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Calcium in PDB 5k31: Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer

Protein crystallography data

The structure of Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer, PDB code: 5k31 was solved by U.Sharma, D.J.S.Hulmes, N.Aghajari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.07 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.820, 149.630, 105.950, 90.00, 101.68, 90.00
R / Rfree (%) 19.6 / 23.8

Other elements in 5k31:

The structure of Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer (pdb code 5k31). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer, PDB code: 5k31:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5k31

Go back to Calcium Binding Sites List in 5k31
Calcium binding site 1 out of 6 in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer


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 Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:16.4
occ:1.00
 OD1 A:ASP67 2.2 27.2 1.0
O A:GLN62 2.3 31.0 1.0
OD1 A:ASN61 2.3 26.2 1.0
O A:CYS64 2.4 26.9 1.0
OD1 A:ASP59 2.4 30.1 1.0
OD2 A:ASP59 2.6 29.3 1.0
CG A:ASP59 2.8 28.4 1.0
CG A:ASP67 3.3 28.8 1.0
C A:GLN62 3.4 32.4 1.0
CG A:ASN61 3.4 27.3 1.0
C A:CYS64 3.5 30.1 1.0
OD2 A:ASP67 3.7 29.2 1.0
N A:GLN62 3.9 29.9 1.0
ND2 A:ASN61 3.9 27.7 1.0
CA A:GLN62 4.0 33.9 1.0
NE2 A:GLN133 4.1 29.7 1.0
CA A:ASN65 4.1 30.5 1.0
N A:ASN65 4.2 31.0 1.0
C A:ASN61 4.3 28.1 1.0
N A:CYS64 4.3 30.0 1.0
C A:GLY63 4.4 30.3 1.0
CB A:ASP59 4.4 27.4 1.0
CA A:CYS64 4.5 29.7 1.0
O A:HOH434 4.5 29.7 1.0
N A:GLY63 4.5 30.2 1.0
O A:ASN61 4.5 27.1 1.0
CB A:ASP67 4.6 28.8 1.0
O A:GLY63 4.7 31.8 1.0
CB A:ASN61 4.7 27.0 1.0
CA A:GLY63 4.7 30.1 1.0
N A:ASP67 4.8 29.4 1.0
C A:ASN65 4.8 30.8 1.0
CA A:ASN61 4.9 27.5 1.0
CD A:GLN133 4.9 26.9 1.0
O A:HOH416 4.9 22.6 1.0
C A:ASP67 5.0 26.8 1.0
CA A:ASP67 5.0 28.4 1.0

Calcium binding site 2 out of 6 in 5k31

Go back to Calcium Binding Sites List in 5k31
Calcium binding site 2 out of 6 in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer


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 Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:19.7
occ:1.00
 O B:GLN62 2.2 36.1 1.0
OD1 B:ASP67 2.2 35.0 1.0
O F:HOH408 2.3 12.9 1.0
OD1 B:ASN61 2.4 27.0 1.0
OD1 B:ASP59 2.4 35.2 1.0
O B:CYS64 2.4 33.1 1.0
OD2 B:ASP59 2.8 33.5 1.0
CG B:ASP59 3.0 33.7 1.0
CG B:ASP67 3.2 39.4 1.0
C B:GLN62 3.4 36.4 1.0
CG B:ASN61 3.4 28.5 1.0
OD2 B:ASP67 3.4 39.5 1.0
C B:CYS64 3.6 37.1 1.0
ND2 B:ASN61 3.9 28.2 1.0
N B:GLN62 4.0 32.4 1.0
CA B:GLN62 4.1 37.8 1.0
N B:CYS64 4.2 35.6 1.0
C B:ASN61 4.2 30.4 1.0
NE2 B:GLN133 4.2 28.9 1.0
O F:HOH437 4.3 30.7 1.0
OD1 F:ASP43 4.3 39.2 1.0
C B:GLY63 4.3 34.1 1.0
CA B:ASN65 4.3 38.1 1.0
N B:ASN65 4.4 38.6 1.0
N B:GLY63 4.4 36.7 1.0
CB B:ASP59 4.5 31.8 1.0
CA B:CYS64 4.5 36.6 1.0
O B:ASN61 4.5 30.3 1.0
CB B:ASP67 4.6 41.2 1.0
CB B:ASN61 4.6 27.3 1.0
CA B:GLY63 4.6 35.7 1.0
O B:GLY63 4.7 34.0 1.0
CA B:ASN61 4.8 28.2 1.0
N B:ASP67 4.8 41.0 1.0
C B:ASN65 4.9 38.2 1.0
CD B:GLN133 5.0 29.1 1.0

