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

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

Resolution Low / High (Å)	79.37 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.090, 144.120, 158.740, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 25.8

The structure of Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Short) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Metalloproteinase Enhancer Pcpe-1 Bound to the Procollagen C Propeptide Trimer (Short) (pdb code 6fzv). 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 (Short), PDB code: 6fzv:
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 (Short)


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 (Short) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:60.8 occ:1.00 O A:CYS64 2.2 71.5 1.0 O A:GLN62 2.3 72.2 1.0 OD1 A:ASP67 2.3 65.9 1.0 OD2 A:ASP59 2.7 61.5 1.0 OD1 A:ASP59 2.7 61.1 1.0 OD1 A:ASN61 2.7 65.4 1.0 CG A:ASP59 3.0 61.5 1.0 CG A:ASP67 3.2 65.7 1.0 HD21 A:ASN61 3.2 81.8 1.0 OD2 A:ASP67 3.3 66.0 1.0 C A:CYS64 3.4 70.3 1.0 CG A:ASN61 3.4 66.8 1.0 C A:GLN62 3.5 73.0 1.0 ND2 A:ASN61 3.6 68.1 1.0 HB3 A:CYS64 3.8 74.7 1.0 N A:CYS64 3.9 62.3 1.0 H A:CYS64 3.9 74.8 1.0 HE22 A:GLN132 4.0 71.3 1.0 H A:ASP67 4.0 74.6 1.0 OD2 B:ASP43 4.0 82.5 1.0 N A:GLN62 4.1 73.8 1.0 HA A:LYS65 4.1 94.7 1.0 CA A:CYS64 4.1 62.5 1.0 C A:ASN61 4.2 69.9 1.0 C A:GLY63 4.2 69.3 1.0 CA A:GLN62 4.2 75.0 1.0 H A:GLN62 4.3 88.6 1.0 HA A:GLN62 4.4 90.0 1.0 O A:ASN61 4.4 72.0 1.0 HD22 A:ASN61 4.4 81.8 1.0 HA3 A:GLY63 4.5 82.9 1.0 N A:LYS65 4.5 72.9 1.0 N A:GLY63 4.5 72.8 1.0 CB A:CYS64 4.5 62.3 1.0 CB A:ASP59 4.6 61.8 1.0 NE2 A:GLN132 4.6 59.4 1.0 CB A:ASP67 4.6 66.3 1.0 CA A:GLY63 4.6 69.1 1.0 CA A:LYS65 4.7 78.9 1.0 CB A:ASN61 4.8 66.8 1.0 H A:ASN61 4.8 79.6 1.0 N A:ASP67 4.8 62.2 1.0 O A:GLY63 4.8 69.7 1.0 H A:LEU66 4.8 85.6 1.0 CG B:ASP43 4.8 80.2 1.0 HE21 A:GLN132 4.9 71.3 1.0 HB2 A:ASP59 4.9 74.2 1.0 HB3 A:ASP59 5.0 74.2 1.0 CA A:ASN61 5.0 67.0 1.0 OD1 B:ASP43 5.0 80.7 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 (Short)


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 (Short) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:66.3 occ:1.00 O B:GLN62 2.3 0.5 1.0 O B:CYS64 2.3 73.0 1.0 OD1 B:ASP67 2.4 71.9 1.0 OD1 B:ASP59 2.5 69.4 1.0 OD1 B:ASN61 2.5 60.5 1.0 OD2 B:ASP59 2.7 69.9 1.0 CG B:ASP59 2.9 69.7 1.0 OD2 B:ASP67 3.1 70.4 1.0 CG B:ASP67 3.1 70.3 1.0 HD21 B:ASN61 3.2 0.9 1.0 CG B:ASN61 3.3 60.6 1.0 C B:GLN62 3.3 61.0 1.0 C B:CYS64 3.5 72.8 1.0 ND2 B:ASN61 3.5 99.1 1.0 HE22 B:GLN132 3.7 88.8 1.0 N B:GLN62 3.8 91.5 1.0 H B:GLN62 3.9 0.8 1.0 HA B:GLN62 3.9 72.7 1.0 CA B:GLN62 3.9 60.6 1.0 N B:CYS64 3.9 72.7 1.0 H B:CYS64 4.0 87.2 1.0 HA B:LYS65 4.1 94.3 1.0 HB3 B:CYS64 4.1 88.1 1.0 H B:ASP67 4.2 84.6 1.0 C B:GLY63 4.2 62.2 1.0 C B:ASN61 4.2 90.4 1.0 CA B:CYS64 4.2 73.1 1.0 HD22 B:ASN61 4.3 0.9 1.0 NE2 B:GLN132 4.3 74.0 1.0 N B:GLY63 4.4 61.3 1.0 OD2 C:ASP43 4.4 83.2 1.0 CB B:ASP59 4.5 63.1 1.0 N B:LYS65 4.5 76.7 1.0 HA3 B:GLY63 4.5 74.2 1.0 H B:ASN61 4.6 71.7 1.0 CB B:ASP67 4.6 70.0 1.0 CB B:ASN61 4.6 60.2 1.0 CA B:GLY63 4.6 61.9 1.0 O B:ASN61 4.6 60.5 1.0 O B:GLY63 4.7 0.0 1.0 HE21 B:GLN132 4.7 88.8 1.0 CA B:LYS65 4.7 78.6 1.0 CB B:CYS64 4.7 73.4 1.0 HB2 B:ASP59 4.8 75.7 1.0 CA B:ASN61 4.8 60.0 1.0 HB3 B:ASP59 4.9 75.7 1.0 N B:ASP67 4.9 70.5 1.0 HA B:ASP59 5.0 75.2 1.0 N B:ASN61 5.0 59.8 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 (Short)


