Calcium in PDB 7s6e: Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium

The structure of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium, PDB code: 7s6e was solved by B.S.Shah, H.Mikolajek, V.Mykhaylyk, C.M.Orr, R.J.Owens, I.T.Paulsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.11 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.76, 117.12, 123.46, 90, 90, 90
R / Rfree (%)	14.7 / 17.4

The structure of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium (pdb code 7s6e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium, PDB code: 7s6e:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca509 b:16.6 occ:1.00 O A:LEU23 2.3 17.3 1.0 O B:HOH780 2.3 14.6 1.0 O B:HOH803 2.4 22.6 1.0 O B:HOH733 2.4 21.5 1.0 O B:HOH641 2.4 27.5 1.0 O A:HOH606 2.4 22.2 1.0 O B:HOH607 2.5 26.2 1.0 C A:LEU23 3.5 17.6 1.0 HB3 A:LEU23 3.7 19.1 1.0 HG A:SER32 4.0 15.8 0.0 HG21 A:THR24 4.1 18.7 1.0 O B:HOH876 4.1 36.4 1.0 HB1 A:ALA28 4.1 15.8 1.0 HA A:LEU23 4.2 18.1 1.0 HA A:THR24 4.2 17.4 1.0 OD1 B:ASP294 4.2 23.7 1.0 CA A:LEU23 4.2 17.9 1.0 HG23 A:THR24 4.3 18.7 1.0 O B:HOH719 4.4 19.0 1.0 HD2 B:ARG295 4.4 19.6 1.0 CB A:LEU23 4.4 19.1 1.0 OG1 B:THR256 4.4 19.6 1.0 OE2 B:GLU252 4.5 20.5 1.0 OG A:SER32 4.5 15.4 0.5 N A:THR24 4.5 16.6 1.0 HG A:SER32 4.5 16.1 0.0 HG B:SER255 4.6 19.6 0.0 CG2 A:THR24 4.6 18.6 1.0 HG1 B:THR256 4.7 20.1 0.0 OG B:SER255 4.7 19.1 1.0 O A:HOH849 4.8 22.9 1.0 HB2 A:LEU23 4.8 19.1 1.0 CA A:THR24 4.8 17.1 1.0 HA B:THR256 4.9 20.3 1.0 HD21 A:LEU23 4.9 21.6 1.0 HB2 A:ALA28 4.9 15.8 1.0 CB A:ALA28 4.9 15.5 1.0 O B:HOH651 4.9 26.9 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca510 b:21.2 occ:1.00 H A:THR379 2.6 21.0 1.0 H A:CYS392 2.7 24.9 1.0 HD22 A:ASN347 2.7 20.4 1.0 HG21 A:THR379 2.8 21.9 1.0 H A:TRP380 2.9 21.7 1.0 HA A:ALA391 3.1 26.8 1.0 O A:HOH851 3.2 35.8 1.0 HA A:GLN378 3.3 21.5 1.0 N A:THR379 3.4 21.4 1.0 N A:CYS392 3.4 24.6 1.0 HB1 A:ALA391 3.5 28.5 1.0 HD1 A:TRP380 3.5 20.1 1.0 HG23 A:THR379 3.5 21.9 1.0 HB3 A:CYS392 3.5 25.6 1.0 CG2 A:THR379 3.6 22.6 1.0 ND2 