8 1.0 CG C:ASP949 4.0 199.8 1.0 N C:TYR946 4.1 199.8 1.0 SG C:CYS975 4.1 219.3 1.0 CB C:GLN953 4.3 199.7 1.0 CG C:GLN953 4.3 199.7 1.0 OD1 C:ASP961 4.3 195.8 1.0 N C:GLN953 4.3 199.7 1.0 N C:ASP949 4.4 199.8 1.0 CB C:ASP961 4.4 195.8 1.0 OD2 C:ASP949 4.4 199.8 1.0 C C:ILE951 4.5 206.4 1.0 CA C:GLY948 4.7 208.4 1.0 O C:CYS947 4.7 218.8 1.0 CB C:GLU958 4.8 196.8 1.0 C C:GLY945 4.8 192.2 1.0 SG C:CYS947 4.8 218.8 1.0 C C:ILE952 4.9 211.7 1.0 CA C:ILE952 4.9 211.7 1.0 CA C:GLN953 4.9 199.7 1.0

Calcium binding site 7 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1708 b:146.8 occ:1.00 O C:ILE966 2.4 157.3 1.0 O C:ASN964 2.4 160.5 1.0 N C:ILE966 2.4 157.3 1.0 C C:ASN964 2.6 160.5 1.0 OD2 C:ASP962 2.8 171.9 1.0 OD2 C:ASP969 2.8 175.3 1.0 CG C:ASN964 2.9 160.5 1.0 ND2 C:ASN964 2.9 160.5 1.0 CB C:ASN964 3.0 160.5 1.0 C C:ILE966 3.1 157.3 1.0 N C:LYS965 3.1 170.1 1.0 CA C:ILE966 3.2 157.3 1.0 C C:LYS965 3.4 170.1 1.0 CA C:ASN964 3.4 160.5 1.0 OD1 C:ASN964 3.5 160.5 1.0 CA C:LYS965 3.5 170.1 1.0 CG C:ASP962 3.6 171.9 1.0 CG C:ASP969 3.6 175.3 1.0 OD1 C:ASP969 3.7 175.3 1.0 OD1 C:ASP962 3.8 171.9 1.0 CB C:ILE966 3.8 157.3 1.0 O C:CYS971 4.0 194.2 1.0 N C:ASN964 4.3 160.5 1.0 N C:ASN967 4.3 173.7 1.0 O C:LYS965 4.5 170.1 1.0 CG1 C:ILE966 4.6 157.3 1.0 O C:SER972 4.7 188.3 1.0 CB C:ASP962 4.9 171.9 1.0

Calcium binding site 8 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1709 b:296.4 occ:1.00 OD2 C:ASP1010 2.3 299.6 1.0 O C:VAL998 2.3 302.9 1.0 O C:HIS993 2.3 233.2 1.0 OE2 C:GLU1003 2.4 295.9 1.0 OD1 C:ASP996 2.4 261.9 1.0 OE1 C:GLU1003 2.8 295.9 1.0 CG C:ASP1010 2.9 299.6 1.0 CD C:GLU1003 2.9 295.9 1.0 CG C:ASP996 3.4 261.9 1.0 C C:HIS993 3.4 233.2 1.0 C C:VAL998 3.5 302.9 1.0 OD1 C:ASP1010 3.6 299.6 1.0 N C:GLY995 3.6 251.9 1.0 CB C:ASP1010 3.7 299.6 1.0 CA C:ASP994 3.7 239.2 1.0 N C:VAL998 3.8 302.9 1.0 OD2 C:ASP996 3.8 261.9 1.0 C C:ASP994 3.9 239.2 1.0 N C:ASP996 3.9 261.9 1.0 N C:GLY997 4.0 276.0 1.0 N C:ASP994 4.0 239.2 1.0 CG1 C:VAL998 4.1 302.9 1.0 CA C:VAL998 4.2 302.9 1.0 OE1 C:GLU1000 4.2 308.3 1.0 CG C:GLU1003 4.4 295.9 1.0 OE2 C:GLU1000 4.5 308.3 1.0 N C:CYS999 4.5 313.1 1.0 CB C:ASP996 4.6 261.9 1.0 CA C:GLY995 4.6 251.9 1.0 C C:GLY995 4.6 251.9 1.0 CA C:HIS993 4.6 233.2 1.0 C C:GLY997 4.6 276.0 1.0 CA C:ASP996 4.7 261.9 1.0 CD C:GLU1000 4.7 308.3 1.0 O C:ASP994 4.7 239.2 1.0 CA C:CYS999 4.7 313.1 1.0 OG C:SER1007 4.8 283.2 1.0 CB C:VAL998 4.8 302.9 1.0 C C:ASP996 4.9 261.9 1.0 CA C:GLY997 4.9 276.0 1.0 OD1 C:ASP994 4.9 239.2 1.0

