Manganese in PDB 7l36: Pepck Steady-State Structure with Mn and Gtp

All present enzymatic activity of Pepck Steady-State Structure with Mn and Gtp:
4.1.1.32;

The structure of Pepck Steady-State Structure with Mn and Gtp, PDB code: 7l36 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)	41.00 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.38, 118.55, 60.233, 90, 109.53, 90
R / Rfree (%)	15.2 / 19.9

The structure of Pepck Steady-State Structure with Mn and Gtp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Pepck Steady-State Structure with Mn and Gtp (pdb code 7l36). 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 Steady-State Structure with Mn and Gtp, PDB code: 7l36:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Pepck Steady-State Structure with Mn and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pepck Steady-State Structure with Mn and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:8.6 occ:1.00 HZ1 A:LYS244 1.4 14.2 1.0 OD1 A:ASP311 2.1 10.3 1.0 O3G A:GTP703 2.2 10.0 1.0 O A:HOH993 2.2 13.9 1.0 NZ A:LYS244 2.3 11.8 1.0 O A:HOH1118 2.3 13.2 1.0 NE2 A:HIS264 2.3 8.3 1.0 HZ3 A:LYS244 2.6 14.2 1.0 HZ2 A:LYS244 2.6 14.2 1.0 CG A:ASP311 3.0 10.2 1.0 OD2 A:ASP311 3.2 9.2 1.0 CE1 A:HIS264 3.3 11.5 1.0 HZ1 A:LYS290 3.3 20.1 1.0 CD2 A:HIS264 3.3 9.5 1.0 CE A:LYS244 3.3 12.3 1.0 PG A:GTP703 3.4 13.9 1.0 HE1 A:HIS264 3.4 13.8 1.0 HD2 A:HIS264 3.4 11.4 1.0 HE2 A:LYS244 3.5 14.8 1.0 HE3 A:LYS244 3.5 14.8 1.0 O1G A:GTP703 3.6 15.0 1.0 HE3 A:LYS290 3.8 9.9 1.0 O2G A:GTP703 4.0 14.5 1.0 NZ A:LYS290 4.1 16.7 1.0 O A:HOH854 4.2 9.8 1.0 HE2 A:LYS290 4.2 9.9 1.0 CE A:LYS290 4.3 8.3 1.0 O A:HOH1002 4.3 13.8 1.0 ND1 A:HIS264 4.4 8.6 1.0 CG A:HIS264 4.4 8.2 1.0 HZ2 A:LYS290 4.4 20.1 1.0 CB A:ASP311 4.4 9.7 1.0 O A:HOH1130 4.5 41.1 1.0 HB2 A:ASP311 4.7 11.6 1.0 CD A:LYS244 4.7 15.6 1.0 HA A:ASP311 4.7 9.5 1.0 HZ3 A:LYS290 4.7 20.1 1.0 HH12 A:ARG405 4.7 20.7 1.0 HH22 A:ARG405 4.7 17.7 1.0 HZ A:PHE485 4.7 14.6 1.0 O3B A:GTP703 4.7 18.5 1.0 HB2 A:SER286 4.7 41.7 1.0 O A:HOH1171 4.7 18.6 1.0 HD2 A:LYS244 4.8 18.8 1.0 HE3 A:LYS243 4.8 28.9 1.0 HE2 A:PHE485 4.9 15.7 1.0 HZ2 A:LYS243 4.9 26.4 1.0 HD3 A:LYS244 4.9 18.8 1.0 HZ3 A:LYS243 5.0 26.4 1.0

