Calcium in PDB 6fzw: Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long)

The structure of Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long), PDB code: 6fzw was solved by E.Hohenester, D.Pulido, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.79 / 2.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.880, 143.650, 156.710, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 27.1

The binding sites of Calcium atom in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long) (pdb code 6fzw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long), PDB code: 6fzw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long)


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 Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:62.9 occ:1.00 O A:CYS64 2.3 69.9 1.0 OD1 A:ASP67 2.3 69.2 1.0 O A:GLN62 2.3 62.8 1.0 OD1 A:ASN61 2.5 63.6 1.0 OD2 A:ASP59 2.5 63.6 1.0 OD1 A:ASP59 2.7 63.4 1.0 CG A:ASP59 2.9 63.6 1.0 CG A:ASP67 3.2 69.0 1.0 HD22 A:ASN61 3.3 75.8 1.0 CG A:ASN61 3.3 63.3 1.0 OD2 A:ASP67 3.3 68.6 1.0 C A:CYS64 3.4 70.2 1.0 C A:GLN62 3.5 63.0 1.0 ND2 A:ASN61 3.6 63.1 1.0 H A:CYS64 3.8 83.6 1.0 HB3 A:CYS64 3.8 83.8 1.0 N A:CYS64 3.8 69.7 1.0 OD2 B:ASP43 4.0 71.2 1.0 H A:ASP67 4.1 84.1 1.0 CA A:CYS64 4.1 70.1 1.0 N A:GLN62 4.1 62.8 1.0 HA A:LYS65 4.1 77.7 1.0 H A:GLN62 4.2 75.3 1.0 C A:GLY63 4.2 66.2 1.0 CA A:GLN62 4.2 63.1 1.0 HA A:GLN62 4.3 75.7 1.0 HE22 A:GLN132 4.3 75.8 1.0 C A:ASN61 4.4 63.5 1.0 HD21 A:ASN61 4.4 75.8 1.0 HA3 A:GLY63 4.4 79.0 1.0 CB A:ASP59 4.4 64.1 1.0 CB A:CYS64 4.5 69.9 1.0 N A:GLY63 4.5 65.8 1.0 N A:LYS65 4.5 64.5 1.0 CB A:ASN61 4.6 63.0 1.0 OD1 B:ASP43 4.6 70.8 1.0 CB A:ASP67 4.6 69.3 1.0 CA A:GLY63 4.6 65.8 1.0 CG B:ASP43 4.6 71.0 1.0 O A:GLY63 4.7 66.7 1.0 O A:ASN61 4.7 63.3 1.0 HH11 B:ARG39 4.7 81.2 1.0 CA A:LYS65 4.8 64.8 1.0 N A:ASP67 4.8 70.0 1.0 H A:ASN61 4.8 76.4 1.0 HB3 A:ASP59 4.8 77.0 1.0 NE2 A:GLN132 4.8 63.1 1.0 HB2 A:ASN61 4.8 75.6 1.0 HB2 A:ASP59 4.9 77.0 1.0 H A:LEU66 4.9 80.6 1.0 CA A:ASN61 5.0 63.3 1.0 C A:ASP67 5.0 69.9 1.0 HA A:CYS64 5.0 84.1 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long)


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 Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:63.3 occ:1.00 O B:GLN62 2.3 65.5 1.0 OD1 B:ASP67 2.3 63.6 1.0 O B:CYS64 2.3 68.0 1.0 OD1 B:ASN61 2.5 66.4 1.0 OD2 B:ASP59 2.5 63.3 1.0 OD1 B:ASP59 2.6 62.9 1.0 CG B:ASP59 2.9 63.0 1.0 OD2 B:ASP67 3.0 63.3 1.0 CG B:ASP67 3.0 63.5 1.0 HD21 B:ASN61 3.1 79.8 1.0 CG B:ASN61 3.3 66.3 1.0 C B:GLN62 3.4 65.5 1.0 ND2 B:ASN61 3.5 66.5 1.0 C B:CYS64 3.5 68.6 1.0 HE22 B:GLN132 3.5 82.0 1.0 OD2 C:ASP43 3.7 73.9 1.0 N B:CYS64 3.8 68.4 1.0 H B:CYS64 3.8 82.1 1.0 HB3 B:CYS64 3.9 82.9 1.0 C B:GLY63 4.1 64.6 1.0 NE2 B:GLN132 4.1 68.3 1.0 N B:GLN62 4.1 64.6 1.0 CA B:CYS64 4.1 68.9 1.0 H B:ASP67 4.2 77.6 1.0 CA B:GLN62 4.2 65.1 1.0 H B:GLN62 4.2 77.6 1.0 HA B:LYS65 4.3 89.0 1.0 HD22 B:ASN61 4.3 79.8 1.0 HA3 B:GLY63 4.3 77.1 1.0 HA B:GLN62 4.3 78.1 1.0 HE21 B:GLN132 4.3 82.0 1.0 C B:ASN61 4.4 66.2 1.0 N B:GLY63 4.4 63.7 1.0 CB B:ASP59 4.4 62.9 1.0 CB B:ASP67 4.5 63.8 1.0 CA B:GLY63 4.5 64.2 1.0 O B:GLY63 4.5 64.8 1.0 CG C:ASP43 4.5 74.1 1.0 N B:LYS65 4.6 74.3 1.0 CB B:CYS64 4.6 69.1 1.0 CB B:ASN61 4.6 65.9 1.0 H B:ASN61 4.6 78.9 1.0 O B:ASN61 4.7 66.5 1.0 OD1 C:ASP43 4.7 73.8 1.0 HB3 B:ASP59 4.8 75.5 1.0 CA B:LYS65 4.8 74.2 1.0 HB2 B:ASP59 4.8 75.5 1.0 N B:ASP67 4.9 64.6 1.0 HB3 B:ASP67 4.9 76.6 1.0 CA B:ASN61 4.9 65.9 1.0 HB2 B:ASN61 4.9 79.1 1.0 CD B:GLN132 4.9 67.9 1.0 HB2 B:ASP67 5.0 76.6 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long)


