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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

Protein crystallography data

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

Calcium Binding Sites:

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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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 4u7k

Go back to Calcium Binding Sites List in 4u7k
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

Reference:

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
Page generated: Wed Jul 9 02:14:45 2025

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