A:ASN347 3.6 20.5 1.0 CA A:ALA391 3.8 27.7 1.0 N A:TRP380 3.8 21.9 1.0 HD21 A:ASN347 4.0 20.4 1.0 HB2 A:TRP380 4.0 22.3 1.0 CB A:ALA391 4.0 28.9 1.0 HB3 A:ASN347 4.0 18.5 1.0 C A:ALA391 4.1 26.5 1.0 HB2 A:ASN347 4.1 18.5 1.0 CA A:GLN378 4.2 21.9 1.0 C A:GLN378 4.2 20.8 1.0 HG22 A:THR379 4.2 21.9 1.0 CA A:THR379 4.2 20.3 1.0 HB2 A:ALA391 4.2 28.5 1.0 CD1 A:TRP380 4.3 19.6 1.0 CB A:CYS392 4.3 26.6 1.0 O A:CYS392 4.3 22.2 1.0 CA A:CYS392 4.4 24.2 1.0 HB2 A:CYS392 4.4 25.6 1.0 CB A:ASN347 4.4 17.7 1.0 CB A:THR379 4.4 20.5 1.0 CG A:ASN347 4.5 20.1 1.0 O A:PRO377 4.5 22.3 1.0 C A:THR379 4.5 20.2 1.0 HB3 A:GLN378 4.7 23.6 1.0 CB A:TRP380 4.7 22.6 1.0 HB A:THR379 4.8 20.5 1.0 CA A:TRP380 4.8 22.7 1.0 C A:CYS392 4.8 23.0 1.0 CG A:TRP380 4.9 21.1 1.0 HG2 A:GLN378 4.9 26.0 1.0 HB3 A:ALA391 4.9 28.6 1.0 O A:TRP380 4.9 23.1 1.0 O A:PHE390 5.0 24.2 1.0 CB A:GLN378 5.0 23.4 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:20.8 occ:1.00 O A:HOH819 2.1 41.7 1.0 O A:HOH864 2.2 28.4 1.0 O A:GLY319 2.3 21.7 1.0 OD2 A:ASP54 2.4 23.4 1.0 O A:HOH800 2.5 32.3 1.0 OD1 A:ASP54 2.5 21.7 1.0 CG A:ASP54 2.8 24.4 1.0 C A:GLY319 3.5 25.0 1.0 HB A:THR320 3.5 25.4 1.0 HA3 A:GLY319 3.8 22.6 1.0 HG13 A:VAL53 4.1 23.1 1.0 CA A:GLY319 4.2 22.2 1.0 HO2 A:EDO506 4.2 50.2 1.0 CB A:ASP54 4.3 23.5 1.0 HA A:THR320 4.4 23.7 1.0 CB A:THR320 4.4 25.9 1.0 N A:THR320 4.5 22.9 1.0 O2 A:EDO506 4.5 49.3 1.0 CA A:THR320 4.6 23.9 1.0 HA2 A:GLY319 4.7 22.6 1.0 HG11 A:VAL53 4.7 23.1 1.0 HB2 A:ASP54 4.7 23.2 1.0 HB3 A:ASP54 4.7 23.2 1.0 CG1 A:VAL53 4.8 24.1 1.0 O A:ALA318 4.8 20.7 1.0 H A:ASP54 5.0 20.4 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:50.2 occ:1.00 OD1 A:ASP323 2.3 32.3 1.0 O A:GLU110 2.3 31.9 1.0 O A:HOH836 2.5 40.1 1.0 OD1 A:ASP324 2.5 45.4 1.0 OD2 A:ASP323 3.0 36.1 1.0 CG A:ASP323 3.0 32.0 1.0 HH21 A:ARG327 3.6 30.4 1.0 C A:GLU110 3.6 34.6 1.0 HA A:ALA111 3.6 31.7 1.0 HG3 A:GLU110 3.7 44.8 1.0 HB3 A:GLU110 3.7 40.3 1.0 CG A:ASP324 3.7 40.7 1.0 H A:ASP324 3.9 25.6 1.0 CG A:GLU110 4.3 47.0 1.0 CB A:GLU110 4.3 41.1 1.0 NH2 A:ARG327 