Calcium binding site 9 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ca1702 b:299.3 occ:1.00 OE2 Q:GLU1003 2.3 298.1 1.0 O Q:HIS993 2.3 229.2 1.0 O Q:VAL998 2.5 298.4 1.0 CG1 Q:VAL998 2.7 298.4 1.0 OD1 Q:ASP996 2.9 253.0 1.0 CD Q:GLU1003 2.9 298.1 1.0 OE1 Q:GLU1003 3.0 298.1 1.0 OE1 Q:GLU1000 3.1 315.8 1.0 C Q:HIS993 3.2 229.2 1.0 C Q:VAL998 3.3 298.4 1.0 OD2 Q:ASP996 3.5 253.0 1.0 CG Q:ASP996 3.6 253.0 1.0 OD2 Q:ASP1010 3.7 294.0 1.0 OE2 Q:GLU1000 3.8 315.8 1.0 CA Q:HIS993 3.8 229.2 1.0 CD Q:GLU1000 3.8 315.8 1.0 CB Q:VAL998 3.9 298.4 1.0 CB Q:HIS993 3.9 229.2 1.0 CA Q:VAL998 3.9 298.4 1.0 N Q:VAL998 4.1 298.4 1.0 N Q:CYS999 4.2 315.9 1.0 N Q:ASP994 4.3 227.2 1.0 CG Q:GLU1003 4.4 298.1 1.0 CA Q:CYS999 4.6 315.9 1.0 CA Q:ASP994 4.6 227.2 1.0 CD2 Q:HIS993 4.6 229.2 1.0 CG Q:ASP1010 4.6 294.0 1.0 CG Q:HIS993 4.7 229.2 1.0 CG2 Q:VAL998 4.8 298.4 1.0 CB Q:ASP996 5.0 253.0 1.0 N Q:ASP996 5.0 253.0 1.0

Calcium binding site 10 out of 16 in the Papp-A Dimer in Complex with Its Inhibitor STC2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Papp-A Dimer in Complex with Its Inhibitor STC2 within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ca1703 b:132.2 occ:1.00 O Q:ILE966 2.4 155.2 1.0 O Q:ASN964 2.4 155.7 1.0 N Q:ILE966 2.5 155.2 1.0 OD2 Q:ASP962 2.5 167.7 1.0 C Q:ASN964 2.7 155.7 1.0 OD2 Q:ASP969 2.7 167.7 1.0 CB Q:ASN964 2.9 155.7 1.0 CG Q:ASN964 2.9 155.7 1.0 ND2 Q:ASN964 3.1 155.7 1.0 C Q:ILE966 3.1 155.2 1.0 CA Q:ILE966 3.2 155.2 1.0 N Q:LYS965 3.2 169.8 1.0 CG Q:ASP962 3.3 167.7 1.0 CA Q:ASN964 3.3 155.7 1.0 C Q:LYS965 3.5 169.8 1.0 CG Q:ASP969 3.5 167.7 1.0 OD1 Q:ASP969 3.5 167.7 1.0 OD1 Q:ASP962 3.6 167.7 1.0 OD1 Q:ASN964 3.6 155.7 1.0 CA Q:LYS965 3.7 169.8 1.0 CB Q:ILE966 3.7 155.2 1.0 N Q:ASN964 4.1 155.7 1.0 O Q:CYS971 4.1 187.3 1.0 N Q:ASN967 4.4 174.4 1.0 CG1 Q:ILE966 4.4 155.2 1.0 CB Q:ASP962 4.5 167.7 1.0 O Q:LYS965 4.6 169.8 1.0 O Q:SER972 4.9 180.1 1.0 CB Q:ASP969 4.9 167.7 1.0 CG2 Q:ILE966 5.0 155.2 1.0

S.D.Kobbero, M.Gajhede, O.A.Mirza, S.Kloverpris, T.R.Kjaer, J.H.Mikkelsen, T.Boesen, C.Oxvig. Structure of the Proteolytic Enzyme Papp-A with the Endogenous Inhibitor Stanniocalcin-2 Reveals Its Inhibitory Mechanism. Nat Commun V. 13 6084 2022.
ISSN: ESSN 2041-1723
PubMed: 36257932
DOI: 10.1038/S41467-022-33698-8