Calcium in PDB 4lp7: Crystal Structure of the Human Metapneumovirus Matrix Protein

The structure of Crystal Structure of the Human Metapneumovirus Matrix Protein, PDB code: 4lp7 was solved by C.Leyrat, K.Harlos, J.M.Grimes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.70 / 2.83
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	62.009, 62.009, 275.385, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 22.9

The structure of Crystal Structure of the Human Metapneumovirus Matrix Protein also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Human Metapneumovirus Matrix Protein (pdb code 4lp7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Human Metapneumovirus Matrix Protein, PDB code: 4lp7:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Human Metapneumovirus Matrix Protein


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 Human Metapneumovirus Matrix Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:70.3 occ:1.00 O A:LEU28 2.2 85.4 1.0 O A:HOH426 2.2 69.9 1.0 OD2 A:ASP26 2.5 91.3 1.0 OD1 A:ASP26 2.7 90.8 1.0 O A:LYS101 2.7 68.6 1.0 OE1 A:GLU24 2.8 62.6 1.0 CG A:ASP26 2.9 89.3 1.0 C A:LEU28 3.3 87.7 1.0 CD A:GLU24 3.3 83.4 1.0 OE2 A:GLU24 3.6 66.1 1.0 C A:LYS101 3.7 69.6 1.0 CB A:LEU28 4.0 88.1 1.0 CA A:LEU28 4.1 87.7 1.0 N A:PRO29 4.2 81.3 1.0 N A:GLU103 4.2 74.2 1.0 CB A:ASP26 4.3 78.2 1.0 CA A:PRO29 4.3 79.2 1.0 N A:LEU28 4.3 88.3 1.0 CG A:GLU24 4.4 76.0 1.0 CA A:LYS101 4.5 70.4 1.0 N A:ALA30 4.5 74.1 1.0 CB A:GLU24 4.6 74.7 1.0 N A:LEU102 4.6 65.4 1.0 CB A:GLU103 4.6 78.5 1.0 CA A:LEU102 4.7 64.2 1.0 C A:PRO29 4.8 81.1 1.0 CB A:LYS101 4.9 71.7 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Human Metapneumovirus Matrix Protein


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 Human Metapneumovirus Matrix Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:69.5 occ:1.00 O B:LEU28 2.1 85.8 1.0 OD2 B:ASP26 2.4 90.2 1.0 OE1 B:GLU24 2.4 79.0 1.0 O B:HOH428 2.4 80.5 1.0 O B:LYS101 2.5 76.0 1.0 OD1 B:ASP26 2.5 85.8 1.0 O B:HOH412 2.7 80.5 1.0 CG B:ASP26 2.8 86.7 1.0 CD B:GLU24 3.1 83.9 1.0 C B:LEU28 3.3 86.7 1.0 OE2 B:GLU24 3.4 71.2 1.0 C B:LYS101 3.7 75.0 1.0 CA B:PRO29 4.1 78.9 1.0 N B:PRO29 4.1 81.2 1.0 CB B:LEU28 4.1 84.8 1.0 CA B:LEU28 4.2 84.7 1.0 CB B:ASP26 4.2 79.7 1.0 CG B:GLU24 4.3 76.2 1.0 N B:ALA30 4.3 74.9 1.0 CB B:GLU24 4.4 74.9 1.0 N B:LEU28 4.4 85.3 1.0 N B:GLU103 4.5 71.0 1.0 C B:PRO29 4.5 78.7 1.0 CA B:LYS101 4.5 73.1 1.0 N B:LEU102 4.6 70.3 1.0 O B:HOH435 4.7 86.5 1.0 CA B:LEU102 4.7 67.8 1.0 CB B:LYS101 4.8 74.3 1.0 CB B:GLU103 4.9 74.9 1.0 CB B:ALA30 5.0 76.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Human Metapneumovirus Matrix Protein


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 Human Metapneumovirus Matrix Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:79.0 occ:1.00 O C:LEU28 2.1 88.6 1.0 O C:HOH423 2.4 76.4 1.0 OD2 C:ASP26 2.4 95.5 1.0 O C:LYS101 2.4 76.5 1.0 OE1 C:GLU24 2.5 79.7 1.0 O C:HOH418 2.5 60.8 1.0 OD1 C:ASP26 2.5 86.6 1.0 CG C:ASP26 2.8 88.8 1.0 CD C:GLU24 3.1 91.0 1.0 OE2 C:GLU24 3.2 87.5 1.0 C C:LEU28 3.2 89.1 1.0 C C:LYS101 3.6 76.3 1.0 N C:PRO29 4.1 81.3 1.0 CA C:PRO29 4.1 78.6 1.0 CB C:LEU28 4.1 87.5 1.0 CA C:LEU28 4.2 87.4 1.0 CB C:ASP26 4.2 79.3 1.0 N C:ALA30 4.3 71.4 1.0 CG C:GLU24 4.3 81.8 1.0 N C:LEU28 4.4 87.1 1.0 CB C:GLU24 4.5 75.2 1.0 O C:HOH437 4.5 68.4 1.0 CA C:LYS101 4.5 75.7 1.0 N C:GLU103 4.5 72.3 1.0 N C:LEU102 4.5 71.5 1.0 C C:PRO29 4.6 78.8 1.0 CA C:LEU102 4.7 70.0 1.0 CB C:LYS101 4.8 76.5 1.0 CB C:GLU103 4.8 75.5 1.0 CB C:ALA30 4.9 70.4 1.0 C C:LEU102 5.0 75.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Human Metapneumovirus Matrix Protein


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 Human Metapneumovirus Matrix Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:74.8 occ:1.00 O D:LEU28 2.3 87.0 1.0 OD2 D:ASP26 2.4 87.4 1.0 O D:LYS101 2.4 74.9 1.0 OE1 D:GLU24 2.5 66.5 1.0 O D:HOH437 2.6 95.5 1.0 OD1 D:ASP26 2.7 90.0 1.0 O D:HOH419 2.8 55.1 1.0 CG D:ASP26 2.8 88.4 1.0 CD D:GLU24 3.1 93.6 1.0 OE2 D:GLU24 3.2 93.3 1.0 C D:LEU28 3.4 88.6 1.0 C D:LYS101 3.6 74.3 1.0 CB D:LEU28 4.1 88.5 1.0 CA D:LEU28 4.2 88.4 1.0 N D:GLU103 4.2 70.1 1.0 CB D:ASP26 4.3 80.6 1.0 N D:PRO29 4.3 82.8 1.0 CG D:GLU24 4.3 76.7 1.0 CA D:PRO29 4.4 80.9 1.0 N D:LEU28 4.4 89.4 1.0 N D:LEU102 4.5 70.3 1.0 N D:ALA30 4.6 71.2 1.0 CA D:LYS101 4.6 71.4 1.0 CA D:LEU102 4.6 68.5 1.0 CB D:GLU103 4.6 73.8 1.0 O D:HOH441 4.6 88.7 1.0 CB D:GLU24 4.7 74.8 1.0 C D:PRO29 4.8 79.2 1.0 C D:LEU102 4.8 72.9 1.0 CG D:GLU103 4.9 92.2 1.0 CB D:LYS101 5.0 72.3 1.0

C.Leyrat, M.Renner, K.Harlos, J.T.Huiskonen, J.M.Grimes. Structure and Self-Assembly of the Calcium Binding Matrix Protein of Human Metapneumovirus. Structure V. 22 136 2014.
ISSN: ISSN 0969-2126
PubMed: 24316400
DOI: 10.1016/J.STR.2013.10.013