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 (Short) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:80.2 occ:1.00 O C:GLN62 2.3 79.4 1.0 OD1 C:ASP67 2.4 0.4 1.0 HD21 C:ASN61 2.5 0.3 1.0 OD2 C:ASP59 2.5 71.8 1.0 OD1 C:ASP59 2.6 74.2 1.0 O C:CYS64 2.7 93.8 1.0 OD2 C:ASP67 2.9 98.8 1.0 CG C:ASP59 2.9 71.9 1.0 OD1 C:ASN61 2.9 82.8 1.0 ND2 C:ASN61 3.0 84.4 1.0 CG C:ASP67 3.0 99.2 1.0 CG C:ASN61 3.2 82.4 1.0 C C:GLN62 3.4 78.7 1.0 C C:CYS64 3.6 96.3 1.0 HD22 C:ASN61 3.6 0.3 1.0 H C:CYS64 3.7 0.8 1.0 HB3 C:CYS64 3.8 0.6 1.0 N C:CYS64 3.8 90.6 1.0 N C:GLN62 3.9 77.3 1.0 H C:GLN62 4.0 92.7 1.0 CA C:GLN62 4.1 78.5 1.0 C C:ASN61 4.1 88.0 1.0 H C:ASP67 4.1 0.3 1.0 CA C:CYS64 4.2 93.0 1.0 HE22 C:GLN132 4.2 88.2 1.0 HA C:GLN62 4.2 94.2 1.0 OD2 A:ASP43 4.3 97.5 1.0 C C:GLY63 4.3 84.7 1.0 O C:ASN61 4.3 88.4 1.0 HA C:LYS65 4.4 0.7 1.0 N C:GLY63 4.4 87.5 1.0 CB C:CYS64 4.4 95.5 1.0 CB C:ASP59 4.4 73.0 1.0 HA3 C:GLY63 4.5 0.5 1.0 CB C:ASP67 4.5 0.9 1.0 CB C:ASN61 4.5 81.9 1.0 N C:LYS65 4.6 0.3 1.0 H C:ASN61 4.6 98.2 1.0 CA C:GLY63 4.7 84.6 1.0 NE2 C:GLN132 4.8 73.5 1.0 CA C:ASN61 4.8 83.9 1.0 HB2 C:ASP59 4.8 87.6 1.0 HB2 C:CYS64 4.8 0.6 1.0 HB3 C:ASP59 4.8 87.6 1.0 HB2 C:ASP67 4.8 0.1 1.0 CA C:LYS65 4.9 0.6 1.0 N C:ASP67 4.9 0.9 1.0 H C:LEU66 5.0 0.8 1.0 O C:GLY63 5.0 82.5 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 (Short)


