Manganese in PDB 7l3v: Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid

All present enzymatic activity of Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid:
4.1.1.32;

The structure of Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid, PDB code: 7l3v was solved by J.A.Clinger, D.W.Moreau, M.J.Mcleod, T.Holyoak, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.67 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.159, 118.787, 61.307, 90, 107.25, 90
R / Rfree (%)	18.6 / 20.6

The binding sites of Manganese atom in the Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid (pdb code 7l3v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid, PDB code: 7l3v:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn904 b:43.1 occ:1.00 O A:HOH1117 2.2 42.9 1.0 O3P A:PEP903 2.2 60.1 1.0 OG1 A:THR291 2.3 35.5 1.0 O1B A:GDP902 2.4 43.9 1.0 O A:HOH1060 2.4 39.8 1.0 O A:HOH1031 2.5 36.4 1.0 HG1 A:THR291 2.6 42.6 1.0 PB A:GDP902 3.4 41.4 1.0 O2B A:GDP902 3.4 74.0 1.0 H A:THR291 3.4 42.2 1.0 CB A:THR291 3.5 38.6 1.0 P A:PEP903 3.5 59.8 1.0 HB A:THR291 3.6 46.3 1.0 HA2 A:GLY334 3.6 41.2 1.0 O1P A:PEP903 3.7 48.0 1.0 H A:VAL335 3.9 48.2 1.0 OD2 A:ASP310 4.0 44.5 1.0 N A:THR291 4.1 35.2 1.0 HB2 A:LYS290 4.1 34.9 1.0 O A:HOH1194 4.2 45.8 1.0 O1A A:GDP902 4.2 61.4 1.0 O2P A:PEP903 4.3 63.9 1.0 CA A:THR291 4.3 47.0 1.0 HG21 A:THR291 4.4 51.9 1.0 HE2 A:LYS290 4.4 38.0 1.0 HG23 A:VAL335 4.4 52.2 1.0 O A:HOH1097 4.4 41.3 1.0 O A:ASP310 4.5 34.8 1.0 O3A A:GDP902 4.5 40.5 1.0 CG2 A:THR291 4.5 43.2 1.0 O3B A:GDP902 4.5 51.1 1.0 CA A:GLY334 4.5 34.3 1.0 HZ3 A:LYS290 4.5 37.5 1.0 HZ1 A:LYS290 4.6 37.5 1.0 HA A:THR291 4.6 56.3 1.0 HA3 A:GLY334 4.6 41.2 1.0 N A:VAL335 4.7 40.1 1.0 PA A:GDP902 4.7 61.6 1.0 O2 A:PEP903 4.7 60.7 1.0 CG A:ASP310 4.8 42.4 1.0 HG23 A:THR291 4.8 51.9 1.0 O2A A:GDP902 4.8 48.4 1.0 HB2 A:ASP311 4.8 38.5 1.0 OD1 A:ASP311 4.8 34.1 1.0 HH12 A:ARG405 4.9 59.2 1.0 NZ A:LYS290 4.9 31.3 1.0 CB A:LYS290 4.9 29.1 1.0 HB3 A:LYS290 4.9 34.9 1.0 O A:PHE333 4.9 35.6 1.0 HB2 A:ASP310 5.0 43.5 1.0

Manganese binding site 2 out of 4 in the Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn905 b:108.3 occ:1.00 HE1 A:HIS502 1.6 104.5 1.0 CE1 A:HIS502 2.3 87.1 1.0 OE2 A:GLU607 2.5 52.2 1.0 HE2 A:HIS502 2.9 101.0 1.0 NE2 A:HIS502 3.0 84.2 1.0 O A:HOH1227 3.0 36.7 1.0 HG2 A:GLU607 3.2 46.4 1.0 O A:HOH1210 3.4 52.4 1.0 ND1 A:HIS502 3.4 80.8 1.0 CD A:GLU607 3.6 53.1 1.0 CG A:GLU607 3.8 38.6 1.0 HB3 A:LEU498 4.0 23.8 1.0 HE21 A:GLN451 4.1 47.4 1.0 CD2 A:HIS502 4.2 73.3 1.0 HG3 A:GLU607 4.2 46.4 1.0 CG A:HIS502 4.4 69.1 1.0 OE1 A:GLU607 4.7 34.4 1.0 HG3 A:GLN451 4.7 41.8 1.0 HD22 A:LEU498 4.8 24.2 1.0 O A:LEU498 4.8 28.8 1.0 HG2 A:GLN451 4.9 41.8 1.0 NE2 A:GLN451 4.9 39.5 1.0 HD2 A:HIS502 5.0 88.0 1.0 CB A:LEU498 5.0 19.9 1.0 HB3 A:ALA501 5.0 42.2 1.0

