Manganese in PDB 7l3m: Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid

All present enzymatic activity of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid:
4.1.1.32;

The structure of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid, PDB code: 7l3m 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)	51.33 / 2.07
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.389, 118.935, 60.3, 90, 109.42, 90
R / Rfree (%)	17.2 / 18.6

The structure of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid (pdb code 7l3m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid, PDB code: 7l3m:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Pepck Mmqx Structure 40MS 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 40MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:14.8 occ:1.00 O1 A:PEP703 1.6 33.7 1.0 OD1 A:ASP311 2.1 10.6 1.0 NZ A:LYS244 2.3 16.2 1.0 NE2 A:HIS264 2.4 11.6 1.0 O1P A:PEP703 2.4 30.0 1.0 O A:HOH805 2.5 21.0 1.0 C1 A:PEP703 2.6 42.6 1.0 CG A:ASP311 2.9 12.9 1.0 OD2 A:ASP311 3.0 16.2 1.0 O2 A:PEP703 3.1 54.7 1.0 C2 A:PEP703 3.2 50.9 1.0 P A:PEP703 3.3 58.4 1.0 CE1 A:HIS264 3.3 11.2 1.0 CE A:LYS244 3.3 21.7 1.0 CD2 A:HIS264 3.3 12.8 1.0 O2' A:PEP703 3.7 51.8 1.0 O3P A:PEP703 4.0 43.0 1.0 NZ A:LYS290 4.1 19.2 1.0 O A:HOH836 4.2 22.0 1.0 O A:HOH1032 4.2 24.2 1.0 CE A:LYS290 4.2 16.1 1.0 CB A:ASP311 4.3 10.9 1.0 ND1 A:HIS264 4.4 16.3 1.0 C3 A:PEP703 4.4 43.3 1.0 CG A:HIS264 4.4 9.8 1.0 O2P A:PEP703 4.5 54.0 1.0 CD A:LYS244 4.6 16.4 1.0 O A:HOH803 4.8 37.5 1.0 CA A:ASP311 5.0 12.2 1.0

Manganese binding site 2 out of 3 in the Pepck Mmqx Structure 40MS 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 40MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn706 b:33.7 occ:1.00 O A:HOH987 2.2 28.1 1.0 O1B A:GDP704 2.3 26.5 1.0 O A:HOH819 2.3 27.4 1.0 O A:HOH836 2.3 22.0 1.0 O3P A:PEP703 2.4 43.0 1.0 OG1 A:THR291 2.5 17.1 1.0 PB A:GDP704 3.4 25.2 1.0 P A:PEP703 3.5 58.4 1.0 CB A:THR291 3.6 22.0 1.0 O2B A:GDP704 3.6 40.8 1.0 O1P A:PEP703 3.7 30.0 1.0 OD2 A:ASP310 3.9 28.4 1.0 O A:HOH1032 4.0 24.2 1.0 O2P A:PEP703 4.1 54.0 1.0 N A:THR291 4.2 18.9 1.0 O1A A:GDP704 4.3 32.9 1.0 O3B A:GDP704 4.3 28.6 1.0 O A:ASP310 4.4 16.8 1.0 CA A:THR291 4.5 21.0 1.0 O A:HOH1036 4.5 22.9 1.0 CA A:GLY334 4.5 18.5 1.0 O3A A:GDP704 4.6 34.0 1.0 CG2 A:THR291 4.6 22.0 1.0 CG A:ASP310 4.6 18.4 1.0 PA A:GDP704 4.8 37.9 1.0 OD1 A:ASP311 4.8 10.6 1.0 O2 A:PEP703 4.8 54.7 1.0 N A:VAL335 4.8 16.1 1.0 CB A:LYS290 4.9 11.4 1.0 O A:PHE333 4.9 19.9 1.0 NZ A:LYS290 4.9 19.2 1.0 O2A A:GDP704 4.9 29.7 1.0 O A:HOH805 5.0 21.0 1.0

Manganese binding site 3 out of 3 in the Pepck Mmqx Structure 40MS 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 40MS Post-Mixing with Oxaloacetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn707 b:79.3 occ:1.00 NE2 A:HIS502 2.4 54.7 1.0 CE1 A:HIS502 2.5 48.1 1.0 OE1 A:GLU607 2.5 41.5 1.0 OE2 A:GLU607 2.8 55.1 1.0 CD A:GLU607 2.8 42.2 1.0 O A:HOH870 2.9 25.1 1.0 O A:HOH1072 3.4 44.2 1.0 O A:HOH862 3.5 39.0 1.0 CD2 A:HIS502 3.7 45.6 1.0 ND1 A:HIS502 3.8 49.5 1.0 CG A:GLU607 4.2 31.4 1.0 CG A:HIS502 4.4 44.7 1.0 NE2 A:GLN451 4.5 20.1 1.0 O A:LEU498 4.8 17.6 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