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 Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:71.0 occ:1.00 OD1 C:ASP67 2.3 88.8 1.0 O C:GLN62 2.4 69.5 1.0 OD2 C:ASP59 2.4 71.2 1.0 O C:CYS64 2.5 80.7 1.0 OD1 C:ASP59 2.6 71.0 1.0 OD1 C:ASN61 2.6 75.9 1.0 CG C:ASP59 2.8 71.1 1.0 OD2 C:ASP67 2.9 88.0 1.0 CG C:ASP67 2.9 88.7 1.0 HD21 C:ASN61 3.1 91.4 1.0 CG C:ASN61 3.3 75.7 1.0 C C:GLN62 3.4 69.2 1.0 ND2 C:ASN61 3.5 76.1 1.0 C C:CYS64 3.7 81.3 1.0 N C:GLN62 3.9 68.5 1.0 OD1 A:ASP43 4.0 91.7 1.0 H C:GLN62 4.0 82.3 1.0 CA C:GLN62 4.1 68.8 1.0 N C:CYS64 4.1 80.3 1.0 HE22 C:GLN132 4.1 89.2 1.0 HA C:GLN62 4.2 82.6 1.0 C C:ASN61 4.2 74.9 1.0 H C:CYS64 4.2 96.4 1.0 HB3 C:CYS64 4.2 98.0 1.0 H C:ASP67 4.2 0.5 1.0 HA C:LYS65 4.3 0.3 1.0 C C:GLY63 4.3 68.0 1.0 HD22 C:ASN61 4.3 91.4 1.0 CB C:ASP59 4.4 71.2 1.0 CB C:ASP67 4.4 89.5 1.0 CA C:CYS64 4.4 81.2 1.0 N C:GLY63 4.4 66.8 1.0 HA3 C:GLY63 4.5 80.7 1.0 O C:ASN61 4.5 74.8 1.0 H C:ASN61 4.6 89.9 1.0 CB C:ASN61 4.6 75.0 1.0 CA C:GLY63 4.7 67.2 1.0 O C:GLY63 4.7 68.3 1.0 HB3 C:ASP59 4.7 85.4 1.0 N C:LYS65 4.7 90.2 1.0 NE2 C:GLN132 4.7 74.3 1.0 HB2 C:ASP59 4.8 85.4 1.0 HB3 C:ASP67 4.8 0.4 1.0 CA C:ASN61 4.8 74.7 1.0 CB C:CYS64 4.9 81.7 1.0 CA C:LYS65 4.9 90.3 1.0 HB2 C:ASP67 4.9 0.4 1.0 N C:ASP67 4.9 90.5 1.0 C C:ASP67 5.0 89.7 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long)