4.3 28.6 1.0 HG2 A:GLU110 4.4 44.9 1.0 N A:ASP324 4.4 24.6 1.0 HH22 A:ARG327 4.4 30.4 1.0 CB A:ASP323 4.4 29.1 1.0 OD2 A:ASP324 4.4 56.0 1.0 N A:ALA111 4.4 31.3 1.0 CA A:ALA111 4.5 32.9 1.0 H A:ASP323 4.5 24.9 1.0 O A:HOH742 4.6 33.4 1.0 CA A:GLU110 4.6 33.3 1.0 O A:LYS109 4.6 37.4 1.0 OD1 A:ASP322 4.7 27.7 1.0 HB3 A:ASP323 4.8 29.1 1.0 CB A:ASP324 4.8 32.4 1.0 O A:HOH834 4.8 39.2 1.0 HB2 A:ASP324 4.9 33.2 1.0 HA A:ASP324 5.0 28.1 1.0 HB2 A:ASP323 5.0 29.1 1.0 C A:ASP323 5.0 24.9 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca513 b:36.8 occ:1.00 O A:HOH770 2.3 37.4 1.0 O A:HOH743 2.4 33.6 1.0 OD1 A:ASP13 2.5 25.8 1.0 OD2 A:ASP13 2.6 25.9 1.0 CG A:ASP13 2.9 23.7 1.0 H A:SER14 4.2 21.6 1.0 CB A:ASP13 4.4 22.0 1.0 O A:SER14 4.6 19.2 1.0 HE2 A:TYR58 4.8 18.9 1.0 HB3 A:ASP13 4.8 22.0 1.0 HB2 A:ASP13 4.8 22.0 1.0 O A:HOH630 4.9 26.6 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca514 b:22.2 occ:1.00 HE21 A:GLN352 2.0 17.2 1.0 O A:HOH679 2.3 18.9 1.0 O A:THR131 2.4 16.5 1.0 OG A:SER303 2.4 14.9 1.0 NE2 A:GLN352 2.4 15.9 1.0 O A:HOH741 2.5 16.6 1.0 O A:HOH779 2.5 19.1 1.0 HG A:SER303 2.6 16.0 0.0 HE22 A:GLN352 2.6 17.2 1.0 HA2 A:GLY132 3.3 17.0 1.0 HD12 A:ILE350 3.4 18.5 1.0 CB A:SER303 3.4 16.9 1.0 CD A:GLN352 3.4 20.3 1.0 HA A:SER303 3.5 16.4 1.0 HB3 A:SER303 3.5 16.2 1.0 C A:THR131 3.5 16.9 1.0 HB2 A:ASN270 3.7 19.8 1.0 OE1 A:GLN352 3.7 24.6 1.0 OD1 A:ASP299 3.8 16.1 1.0 HB A:THR131 3.9 17.2 1.0 CA A:SER303 4.0 16.1 1.0 OE1 A:GLN339 4.0 21.6 1.0 CA A:GLY132 4.0 16.9 1.0 OE1 A:GLU302 4.1 19.3 1.0 OD2 A:ASP299 4.1 18.9 1.0 OD1 A:ASN270 4.1 19.3 1.0 H A:ALA133 4.1 17.6 1.0 N A:GLY132 4.2 17.1 1.0 HB2 A:SER303 4.2 16.2 1.0 CG A:ASP299 4.3 18.5 1.0 CD1 A:ILE350 4.4 18.2 1.0 H A:SER303 4.5 16.4 1.0 C A:GLY132 4.5 17.1 1.0 N A:ALA133 4.5 18.1 1.0 CB A:ASN270 4.5 18.8 1.0 N A:SER303 4.5 16.1 1.0 HD11 A:ILE350 4.6 18.5 1.0 CA A:THR131 4.6 17.1 1.0 CB A:THR131 4.6 17.3 1.0 HD22 A:ASN306 4.7 21.1 1.0 O A:ASP299 4.7 17.2 1.0 CG A:ASN270 4.7 22.1 1.0 HG2 A:GLN352 4.7 20.5 1.0 O A:HOH750 4.7 17.1 1.0 CG