Calcium in PDB 4u7k: Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution

The structure of Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution, PDB code: 4u7k was solved by R.Bauer, K.Janowska, J.Sakon, O.Matsushita, E.Latimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.76 / 1.91
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.320, 87.610, 104.350, 90.00, 116.04, 90.00
R / Rfree (%)	16.3 / 20.7

The binding sites of Calcium atom in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution (pdb code 4u7k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution, PDB code: 4u7k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:33.5 occ:1.00 O A:SER686 2.4 31.7 1.0 OD2 A:ASP754 2.4 32.2 1.0 OD1 A:ASP715 2.4 35.5 1.0 O A:HOH927 2.4 37.3 1.0 OD2 A:ASP713 2.5 34.2 1.0 OD1 A:ASP713 2.5 34.1 1.0 OD1 A:ASN685 2.5 37.0 1.0 CG A:ASP713 2.8 34.9 1.0 CG A:ASP754 3.4 34.5 1.0 CG A:ASN685 3.4 44.0 1.0 CG A:ASP715 3.5 41.8 1.0 C A:SER686 3.5 36.6 1.0 ND2 A:ASN685 3.6 35.5 1.0 CB A:ASP754 3.9 26.6 1.0 OD2 A:ASP715 4.0 40.3 1.0 N A:SER686 4.1 37.7 1.0 O A:HOH954 4.2 51.5 1.0 OD1 A:ASP754 4.3 33.0 1.0 CA A:SER686 4.3 36.3 1.0 C A:ASP715 4.4 37.3 1.0 CB A:ASP713 4.4 28.9 1.0 N A:GLY716 4.5 33.1 1.0 O A:ASP715 4.5 38.1 1.0 N A:LEU687 4.6 31.4 1.0 N A:ASP715 4.6 31.4 1.0 C A:LEU687 4.6 28.7 1.0 OD1 A:ASP755 4.6 39.2 1.0 CB A:SER686 4.7 41.1 1.0 N A:PRO688 4.7 29.0 1.0 CA A:LEU687 4.7 33.0 1.0 CB A:ASP715 4.8 32.8 1.0 CD A:PRO688 4.8 29.9 1.0 CB A:ASN685 4.8 42.9 1.0 CA A:ASP715 4.8 32.5 1.0 C A:ASN685 4.9 39.8 1.0 CA A:GLY716 4.9 37.0 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:33.8 occ:1.00 O B:SER686 2.4 32.1 1.0 OD2 B:ASP754 2.4 33.5 1.0 OD1 B:ASP715 2.4 35.4 1.0 OD1 B:ASP713 2.5 35.5 1.0 OD1 B:ASN685 2.5 37.3 1.0 OD2 B:ASP713 2.5 36.5 1.0 O B:HOH940 2.5 40.9 1.0 CG B:ASP713 2.8 34.4 1.0 CG B:ASP754 3.4 35.2 1.0 CG B:ASN685 3.4 43.3 1.0 CG B:ASP715 3.5 44.2 1.0 C B:SER686 3.6 36.2 1.0 ND2 B:ASN685 3.7 36.9 1.0 CB B:ASP754 3.9 29.9 1.0 OD2 B:ASP715 4.0 42.1 1.0 N B:SER686 4.1 38.6 1.0 O B:HOH985 4.2 54.8 1.0 CA B:SER686 4.3 37.2 1.0 OD1 B:ASP754 4.3 34.8 1.0 C B:ASP715 4.4 37.7 1.0 CB B:ASP713 4.4 30.5 1.0 N B:GLY716 4.5 33.1 1.0 O B:ASP715 4.5 38.5 1.0 CB