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 Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:79.3 occ:1.00 OD1 D:ASP109 2.4 95.0 1.0 O D:THR112 2.5 87.8 1.0 O D:GLY111 2.5 83.3 1.0 OD1 D:ASP68 2.6 97.9 1.0 OE1 D:GLU60 2.6 75.3 1.0 OD2 D:ASP68 2.7 98.9 1.0 CG D:ASP68 3.0 98.5 1.0 H D:ASP109 3.3 0.7 1.0 C D:GLY111 3.3 84.0 1.0 C D:THR112 3.6 88.3 1.0 H D:GLY111 3.6 99.8 1.0 HZ1 A:LYS35 3.7 96.7 1.0 CG D:ASP109 3.7 94.1 1.0 HE1 D:TYR32 3.8 97.5 1.0 CD D:GLU60 3.8 74.8 1.0 HB2 D:GLU60 4.0 91.9 1.0 CA D:GLY111 4.0 84.0 1.0 HB D:THR112 4.0 0.7 1.0 N D:GLY111 4.0 83.2 1.0 N D:THR112 4.0 87.4 1.0 N D:ASP109 4.1 96.4 1.0 HA2 D:GLY111 4.1 0.9 1.0 HH D:TYR32 4.1 96.6 1.0 HB3 D:TYR67 4.1 0.7 1.0 HB D:THR108 4.2 95.2 1.0 HZ3 A:LYS35 4.2 96.7 1.0 NZ A:LYS35 4.2 80.5 1.0 O D:ASP109 4.3 96.6 1.0 HZ2 A:LYS35 4.3 96.7 1.0 CA D:THR112 4.3 87.6 1.0 OD2 D:ASP109 4.4 93.1 1.0 HB3 D:GLU60 4.4 91.9 1.0 C D:ASP109 4.4 95.6 1.0 CB D:ASP68 4.5 98.8 1.0 HA2 D:GLY113 4.5 1.0 1.0 OE2 D:GLU60 4.5 74.0 1.0 CB D:GLU60 4.6 76.6 1.0 HB3 D:PRO34 4.6 94.9 1.0 CA D:ASP109 4.6 95.4 1.0 N D:GLY113 4.6 99.1 1.0 HG21 D:THR108 4.7 96.4 1.0 HA3 D:GLY113 4.7 1.0 1.0 CB D:THR112 4.7 86.4 1.0 HA D:THR108 4.7 93.9 1.0 CE1 D:TYR32 4.7 81.2 1.0 CB D:ASP109 4.7 94.2 1.0 H D:THR112 4.7 0.9 1.0 CG D:GLU60 4.8 75.4 1.0 HB2 D:ASP68 4.8 0.6 1.0 CA D:GLY113 4.9 100.0 1.0 OH D:TYR32 4.9 80.5 1.0 HA3 D:GLY111 4.9 0.9 1.0 CB D:THR108 4.9 79.4 1.0 N D:ASP68 5.0 96.6 1.0 HB3 D:ASP68 5.0 0.6 1.0 N D:GLU110 5.0 93.0 1.0 H D:ASP68 5.0 1.0 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long)


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 Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Long) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:89.8 occ:1.00 O D:VAL236 2.4 0.3 1.0 OD2 D:ASP191 2.4 0.4 1.0 O D:SER235 2.4 0.2 1.0 OE1 D:GLU183 2.5 0.1 1.0 OD1 D:ASP191 2.5 0.8 1.0 OD1 D:ASP233 2.6 97.4 1.0 CG D:ASP191 2.8 0.7 1.0 CD D:GLU183 3.5 0.2 1.0 HB D:VAL236 3.5 0.9 1.0 C D:SER235 3.5 0.2 1.0 C D:VAL236 3.5 0.8 1.0 HB2 D:GLU183 3.6 0.1 1.0 H D:ASP233 3.6 0.4 1.0 H D:SER235 3.9 0.5 1.0 CG D:ASP233 3.9 96.8 1.0 HH D:TYR155 3.9 0.6 1.0 HE1 D:TYR155 4.1 0.1 1.0 HZ3 B:LYS18 4.1 0.7 1.0 OE2 D:GLU183 4.1 0.9 1.0 HB3 D:TYR190 4.2 0.3 1.0 CA D:VAL236 4.2 0.0 1.0 HB3 D:GLU183 4.2 0.1 1.0 N D:VAL236 4.2 0.5 1.0 CB D:GLU183 4.2 0.6 1.0 CB D:ASP191 4.2 0.8 1.0 CB D:VAL236 4.2 0.9 1.0 HA D:THR237 4.3 0.3 1.0 N D:ASP233 4.3 99.5 1.0 OG D:SER232 4.3 1.0 1.0 O D:ASP233 4.3 0.9 1.0 HA D:SER232 4.4 0.2 1.0 CG D:GLU183 4.4 0.8 1.0 HB2 D:ASP191 4.5 0.3 1.0 H D:ASP191 4.5 0.6 1.0 OD2 D:ASP233 4.5 95.6 1.0 N D:SER235 4.5 0.5 1.0 CA D:SER235 4.6 0.8 1.0 N D:THR237 4.6 0.4 1.0 HZ2 B:LYS18 4.7 0.7 1.0 HG3 D:GLU183 4.7 0.1 1.0 HG13 D:VAL236 4.7 0.5 1.0 NZ B:LYS18 4.7 92.2 1.0 HG D:SER232 4.7 0.6 1.0 OH D:TYR155 4.7 0.8 1.0 HZ1 B:LYS18 4.7 0.7 1.0 N D:ASP191 4.7 0.5 1.0 C D:ASP233 4.8 0.8 1.0 HB3 D:ASP191 4.8 0.3 1.0 HB3 D:SER235 4.8 0.6 1.0 CA D:ASP233 4.9 99.5 1.0 CE1 D:TYR155 4.9 0.8 1.0 CA D:THR237 4.9 0.4 1.0 CB D:ASP233 5.0 97.6 1.0 H D:VAL236 5.0 1.0 1.0 CA D:ASP191 5.0 0.7 1.0

D.Pulido, U.Sharma, S.Vadon-Le Goff, S.A.Hussain, S.Cordes, N.Mariano, E.Bettler, C.Moali, N.Aghajari, E.Hohenester, D.J.S.Hulmes. Structural Basis For the Acceleration of Procollagen Processing By Procollagen C-Proteinase Enhancer-1. Structure V. 26 1384 2018.
ISSN: ISSN 1878-4186
PubMed: 30078642
DOI: 10.1016/J.STR.2018.06.011