Manganese binding site 3 out of 4 in the Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn906 b:33.6 occ:1.00 O1 A:PEP903 1.4 28.0 1.0 HZ1 A:LYS244 1.4 45.2 1.0 OD1 A:ASP311 1.9 34.1 1.0 NZ A:LYS244 2.2 37.7 1.0 NE2 A:HIS264 2.2 20.6 1.0 O A:HOH1022 2.3 36.1 1.0 HZ3 A:LYS244 2.3 45.2 1.0 HZ2 A:LYS244 2.6 45.2 1.0 C1 A:PEP903 2.6 55.5 1.0 CG A:ASP311 2.7 29.4 1.0 O1P A:PEP903 2.8 48.0 1.0 OD2 A:ASP311 2.9 28.6 1.0 CD2 A:HIS264 3.0 22.5 1.0 HD2 A:HIS264 3.0 27.0 1.0 CE1 A:HIS264 3.3 28.1 1.0 CE A:LYS244 3.3 32.5 1.0 HZ1 A:LYS290 3.4 37.5 1.0 HE2 A:LYS244 3.4 39.0 1.0 C2 A:PEP903 3.5 56.1 1.0 O2' A:PEP903 3.6 59.5 1.0 HE3 A:LYS244 3.6 39.0 1.0 HE1 A:HIS264 3.6 33.7 1.0 HE3 A:LYS290 3.6 38.0 1.0 O2 A:PEP903 3.6 60.7 1.0 P A:PEP903 3.8 59.8 1.0 NZ A:LYS290 4.1 31.3 1.0 CB A:ASP311 4.1 32.1 1.0 O A:HOH1031 4.2 36.4 1.0 CE A:LYS290 4.2 31.7 1.0 HE2 A:LYS290 4.2 38.0 1.0 CG A:HIS264 4.2 27.7 1.0 HZ1 A:LYS243 4.2 49.6 1.0 O A:HOH1194 4.3 45.8 1.0 ND1 A:HIS264 4.4 25.5 1.0 HB2 A:ASP311 4.4 38.5 1.0 HA A:ASP311 4.4 35.0 1.0 HZ2 A:LYS290 4.5 37.5 1.0 O3P A:PEP903 4.5 60.1 1.0 HZ2 A:LYS243 4.6 49.6 1.0 C3 A:PEP903 4.6 66.6 1.0 HD11 A:ILE312 4.6 39.8 1.0 CD A:LYS244 4.6 30.7 1.0 O A:ASP311 4.7 31.0 1.0 HB3 A:ASP311 4.7 38.5 1.0 CA A:ASP311 4.8 29.2 1.0 HZ3 A:LYS290 4.8 37.5 1.0 HE3 A:LYS243 4.8 47.6 1.0 HD13 A:ILE312 4.8 39.8 1.0 HE2 A:PHE485 4.8 32.3 1.0 HD3 A:LYS244 4.8 36.9 1.0 HD2 A:LYS244 4.8 36.9 1.0 NZ A:LYS243 4.8 41.3 1.0 HZ A:PHE485 4.9 35.0 1.0 HG A:SER286 5.0 65.5 1.0 O2P A:PEP903 5.0 63.9 1.0

Manganese binding site 4 out of 4 in the Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Pepck Mmqx Structure 120MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn907 b:72.6 occ:1.00 O A:LEU79 2.3 35.1 1.0 O A:HOH1061 2.3 43.1 1.0 O A:HOH1258 2.3 51.3 1.0 O A:ASN208 2.5 37.7 1.0 H A:LEU79 3.0 52.2 1.0 HB2 A:LEU79 3.2 54.8 1.0 C A:LEU79 3.3 37.1 1.0 HB3 A:ASN208 3.4 56.3 1.0 N A:LEU79 3.6 43.5 1.0 C A:ASN208 3.7 46.1 1.0 O A:VAL65 3.8 45.5 1.0 CA A:LEU79 3.8 42.4 1.0 HB2 A:TRP210 3.9 41.8 1.0 HB2 A:ASN209 3.9 51.6 1.0 CB A:LEU79 3.9 45.7 1.0 HE3 A:TRP210 4.1 41.4 1.0 HA A:VAL65 4.1 43.1 1.0 CB A:ASN208 4.3 46.9 1.0 HA A:THR80 4.3 49.3 1.0 O A:ASN209 4.3 40.1 1.0 O A:HOH1076 4.3 61.1 1.0 O A:GLY64 4.4 47.4 1.0 CA A:ASN208 4.5 42.8 1.0 HA A:ALA78 4.5 43.7 1.0 HB3 A:LEU79 4.5 54.8 1.0 C A:ASN209 4.5 37.8 1.0 N A:THR80 4.5 44.7 1.0 C A:VAL65 4.6 39.2 1.0 HB2 A:ASN208 4.6 56.3 1.0 HA A:ASN208 4.6 51.3 1.0 N A:ASN209 4.6 41.1 1.0 CB A:ASN209 4.7 43.0 1.0 HG A:LEU79 4.8 55.2 1.0 C A:ALA78 4.8 37.1 1.0 HA A:LEU79 4.8 50.9 1.0 CB A:TRP210 4.8 34.8 1.0 CA A:VAL65 4.8 35.9 1.0 CA A:ASN209 4.8 43.2 1.0 CA A:THR80 4.9 41.1 1.0 CE3 A:TRP210 4.9 34.5 1.0 HB1 A:ALA78 4.9 47.8 1.0 HG13 A:VAL65 5.0 42.6 1.0

J.A.Clinger, D.W.Moreau, M.J.Mcleod, T.Holyoak, R.E.Thorne. Millisecond Mix-and-Quench Crystallography (Mmqx) Enables Time-Resolved Studies of Pepck with Remote Data Collection. Iucrj V. 8 784 2021.
ISSN: ESSN 2052-2525
PubMed: 34584739
DOI: 10.1107/S2052252521007053