B:SER686 4.6 42.8 1.0 N B:ASP715 4.6 31.6 1.0 N B:LEU687 4.6 32.0 1.0 OD1 B:ASP755 4.6 39.1 1.0 C B:LEU687 4.7 28.3 1.0 CB B:ASP715 4.7 33.5 1.0 CA B:GLY716 4.7 40.8 1.0 CB B:ASN685 4.8 44.0 1.0 CA B:ASP715 4.8 33.8 1.0 N B:PRO688 4.8 30.1 1.0 C B:ASN685 4.8 40.2 1.0 CA B:LEU687 4.8 31.3 1.0 CD B:PRO688 4.9 30.2 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca801 b:33.2 occ:1.00 OD2 C:ASP754 2.3 30.8 1.0 O C:HOH948 2.4 40.0 1.0 O C:SER686 2.4 31.6 1.0 OD1 C:ASP715 2.4 34.6 1.0 OD1 C:ASP713 2.5 33.2 1.0 OD2 C:ASP713 2.5 33.2 1.0 OD1 C:ASN685 2.5 34.7 1.0 CG C:ASP713 2.8 33.7 1.0 CG C:ASP754 3.3 33.3 1.0 CG C:ASN685 3.4 41.0 1.0 CG C:ASP715 3.6 40.3 1.0 C C:SER686 3.6 33.4 1.0 ND2 C:ASN685 3.6 33.1 1.0 CB C:ASP754 3.8 26.9 1.0 OD2 C:ASP715 4.0 39.1 1.0 N C:SER686 4.2 38.1 1.0 OD1 C:ASP754 4.2 32.3 1.0 CA C:SER686 4.3 35.3 1.0 CB C:ASP713 4.3 28.2 1.0 O C:HOH968 4.4 47.6 1.0 C C:ASP715 4.4 34.2 1.0 O C:ASP715 4.5 35.5 1.0 N C:GLY716 4.5 31.5 1.0 N C:LEU687 4.6 32.5 1.0 N C:ASP715 4.6 29.5 1.0 C C:LEU687 4.6 27.5 1.0 OD1 C:ASP755 4.6 36.1 1.0 CB C:SER686 4.6 41.1 1.0 N C:PRO688 4.7 27.0 1.0 CB C:ASP715 4.8 32.1 1.0 CA C:LEU687 4.8 30.9 1.0 CB C:ASN685 4.8 40.8 1.0 CA C:ASP715 4.8 31.6 1.0 CA C:GLY716 4.8 35.2 1.0 C C:ASN685 4.9 37.8 1.0 CD C:PRO688 4.9 29.1 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:33.0 occ:1.00 O D:SER686 2.3 30.8 1.0 OD2 D:ASP754 2.4 32.3 1.0 OD2 D:ASP713 2.4 34.3 1.0 OD1 D:ASP715 2.4 35.6 1.0 OD1 D:ASN685 2.4 37.0 1.0 OD1 D:ASP713 2.5 34.3 1.0 O D:HOH929 2.5 38.6 1.0 CG D:ASP713 2.8 32.9 1.0 CG D:ASP754 3.3 35.0 1.0 CG D:ASN685 3.3 43.5 1.0 C D:SER686 3.5 35.2 1.0 CG D:ASP715 3.5 42.3 1.0 ND2 D:ASN685 3.6 36.0 1.0 CB D:ASP754 3.8 27.7 1.0 OD2 D:ASP715 4.0 40.9 1.0 N D:SER686 4.2 40.2 1.0 O D:HOH949 4.2 47.3 1.0 CA D:SER686 4.2 37.1 1.0 OD1 D:ASP754 4.3 33.4 1.0 CB D:ASP713 4.3 29.8 1.0 C D:ASP715 4.3 36.5 1.0 N D:GLY716 4.4 32.0 1.0 O D:ASP715 4.4 37.3 1.0 CB D:SER686 4.5 42.4 1.0 N D:LEU687 4.6 32.4 1.0 N D:ASP715 4.6 31.1 1.0 OD1 D:ASP755 4.7 36.4 1.0 C D:LEU687 4.7 30.2 1.0 N D:PRO688 4.7 27.8 1.0 CB D:ASN685 4.7 43.3 1.0 CA D:LEU687 4.8 31.7 1.0 CB D:ASP715 4.8 32.6 1.0 CA D:GLY716 4.8 36.3 1.0 CA D:ASP715 4.8 33.3 1.0 C D:ASN685 4.8 41.2 1.0 CD