Calcium binding site 3 out of 6 in 5k31

Go back to Calcium Binding Sites List in 5k31
Calcium binding site 3 out of 6 in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer


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 Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:17.2
occ:1.00
 O C:GLN62 2.2 31.6 1.0
OD1 C:ASP67 2.2 30.2 1.0
OD1 C:ASN61 2.3 29.2 1.0
O C:CYS64 2.3 30.1 1.0
O B:HOH406 2.4 13.6 1.0
OD1 C:ASP59 2.4 29.2 1.0
OD2 C:ASP59 2.7 29.8 1.0
CG C:ASP59 2.9 27.8 1.0
CG C:ASP67 3.2 29.9 1.0
C C:GLN62 3.4 34.0 1.0
CG C:ASN61 3.4 31.8 1.0
OD2 C:ASP67 3.5 32.5 1.0
C C:CYS64 3.6 35.2 1.0
N C:GLN62 3.9 33.0 1.0
ND2 C:ASN61 4.0 31.4 1.0
CA C:GLN62 4.1 35.7 1.0
NE2 C:GLN133 4.1 30.5 1.0
C C:ASN61 4.2 31.4 1.0
N C:CYS64 4.3 36.6 1.0
C C:GLY63 4.3 36.0 1.0
CA C:ASN65 4.3 31.6 1.0
O B:HOH417 4.4 32.8 1.0
OD1 B:ASP43 4.4 36.2 1.0
N C:GLY63 4.4 33.8 1.0
CB C:ASP59 4.4 26.5 1.0
N C:ASN65 4.4 31.7 1.0
O C:ASN61 4.5 29.7 1.0
CA C:CYS64 4.5 36.8 1.0
O C:GLY63 4.5 37.2 1.0
CB C:ASP67 4.6 31.1 1.0
O C:HOH401 4.6 27.7 1.0
CB C:ASN61 4.7 30.6 1.0
CA C:GLY63 4.7 35.3 1.0
N C:ASP67 4.8 29.8 1.0
CA C:ASN61 4.8 30.1 1.0
C C:ASN65 4.9 31.2 1.0
CD C:GLN133 4.9 29.9 1.0
NH2 B:ARG42 4.9 43.1 1.0
C C:ASP67 5.0 27.9 1.0
OE1 C:GLN133 5.0 28.3 1.0

Calcium binding site 4 out of 6 in 5k31

Go back to Calcium Binding Sites List in 5k31
Calcium binding site 4 out of 6 in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer


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 Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:15.0
occ:1.00
 O D:GLN62 2.1 31.8 1.0
O D:CYS64 2.3 27.5 1.0
OD1 D:ASP67 2.3 27.0 1.0
OD1 D:ASN61 2.4 25.1 1.0
OD1 D:ASP59 2.4 26.1 1.0
OD2 D:ASP59 2.5 25.7 1.0
CG D:ASP59 2.8 24.9 1.0
C D:GLN62 3.3 30.5 1.0
CG D:ASP67 3.3 27.6 1.0
CG D:ASN61 3.4 26.8 1.0
C D:CYS64 3.5 30.9 1.0
OD2 D:ASP67 3.5 28.6 1.0
N D:GLN62 3.9 28.3 1.0
ND2 D:ASN61 3.9 26.4 1.0
CA D:GLN62 4.0 31.8 1.0
NE2 D:GLN133 4.1 26.9 1.0
N D:CYS64 4.2 32.2 1.0
C D:GLY63 4.3 30.8 1.0
C D:ASN61 4.3 27.4 1.0
CA D:ASN65 4.3 29.6 1.0
N D:GLY63 4.3 30.7 1.0
N D:ASN65 4.3 29.8 1.0
CB D:ASP59 4.3 24.4 1.0
CA D:CYS64 4.4 32.3 1.0
O D:GLY63 4.5 31.1 1.0
O D:ASN61 4.6 26.7 1.0
CA D:GLY63 4.6 31.8 1.0
CB D:ASN61 4.7 26.6 1.0
CB D:ASP67 4.7 27.4 1.0
C D:ASN65 4.9 29.3 1.0
N D:ASP67 4.9 28.4 1.0
CA D:ASN61 4.9 26.2 1.0

Calcium binding site 5 out of 6 in 5k31

Go back to Calcium Binding Sites List in 5k31
Calcium binding site 5 out of 6 in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer