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 (Short) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:82.8 occ:1.00 OD1 D:ASP109 2.4 78.8 1.0 O D:THR112 2.4 80.7 1.0 O D:GLY111 2.4 83.2 1.0 OD2 D:ASP68 2.5 86.1 1.0 OE1 D:GLU60 2.6 0.5 1.0 OD1 D:ASP68 2.8 86.3 1.0 CG D:ASP68 3.0 86.4 1.0 C D:GLY111 3.3 83.2 1.0 H D:ASP109 3.3 0.8 1.0 C D:THR112 3.5 82.0 1.0 CG D:ASP109 3.6 77.0 1.0 H D:GLY111 3.7 99.5 1.0 HB D:THR112 3.7 99.0 1.0 CD D:GLU60 3.8 0.4 1.0 HE1 D:TYR32 4.0 88.2 1.0 HB2 D:GLU60 4.0 83.9 1.0 N D:THR112 4.0 84.4 1.0 HB3 D:TYR67 4.1 99.2 1.0 N D:ASP109 4.1 95.7 1.0 HH D:TYR32 4.1 0.7 1.0 CA D:GLY111 4.1 71.4 1.0 HZ3 A:LYS35 4.1 94.2 1.0 N D:GLY111 4.2 82.9 1.0 CA D:THR112 4.2 83.2 1.0 OD2 D:ASP109 4.2 73.3 1.0 HB D:THR108 4.3 88.3 1.0 HB3 D:GLU60 4.3 83.9 1.0 HA2 D:GLY111 4.3 85.7 1.0 O D:ASP109 4.3 96.9 1.0 HZ2 A:LYS35 4.3 94.2 1.0 CB D:THR112 4.4 82.5 1.0 CB D:ASP68 4.4 89.2 1.0 OE2 D:GLU60 4.5 0.9 1.0 C D:ASP109 4.5 97.9 1.0 CB D:GLU60 4.5 69.9 1.0 HA3 D:GLY113 4.5 0.8 1.0 HA2 D:GLY113 4.6 0.8 1.0 NZ A:LYS35 4.6 78.5 1.0 N D:GLY113 4.6 87.3 1.0 CA D:ASP109 4.6 91.8 1.0 CB D:ASP109 4.7 88.0 1.0 HB2 D:ASP68 4.7 0.1 1.0 HA D:THR108 4.7 87.2 1.0 HZ1 A:LYS35 4.8 94.2 1.0 CG D:GLU60 4.8 68.9 1.0 H D:THR112 4.8 0.2 1.0 CE1 D:TYR32 4.8 73.5 1.0 CA D:GLY113 4.9 85.7 1.0 OH D:TYR32 4.9 88.9 1.0 HB3 D:ASP68 4.9 0.1 1.0 CB D:TYR67 5.0 82.7 1.0 HB3 D:ASP109 5.0 0.6 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 (Short)


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 (Short) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:89.9 occ:1.00 OD1 D:ASP233 2.3 0.5 1.0 OE1 D:GLU183 2.3 0.6 1.0 O D:SER235 2.4 0.4 1.0 O D:VAL236 2.4 0.3 1.0 OD2 D:ASP191 2.5 0.2 1.0 OD1 D:ASP191 2.6 97.3 1.0 CG D:ASP191 2.8 0.2 1.0 HB D:VAL236 3.2 0.3 1.0 H D:ASP233 3.4 0.4 1.0 CD D:GLU183 3.4 0.0 1.0 C D:SER235 3.4 0.3 1.0 CG D:ASP233 3.5 0.3 1.0 C D:VAL236 3.5 99.5 1.0 HB2 D:GLU183 3.7 0.4 1.0 H D:SER235 3.8 0.9 1.0 HB3 D:TYR190 3.9 0.7 1.0 HB3 D:GLU183 3.9 0.4 1.0 HH D:TYR155 3.9 0.7 1.0 CB D:VAL236 4.1 95.2 1.0 OD2 D:ASP233 4.1 99.9 1.0 HZ1 B:LYS18 4.1 0.1 1.0 CA D:VAL236 4.1 99.7 1.0 O D:ASP233 4.1 0.2 1.0 N D:ASP233 4.1 0.5 1.0 N D:VAL236 4.1 0.1 1.0 OE2 D:GLU183 4.2 0.8 1.0 CB D:GLU183 4.2 96.2 1.0 CB D:ASP191 4.2 0.5 1.0 HE1 D:TYR155 4.3 0.7 1.0 HA D:THR237 4.3 0.9 1.0 HZ3 B:LYS18 4.4 0.1 1.0 HZ2 B:LYS18 4.4 0.1 1.0 CG D:GLU183 4.4 99.0 1.0 HB2 D:ASP191 4.4 0.8 1.0 N D:SER235 4.5 0.5 1.0 NZ B:LYS18 4.5 94.2 1.0 OG D:SER232 4.5 0.8 1.0 CA D:SER235 4.5 0.1 1.0 HA D:SER232 4.5 0.4 1.0 C D:ASP233 4.6 0.7 1.0 CB D:ASP233 4.6 0.4 1.0 HG12 D:VAL236 4.6 0.8 1.0 H D:ASP191 4.6 0.6 1.0 CA D:ASP233 4.7 0.8 1.0 N D:THR237 4.7 0.6 1.0 N D:ASP191 4.7 0.2 1.0 OH D:TYR155 4.8 0.3 1.0 CB D:TYR190 4.8 96.4 1.0 HB3 D:ASP191 4.8 0.8 1.0 HG3 D:GLU183 4.9 0.8 1.0 HG23 D:VAL236 4.9 0.8 1.0 CG1 D:VAL236 4.9 94.0 1.0 HB2 D:TYR190 4.9 0.7 1.0 HG D:SER232 4.9 1.0 1.0 H D:VAL236 4.9 0.3 1.0 C D:TYR190 5.0 97.7 1.0 CA D:ASP191 5.0 0.2 1.0 HB3 D:SER235 5.0 0.1 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