D:PRO688 4.9 29.8 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca801 b:34.0 occ:1.00 O E:SER686 2.3 32.5 1.0 OD1 E:ASP715 2.4 36.1 1.0 O E:HOH929 2.4 35.3 1.0 OD2 E:ASP754 2.4 33.1 1.0 OD2 E:ASP713 2.5 34.2 1.0 OD1 E:ASP713 2.5 34.8 1.0 OD1 E:ASN685 2.5 37.8 1.0 CG E:ASP713 2.8 33.4 1.0 CG E:ASN685 3.4 43.6 1.0 CG E:ASP754 3.4 35.5 1.0 CG E:ASP715 3.5 42.0 1.0 C E:SER686 3.5 35.9 1.0 ND2 E:ASN685 3.6 35.3 1.0 CB E:ASP754 3.8 28.2 1.0 OD2 E:ASP715 4.0 41.8 1.0 N E:SER686 4.1 38.3 1.0 CA E:SER686 4.3 36.3 1.0 CB E:ASP713 4.3 29.6 1.0 O E:HOH988 4.3 59.7 1.0 OD1 E:ASP754 4.3 33.0 1.0 C E:ASP715 4.4 36.4 1.0 O E:ASP715 4.4 37.2 1.0 N E:GLY716 4.5 31.1 1.0 N E:LEU687 4.6 31.9 1.0 N E:ASP715 4.6 30.8 1.0 OD1 E:ASP755 4.6 36.3 1.0 C E:LEU687 4.7 28.3 1.0 CB E:SER686 4.7 42.3 1.0 CB E:ASN685 4.7 42.7 1.0 N E:PRO688 4.7 28.4 1.0 CB E:ASP715 4.8 32.5 1.0 CA E:LEU687 4.8 31.4 1.0 CA E:ASP715 4.8 33.2 1.0 C E:ASN685 4.8 39.6 1.0 CD E:PRO688 4.9 28.2 1.0 CA E:GLY716 4.9 37.4 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca801 b:32.5 occ:1.00 OD2 F:ASP754 2.3 32.8 1.0 OD1 F:ASP715 2.4 34.5 1.0 O F:SER686 2.4 32.8 1.0 OD1 F:ASN685 2.4 37.2 1.0 O F:HOH934 2.5 35.4 1.0 OD2 F:ASP713 2.5 34.9 1.0 OD1 F:ASP713 2.5 35.1 1.0 CG F:ASP713 2.9 34.9 1.0 CG F:ASP754 3.3 33.9 1.0 CG F:ASN685 3.4 45.0 1.0 CG F:ASP715 3.5 42.5 1.0 C F:SER686 3.6 36.2 1.0 ND2 F:ASN685 3.6 36.9 1.0 CB F:ASP754 3.9 26.7 1.0 OD2 F:ASP715 4.0 41.7 1.0 N F:SER686 4.2 38.9 1.0 O F:HOH946 4.2 44.8 1.0 OD1 F:ASP754 4.3 33.2 1.0 CA F:SER686 4.3 37.3 1.0 CB F:ASP713 4.4 30.8 1.0 C F:ASP715 4.4 36.6 1.0 O F:ASP715 4.5 37.1 1.0 N F:GLY716 4.6 34.4 1.0 N F:LEU687 4.6 32.2 1.0 CB F:SER686 4.6 42.9 1.0 C F:LEU687 4.6 29.4 1.0 OD1 F:ASP755 4.6 39.5 1.0 N F:ASP715 4.6 31.6 1.0 N F:PRO688 4.7 29.6 1.0 CA F:LEU687 4.7 34.2 1.0 CB F:ASP715 4.8 33.5 1.0 CB F:ASN685 4.8 43.0 1.0 C F:ASN685 4.8 40.4 1.0 CA F:ASP715 4.8 34.0 1.0 CA F:GLY716 4.8 37.7 1.0 CD F:PRO688 4.9 29.3 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca801 b:35.1 occ:1.00 OD2 G:ASP754 2.4 32.8 1.0 OD1 G:ASP715 2.4 36.8 1.0 O G:SER686 2.4 32.8 1.0 OD1 G:ASP713 2.5 35.4 1.0 O G:HOH954 2.5 42.7 1.0 OD1 G:ASN685 2.5 38.2 1.0 OD2 G:ASP713 2.6 34.5 1.0 CG G:ASP713 