Magnesium in PDB 3zlb: Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae

All present enzymatic activity of Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae:
2.7.2.3;

The structure of Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae, PDB code: 3zlb was solved by N.Bernardo-Garcia, J.A.Hermoso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.937 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.347, 78.227, 59.033, 90.00, 96.34, 90.00
R / Rfree (%)	14.52 / 19.21

The binding sites of Magnesium atom in the Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae (pdb code 3zlb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae, PDB code: 3zlb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1399 b:37.0 occ:1.00 HZ3 A:LYS398 1.5 54.2 1.0 HZ2 A:LYS398 1.9 54.2 1.0 NZ A:LYS398 2.0 45.2 1.0 H31 A:GOL1403 2.6 39.7 1.0 HZ1 A:LYS398 2.6 54.2 1.0 OD2 A:ASP8 2.7 17.5 1.0 HG21 A:THR5 2.9 23.2 1.0 H2 A:MET1 3.0 51.4 1.0 O A:MET1 3.1 29.4 1.0 HE3 A:LYS398 3.1 52.0 1.0 HO2 A:GOL1403 3.1 41.9 1.0 O A:LYS3 3.1 16.0 1.0 CE A:LYS398 3.2 43.3 1.0 HB3 A:MET1 3.4 47.2 1.0 C3 A:GOL1403 3.5 33.0 1.0 HA A:LEU4 3.5 14.9 1.0 H A:THR5 3.5 14.5 1.0 O3 A:GOL1403 3.6 35.6 1.0 HB2 A:MET1 3.7 47.2 1.0 CG A:ASP8 3.7 19.2 1.0 N A:MET1 3.7 42.8 1.0 H1 A:MET1 3.8 51.4 1.0 CB A:MET1 3.8 39.3 1.0 CG2 A:THR5 3.8 19.3 1.0 HE2 A:LYS398 3.8 52.0 1.0 HD2 A:LYS398 3.9 47.2 1.0 C A:MET1 3.9 37.2 1.0 HB2 A:LYS398 3.9 26.2 1.0 O2 A:GOL1403 4.0 34.9 1.0 OD1 A:ASP8 4.0 16.7 1.0 CA A:MET1 4.0 38.3 1.0 HO3 A:GOL1403 4.0 42.8 1.0 N A:THR5 4.0 12.1 1.0 CD A:LYS398 4.0 39.3 1.0 HG22 A:THR5 4.0 23.2 1.0 HG3 A:LYS398 4.1 37.1 1.0 H12 A:GOL1403 4.1 44.6 1.0 C2 A:GOL1403 4.2 39.8 1.0 C A:LYS3 4.2 17.0 1.0 CA A:LEU4 4.2 12.4 1.0 H32 A:GOL1403 4.3 39.7 1.0 OG1 A:THR5 4.3 13.3 1.0 H11 A:GOL1403 4.4 44.6 1.0 C A:LEU4 4.4 13.1 1.0 HG23 A:THR5 4.4 23.2 1.0 HG1 A:THR5 4.4 15.9 1.0 CG A:LYS398 4.4 30.9 1.0 C1 A:GOL1403 4.5 37.2 1.0 HD21 A:LEU4 4.5 20.8 1.0 H3 A:MET1 4.5 51.4 1.0 CB A:THR5 4.6 11.6 1.0 N A:LEU4 4.6 12.7 1.0 CB A:LYS398 4.7 21.8 1.0 HD3 A:LYS398 4.9 47.2 1.0 CA A:THR5 4.9 9.5 1.0 CB A:ASP8 5.0 17.3 1.0 HA A:MET1 5.0 45.9 1.0 HB2 A:ASP8 5.0 20.