A:GLN352 4.7 20.6 1.0 HA A:THR131 4.8 17.0 1.0 HB3 A:ASN270 4.8 19.8 1.0 HA3 A:GLY132 4.8 17.0 1.0 HD13 A:ILE350 4.9 18.5 1.0 O A:PRO116 4.9 17.5 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca515 b:34.7 occ:1.00 O A:HOH762 2.4 34.7 1.0 O A:GLY182 2.4 24.5 1.0 O A:HOH839 2.5 40.3 1.0 C A:GLY182 3.6 25.8 1.0 HZ A:PHE147 3.8 21.0 1.0 HA2 A:GLY183 3.9 20.0 1.0 O A:HOH647 4.0 40.2 1.0 HA3 A:GLY182 4.1 25.4 1.0 O A:HOH758 4.2 40.9 1.0 CA A:GLY182 4.5 26.3 1.0 O A:HOH665 4.5 31.5 1.0 N A:GLY183 4.5 21.6 1.0 CA A:GLY183 4.7 19.4 1.0 CZ A:PHE147 4.7 20.0 1.0 HE1 A:PHE147 4.8 20.5 1.0 HA2 A:GLY182 4.9 25.4 1.0 HG3 A:GLU184 5.0 29.1 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:14.0 occ:1.00 O A:HOH791 2.2 15.2 1.0 O A:HOH686 2.3 23.8 1.0 O B:HOH645 2.3 22.9 1.0 O A:HOH830 2.3 21.5 1.0 O B:LEU23 2.3 18.9 1.0 O A:HOH713 2.3 22.2 1.0 O A:HOH747 2.3 23.8 1.0 C B:LEU23 3.5 17.4 1.0 HB3 B:LEU23 3.6 20.1 1.0 HG B:SER32 4.0 14.8 0.0 HG21 B:THR24 4.1 19.9 1.0 OD2 A:ASP294 4.1 26.5 1.0 HA B:LEU23 4.1 18.8 1.0 HB1 B:ALA28 4.2 19.4 1.0 HA B:THR24 4.2 18.6 1.0 CA B:LEU23 4.2 19.4 1.0 HD2 A:ARG295 4.3 17.3 1.0 CB B:LEU23 4.3 20.0 1.0 HG23 B:THR24 4.4 19.9 1.0 O A:HOH709 4.4 24.0 1.0 OE2 A:GLU252 4.5 18.5 1.0 OG1 A:THR256 4.5 21.7 1.0 HG B:SER32 4.5 18.8 0.0 N B:THR24 4.5 19.0 1.0 OG B:SER32 4.6 13.8 0.5 CG2 B:THR24 4.7 20.4 1.0 HG A:SER255 4.7 24.4 0.0 O B:HOH868 4.8 29.2 1.0 HB2 B:LEU23 4.8 20.1 1.0 HD21 B:LEU23 4.8 21.6 1.0 CA B:THR24 4.8 18.4 1.0 HG1 A:THR256 4.9 22.6 0.0 OG A:SER255 4.9 25.3 1.0 HA A:THR256 4.9 21.4 1.0 HD3 A:ARG295 4.9 17.3 1.0 CB B:ALA28 5.0 20.0 1.0 HB2 B:ALA28 5.0 19.4 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:19.6 occ:1.00 H B:THR379 2.6 20.0 1.0 HD22 B:ASN347 2.6 17.7 1.0 H B:CYS392 2.7 21.9 1.0 HG21 B:THR379 2.9 19.3 1.0 H B:TRP380 2.9 21.1 1.0 HA B:ALA391 3.0 26.7 1.0 O B:HOH864 3.2 39.7 1.0 HA B:GLN378 3.2 20.9 1.0 N B:THR379 3.3 20.6 1.0 HB1 B:ALA391 3.4 27.9 1.0 HD1 B:TRP380 3.5 21.0 1.0 N B:CYS392 3.5 21.7 1.0 ND2 B:ASN347 3.5 17.7 1.0 HB3 B:CYS392 3.6 21.5 1.0 HG23 