Manganese binding site 2 out of 3 in the Pepck Steady-State Structure with Mn and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pepck Steady-State Structure with Mn and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:86.7 occ:1.00 O A:HOH919 2.7 20.5 1.0 NE2 A:HIS502 2.8 49.4 1.0 OE2 A:GLU607 2.8 45.6 1.0 HE1 A:HIS502 2.9 64.1 1.0 HG2 A:GLU607 3.0 29.3 1.0 O A:HOH965 3.1 26.8 1.0 CE1 A:HIS502 3.1 53.5 1.0 HE21 A:GLN451 3.6 44.6 1.0 CD A:GLU607 3.7 39.9 1.0 CG A:GLU607 3.8 24.4 1.0 HB3 A:LEU498 3.9 15.6 1.0 CD2 A:HIS502 4.1 51.1 1.0 HG3 A:GLU607 4.2 29.3 1.0 HG2 A:GLN451 4.3 49.5 1.0 HG3 A:GLN451 4.4 49.5 1.0 NE2 A:GLN451 4.4 37.2 1.0 ND1 A:HIS502 4.4 51.9 1.0 HD2 A:HIS502 4.5 61.4 1.0 HD22 A:LEU498 4.5 12.0 1.0 O A:LEU498 4.6 10.9 1.0 HB3 A:ALA501 4.7 31.6 1.0 CG A:GLN451 4.7 41.3 1.0 CB A:LEU498 4.9 13.0 1.0 HE22 A:GLN451 4.9 44.6 1.0 HH22 A:ARG610 4.9 23.5 1.0 OE1 A:GLU607 4.9 16.4 1.0 CG A:HIS502 4.9 46.0 1.0 HD13 A:LEU498 4.9 20.9 1.0 CB A:GLU607 5.0 11.6 1.0

Manganese binding site 3 out of 3 in the Pepck Steady-State Structure with Mn and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pepck Steady-State Structure with Mn and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn704 b:11.9 occ:1.00 O2G A:GTP703 2.1 14.5 1.0 O2B A:GTP703 2.1 8.5 1.0 O A:HOH854 2.2 9.8 1.0 OG1 A:THR291 2.2 9.2 1.0 O A:HOH903 2.2 9.8 1.0 O A:HOH830 2.3 10.2 1.0 PG A:GTP703 3.2 13.9 1.0 PB A:GTP703 3.3 14.7 1.0 CB A:THR291 3.4 11.2 1.0 HB A:THR291 3.4 13.5 1.0 H A:THR291 3.5 10.9 1.0 O3B A:GTP703 3.5 18.5 1.0 HA2 A:GLY334 3.6 12.3 1.0 HH12 A:ARG405 3.7 20.7 1.0 OD2 A:ASP310 3.8 17.5 1.0 O3G A:GTP703 3.8 10.0 1.0 H A:VAL335 3.9 12.9 1.0 O1A A:GTP703 4.0 14.1 1.0 HB2 A:LYS290 4.1 11.0 1.0 N A:THR291 4.1 9.1 1.0 O A:HOH1002 4.1 13.8 1.0 HG23 A:VAL335 4.2 23.8 1.0 HG21 A:THR291 4.2 17.2 1.0 O1B A:GTP703 4.3 15.1 1.0 CA A:THR291 4.3 11.4 1.0 O A:ASP310 4.3 15.4 1.0 HE2 A:LYS290 4.3 9.9 1.0 O3A A:GTP703 4.4 20.1 1.0 NH1 A:ARG405 4.4 17.3 1.0 CG2 A:THR291 4.4 14.4 1.0 O1G A:GTP703 4.5 15.0 1.0 HH11 A:ARG405 4.5 20.7 1.0 CA A:GLY334 4.5 10.3 1.0 CG A:ASP310 4.5 17.3 1.0 HA A:THR291 4.5 13.7 1.0 O A:HOH1021 4.6 12.9 1.0 HB2 A:ASP311 4.6 11.6 1.0 OD1 A:ASP311 4.7 10.3 1.0 HA3 A:GLY334 4.7 12.3 1.0 N A:VAL335 4.7 10.7 1.0 PA A:GTP703 4.7 20.3 1.0 O A:PHE333 4.8 9.6 1.0 O A:HOH1118 4.8 13.2 1.0 HB2 A:ASP310 4.8 10.3 1.0 HZ1 A:LYS290 4.8 20.1 1.0 HG23 A:THR291 4.9 17.2 1.0 HZ3 A:LYS290 4.9 20.1 1.0 CB A:LYS290 4.9 9.2 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