2.9 33.9 1.0 CG G:ASN685 3.4 44.5 1.0 CG G:ASP754 3.4 35.0 1.0 CG G:ASP715 3.5 42.8 1.0 C G:SER686 3.6 36.0 1.0 ND2 G:ASN685 3.6 35.6 1.0 CB G:ASP754 3.9 28.1 1.0 OD2 G:ASP715 4.0 39.7 1.0 N G:SER686 4.1 37.6 1.0 O G:HOH976 4.3 54.1 1.0 CA G:SER686 4.3 36.6 1.0 OD1 G:ASP754 4.3 34.9 1.0 CB G:ASP713 4.4 29.5 1.0 C G:ASP715 4.4 37.4 1.0 O G:ASP715 4.5 38.2 1.0 N G:GLY716 4.5 32.5 1.0 N G:ASP715 4.6 31.8 1.0 N G:LEU687 4.6 31.7 1.0 CB G:SER686 4.6 41.0 1.0 C G:LEU687 4.7 28.8 1.0 OD1 G:ASP755 4.7 39.3 1.0 CB G:ASP715 4.7 34.0 1.0 CB G:ASN685 4.8 43.7 1.0 N G:PRO688 4.8 28.5 1.0 CA G:LEU687 4.8 32.0 1.0 CA G:ASP715 4.8 34.5 1.0 C G:ASN685 4.8 39.0 1.0 CA G:GLY716 4.8 38.9 1.0 CD G:PRO688 4.9 29.4 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution


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 the Clostridium Histolyticum Colh Collagenase Polycystic Kidney Disease-Like Domain 2A in the Presence of Calcium at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca801 b:32.4 occ:1.00 OD2 H:ASP754 2.3 30.0 1.0 O H:HOH961 2.3 41.2 1.0 O H:SER686 2.4 31.3 1.0 OD2 H:ASP713 2.4 30.7 1.0 OD1 H:ASP715 2.4 34.0 1.0 OD1 H:ASP713 2.5 33.5 1.0 OD1 H:ASN685 2.5 34.2 1.0 CG H:ASP713 2.8 32.7 1.0 CG H:ASP754 3.3 33.5 1.0 CG H:ASN685 3.4 40.5 1.0 CG H:ASP715 3.5 41.0 1.0 C H:SER686 3.6 35.6 1.0 ND2 H:ASN685 3.6 33.5 1.0 CB H:ASP754 3.9 27.4 1.0 OD2 H:ASP715 3.9 39.9 1.0 O H:HOH982 4.1 50.5 1.0 N H:SER686 4.2 37.7 1.0 OD1 H:ASP754 4.3 32.0 1.0 CB H:ASP713 4.3 28.5 1.0 CA H:SER686 4.3 37.1 1.0 C H:ASP715 4.4 34.1 1.0 O H:ASP715 4.4 34.7 1.0 N H:GLY716 4.5 33.1 1.0 N H:LEU687 4.6 32.0 1.0 N H:ASP715 4.6 30.2 1.0 OD1 H:ASP755 4.6 36.2 1.0 C H:LEU687 4.6 28.6 1.0 CB H:SER686 4.7 41.5 1.0 N H:PRO688 4.7 28.0 1.0 CB H:ASP715 4.7 31.6 1.0 CB H:ASN685 4.8 41.7 1.0 CA H:GLY716 4.8 37.8 1.0 CA H:LEU687 4.8 30.8 1.0 CA H:ASP715 4.8 32.2 1.0 C H:ASN685 4.8 38.9 1.0 CD H:PRO688 4.9 27.8 1.0

R.Bauer, K.Janowska, K.Taylor, B.Jordan, S.Gann, T.Janowski, E.C.Latimer, O.Matsushita, J.Sakon. Structures of Three Polycystic Kidney Disease-Like Domains From Clostridium Histolyticum Collagenases Colg and Colh Acta Crystallogr.,Sect.D V. 71 Ished 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714027722