B:THR379 3.7 19.3 1.0 CG2 B:THR379 3.7 19.3 1.0 CA B:ALA391 3.7 26.9 1.0 HB2 B:TRP380 3.8 20.6 1.0 N B:TRP380 3.8 22.1 1.0 HD21 B:ASN347 3.9 17.7 1.0 HB3 B:ASN347 3.9 17.1 1.0 CB B:ALA391 3.9 28.5 1.0 CA B:GLN378 4.1 21.5 1.0 C B:ALA391 4.1 23.0 1.0 C B:GLN378 4.1 19.6 1.0 HB2 B:ALA391 4.1 28.0 1.0 HB2 B:ASN347 4.2 17.1 1.0 CD1 B:TRP380 4.2 21.4 1.0 CA B:THR379 4.2 19.0 1.0 CB B:CYS392 4.3 22.1 1.0 O B:HOH602 4.3 41.7 1.0 O B:CYS392 4.4 20.3 1.0 HB2 B:CYS392 4.4 21.5 1.0 CB B:ASN347 4.4 16.6 1.0 HG22 B:THR379 4.4 19.3 1.0 CA B:CYS392 4.4 21.2 1.0 CG B:ASN347 4.5 17.7 1.0 CB B:THR379 4.5 19.4 1.0 O B:PRO377 4.5 19.3 1.0 CB B:TRP380 4.5 20.6 1.0 C B:THR379 4.5 18.8 1.0 O B:HOH924 4.7 43.9 1.0 HB3 B:GLN378 4.7 22.2 1.0 CA B:TRP380 4.7 21.4 1.0 CG B:TRP380 4.8 19.7 1.0 HB B:THR379 4.8 19.4 1.0 HB3 B:ALA391 4.8 28.0 1.0 HG2 B:GLN378 4.8 23.4 1.0 O B:TRP380 4.9 22.4 1.0 O B:PHE390 4.9 23.9 1.0 C B:CYS392 4.9 22.5 1.0 CB B:GLN378 4.9 22.3 1.0 N B:ALA391 5.0 28.8 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca507 b:24.5 occ:1.00 O B:HOH858 2.3 31.6 1.0 OD1 B:ASP323 2.3 21.6 1.0 O B:GLU110 2.3 21.9 1.0 OD1 B:ASP324 2.3 28.0 1.0 O B:HOH614 2.5 23.6 1.0 CG B:ASP323 3.1 20.8 1.0 OD2 B:ASP323 3.2 25.4 1.0 CG B:ASP324 3.5 29.2 1.0 HH21 B:ARG327 3.5 19.9 1.0 C B:GLU110 3.5 21.5 1.0 HA B:ALA111 3.7 19.7 1.0 HB3 B:GLU110 3.7 26.8 1.0 H B:ASP324 3.8 20.6 1.0 HB2 B:GLU110 4.0 26.8 1.0 OD2 B:ASP324 4.0 34.9 1.0 CB B:GLU110 4.2 27.2 1.0 NH2 B:ARG327 4.2 19.3 1.0 N B:ASP324 4.3 20.1 1.0 HH22 B:ARG327 4.3 19.9 1.0 N B:ALA111 4.4 19.3 1.0 OD1 B:ASP322 4.4 24.5 1.0 CA B:ALA111 4.5 19.9 1.0 H B:ASP323 4.5 18.4 1.0 CA B:GLU110 4.5 23.2 1.0 CB B:ASP323 4.5 19.3 1.0 O B:LYS109 4.6 21.2 1.0 CB B:ASP324 4.6 23.6 1.0 HA B:ASP324 4.8 21.6 1.0 HB3 B:ASP323 4.8 19.3 1.0 CA B:ASP324 4.9 22.1 1.0 C B:ASP323 4.9 20.4 1.0 HB2 B:ASP324 5.0 24.4 1.0 N B:ASP323 5.0 18.7 1.0

B.S.Shah, H.Mikolajek, V.Mykhaylyk, C.M.Orr, R.Owens, I.T.Paulsen. Crystal Structure of Urta From Synechococcus CC9311 in Complex with Urea and Calcium To Be Published.