Calcium in PDB 5m6d: Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure

The structure of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure, PDB code: 5m6d was solved by C.Gaboriaud, C.P.Moreau, A.M.Di Guilmi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.52 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.041, 130.237, 79.837, 90.00, 119.64, 90.00
R / Rfree (%)	19.5 / 21.5

The structure of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure (pdb code 5m6d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure, PDB code: 5m6d:

Calcium binding site 1 out of 1 in the Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Streptococcus Pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (Spgapdh) Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:87.0 occ:1.00 O A:VAL47 2.3 54.6 1.0 O A:HOH626 2.4 37.0 1.0 O A:HOH580 2.4 43.0 1.0 O A:VAL44 2.5 58.3 1.0 O A:ILE41 2.6 53.2 1.0 H A:VAL44 3.4 67.9 1.0 C A:VAL47 3.5 54.8 1.0 C A:VAL44 3.5 59.0 1.0 H A:VAL47 3.5 69.0 1.0 HA A:GLN42 3.6 63.3 1.0 HG22 A:ILE41 3.6 61.7 1.0 C A:ILE41 3.7 52.0 1.0 HA A:GLU48 3.8 65.8 1.0 HG23 A:ILE41 3.8 61.7 1.0 HB3 A:GLU48 3.8 67.4 1.0 O A:GLN42 3.9 55.6 1.0 N A:VAL44 4.0 56.6 1.0 C A:GLN42 4.0 54.5 1.0 HA A:GLU45 4.0 76.7 1.0 HB A:VAL44 4.1 67.9 1.0 CA A:GLN42 4.2 52.8 1.0 CG2 A:ILE41 4.2 51.4 1.0 N A:VAL47 4.2 57.5 1.0 CA A:VAL44 4.3 57.8 1.0 CA A:GLU48 4.4 54.8 1.0 N A:GLN42 4.4 52.0 1.0 HB A:VAL47 4.4 66.7 1.0 N A:GLU48 4.4 55.9 1.0 N A:GLU45 4.4 62.8 1.0 CA A:VAL47 4.5 56.0 1.0 CB A:GLU48 4.5 56.2 1.0 O A:HOH614 4.5 31.7 1.0 H A:GLY46 4.6 72.9 1.0 N A:ASN43 4.6 55.3 1.0 CA A:GLU45 4.6 63.9 1.0 HB2 A:GLU48 4.6 67.4 1.0 CB A:VAL44 4.7 56.6 1.0 HA A:ILE41 4.8 61.8 1.0 CA A:ILE41 4.8 51.5 1.0 N A:GLY46 4.8 60.8 1.0 HG21 A:ILE41 4.9 61.7 1.0 C A:ASN43 4.9 58.6 1.0 C A:GLU45 4.9 63.5 1.0 H A:ASN43 5.0 66.3 1.0 CB A:VAL47 5.0 55.6 1.0

C.Moreau, R.Terrasse, N.M.Thielens, T.Vernet, C.Gaboriaud, A.M.Di Guilmi. Deciphering Key Residues Involved in the Virulence-Promoting Interactions Between Streptococcus Pneumoniae and Human Plasminogen. J. Biol. Chem. V. 292 2217 2017.
ISSN: ESSN 1083-351X
PubMed: 28011643
DOI: 10.1074/JBC.M116.764209