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 Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:19.0
occ:1.00
 O E:GLN62 2.2 30.7 1.0
OD1 E:ASP67 2.3 30.0 1.0
O E:CYS64 2.3 29.2 1.0
OD1 E:ASN61 2.4 28.2 1.0
O A:HOH412 2.4 12.9 1.0
OD1 E:ASP59 2.5 32.5 1.0
OD2 E:ASP59 2.7 31.7 1.0
CG E:ASP59 2.9 30.7 1.0
CG E:ASP67 3.3 30.1 1.0
C E:GLN62 3.4 32.6 1.0
CG E:ASN61 3.4 26.5 1.0
C E:CYS64 3.5 32.3 1.0
OD2 E:ASP67 3.5 29.6 1.0
ND2 E:ASN61 3.9 28.0 1.0
N E:GLN62 4.0 28.5 1.0
CA E:GLN62 4.0 33.9 1.0
N E:CYS64 4.2 31.1 1.0
NE2 E:GLN133 4.3 26.3 1.0
C E:ASN61 4.3 27.9 1.0
CA E:ASN65 4.3 33.8 1.0
C E:GLY63 4.3 29.9 1.0
N E:ASN65 4.4 33.5 1.0
OD1 A:ASP43 4.4 32.4 1.0
N E:GLY63 4.4 31.4 1.0
CB E:ASP59 4.4 28.4 1.0
CA E:CYS64 4.5 32.5 1.0
O E:ASN61 4.5 25.1 1.0
CB E:ASP67 4.6 32.0 1.0
CA E:GLY63 4.7 31.8 1.0
CB E:ASN61 4.7 25.7 1.0
O E:GLY63 4.7 29.4 1.0
N E:ASP67 4.8 34.8 1.0
C E:ASN65 4.8 33.0 1.0
CA E:ASN61 4.9 26.6 1.0
C E:ASP67 4.9 32.4 1.0
CA E:ASP67 5.0 33.7 1.0

Calcium binding site 6 out of 6 in 5k31

Go back to Calcium Binding Sites List in 5k31
Calcium binding site 6 out of 6 in the Crystal Structure of Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer


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 Human Fibrillar Procollagen Type I C-Propeptide Homo-Trimer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:16.4
occ:1.00
 O F:GLN62 2.2 32.7 1.0
OD1 F:ASP67 2.2 27.0 1.0
OD1 F:ASN61 2.3 27.4 1.0
O F:CYS64 2.4 31.5 1.0
OD1 F:ASP59 2.4 31.0 1.0
O C:HOH402 2.5 13.2 1.0
OD2 F:ASP59 2.6 32.2 1.0
CG F:ASP59 2.9 31.0 1.0
CG F:ASP67 3.3 29.0 1.0
CG F:ASN61 3.4 29.4 1.0
C F:GLN62 3.4 33.8 1.0
C F:CYS64 3.5 34.0 1.0
OD2 F:ASP67 3.7 28.5 1.0
ND2 F:ASN61 3.9 29.8 1.0
N F:GLN62 4.1 31.4 1.0
NE2 F:GLN133 4.1 33.3 1.0
CA F:ASN65 4.1 31.3 1.0
CA F:GLN62 4.1 35.5 1.0
N F:CYS64 4.2 33.2 1.0
N F:ASN65 4.2 34.0 1.0
OD1 C:ASP43 4.3 31.4 1.0
C F:GLY63 4.3 33.3 1.0
C F:ASN61 4.3 29.5 1.0
CB F:ASP59 4.4 29.4 1.0
N F:GLY63 4.4 33.5 1.0
CA F:CYS64 4.5 33.9 1.0
O F:HOH439 4.5 27.0 1.0
O F:ASN61 4.5 27.6 1.0
O F:GLY63 4.6 34.9 1.0
CA F:GLY63 4.6 34.3 1.0
CB F:ASP67 4.7 29.7 1.0
CB F:ASN61 4.7 29.1 1.0
C F:ASN65 4.7 31.8 1.0
N F:ASP67 4.7 30.2 1.0
NH2 C:ARG42 4.9 33.6 1.0
O F:HOH404 4.9 21.0 1.0
CA F:ASN61 4.9 28.9 1.0
CD F:GLN133 4.9 30.1 1.0
C F:ASP67 5.0 28.4 1.0
CA F:ASP67 5.0 30.0 1.0

Reference:

U.Sharma, L.Carrique, S.Vadon-Le Goff, N.Mariano, R.N.Georges, F.Delolme, P.Koivunen, J.Myllyharju, C.Moali, N.Aghajari, D.J.Hulmes. Structural Basis of Homo- and Heterotrimerization of Collagen I. Nat Commun V. 8 14671 2017.
ISSN: ESSN 2041-1723
PubMed: 28281531
DOI: 10.1038/NCOMMS14671
Page generated: Mon Jul 15 06:39:55 2024

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