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1400 b:17.8 occ:1.00 O A:HOH2396 2.0 22.0 1.0 OE1 A:GLU288 2.1 12.0 1.0 O A:HOH2286 2.1 15.8 1.0 O A:HOH2307 2.1 16.7 1.0 CD A:GLU288 3.1 15.6 1.0 H A:GLU288 3.4 13.9 1.0 OE2 A:GLU288 3.4 11.7 1.0 HA3 A:GLY287 3.7 15.8 1.0 O A:HOH2305 4.0 28.5 1.0 HB A:VAL268 4.1 10.9 1.0 N A:GLU288 4.1 11.6 1.0 O A:HOH2152 4.1 21.7 1.0 HA2 A:GLY287 4.2 15.8 1.0 CA A:GLY287 4.3 13.1 1.0 HB2 A:GLU288 4.3 14.5 1.0 O A:VAL268 4.4 10.8 1.0 CG A:GLU288 4.4 14.9 1.0 C A:GLY287 4.7 11.6 1.0 CB A:GLU288 4.8 12.1 1.0 O A:HOH2153 4.8 39.8 1.0 HG13 A:VAL268 4.9 11.8 1.0 HA A:VAL268 4.9 13.2 1.0 HG3 A:GLU288 4.9 17.9 1.0 CB A:VAL268 5.0 9.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1406 b:24.1 occ:1.00 O A:HOH2403 2.1 21.2 1.0 O A:HOH2390 2.1 26.4 1.0 O A:HOH2401 2.1 26.5 1.0 O A:HOH2388 2.2 24.1 1.0 O A:HOH2404 2.2 21.5 1.0 O A:HOH2402 2.3 29.9 1.0 OE1 A:GLU397 4.2 21.4 1.0 OE2 A:GLU397 4.2 18.9 1.0 O A:HOH2389 4.3 38.6 1.0 CD A:GLU397 4.7 24.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Phosphoglycerate Kinase From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1407 b:9.4 occ:1.00 O A:HOH2361 2.0 14.8 1.0 O2A A:ANP1401 2.1 10.4 1.0 O1B A:ANP1401 2.1 13.2 1.0 O1G A:ANP1401 2.1 11.5 1.0 O A:HOH2397 2.1 11.2 1.0 PB A:ANP1401 3.2 12.0 1.0 PG A:ANP1401 3.2 12.6 1.0 PA A:ANP1401 3.3 10.9 1.0 HOG2 A:ANP1401 3.6 16.4 1.0 O3A A:ANP1401 3.6 9.2 1.0 N3B A:ANP1401 3.6 8.3 1.0 H A:ASP356 3.7 9.2 1.0 O2G A:ANP1401 3.8 13.7 1.0 H5'1 A:ANP1401 3.8 9.2 1.0 O A:HOH2249 4.0 24.2 1.0 HB2 A:ASP356 4.1 8.7 1.0 O A:HOH2360 4.2 43.1 1.0 O1A A:ANP1401 4.2 13.6 1.0 O A:HOH2398 4.2 24.5 1.0 H A:GLY355 4.3 17.4 1.0 O A:HOH2362 4.3 24.1 1.0 O A:HOH2244 4.4 16.5 1.0 O5' A:ANP1401 4.4 9.7 1.0 HNB1 A:ANP1401 4.4 10.0 1.0 O2B A:ANP1401 4.5 12.1 1.0 N A:ASP356 4.6 7.7 1.0 C5' A:ANP1401 4.6 7.7 1.0 HA3 A:GLY355 4.6 16.7 1.0 CG A:ASP356 4.6 12.1 1.0 O3G A:ANP1401 4.6 10.5 1.0 OD1 A:ASP356 4.6 16.9 1.0 HOG3 A:ANP1401 4.8 12.6 1.0 CB A:ASP356 4.8 7.2 1.0 HOB2 A:ANP1401 4.8 14.5 1.0 N A:GLY355 4.9 14.5 1.0 OD2 A:ASP356 5.0 13.3 1.0

M.Fulde, N.Bernardo-Garcia, M.Rohde, N.Nachtigall, R.Frank, K.T.Preissner, J.Klett, A.Morreale, G.S.Chhatwal, J.A.Hermoso, S.Bergmann. Pneumococcal Phosphoglycerate Kinase Interacts with Plasminogen and Its Tissue Activator. Thromb.Haemost. V. 111 2013.
ISSN: ESSN 0340-6245
PubMed: 24196407
DOI: 10.1160/TH13-05-0421