Magnesium in PDB 6k0k: Crystal Structure of Escherichia Coli Pyruvate Kinase II

All present enzymatic activity of Crystal Structure of Escherichia Coli Pyruvate Kinase II:
2.7.1.40;

The structure of Crystal Structure of Escherichia Coli Pyruvate Kinase II, PDB code: 6k0k was solved by C.H.Zhao, Y.P.Zhang, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.95 / 2.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	117.693, 137.300, 139.221, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.9

The binding sites of Magnesium atom in the Crystal Structure of Escherichia Coli Pyruvate Kinase II (pdb code 6k0k). 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 Escherichia Coli Pyruvate Kinase II, PDB code: 6k0k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Escherichia Coli Pyruvate Kinase II


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 Escherichia Coli Pyruvate Kinase II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:43.8 occ:1.00 O A:HOH623 2.2 49.7 1.0 SG A:CYS216 2.4 43.1 1.0 NH2 A:ARG412 3.1 57.4 1.0 O A:VAL190 3.3 33.8 1.0 CB A:CYS216 3.3 38.8 1.0 CA A:GLY189 3.4 35.9 1.0 C A:GLY189 3.6 38.4 1.0 CA A:CYS216 3.8 43.3 1.0 N A:VAL190 3.8 36.6 1.0 O A:ALA185 4.2 37.4 1.0 O A:GLY189 4.3 41.7 1.0 O A:ALA186 4.3 37.1 1.0 CZ A:ARG412 4.3 66.8 1.0 C A:VAL190 4.3 34.9 1.0 N A:GLY189 4.3 35.7 1.0 CB A:ALA218 4.4 30.8 1.0 CA A:ALA186 4.4 34.2 1.0 C A:CYS216 4.4 41.4 1.0 N A:ASP217 4.5 41.6 1.0 N A:ALA218 4.5 43.9 1.0 CA A:VAL190 4.6 38.6 1.0 CG2 A:VAL190 4.6 33.9 1.0 NH1 A:ARG412 4.8 53.9 1.0 C A:ALA186 4.8 32.6 1.0 CA A:ALA218 4.9 36.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Escherichia Coli Pyruvate Kinase II


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 Escherichia Coli Pyruvate Kinase II within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:58.5 occ:1.00 CD C:ARG274 2.7 58.6 1.0 NH1 C:ARG274 2.7 68.2 1.0 NH1 C:ARG397 3.5 44.1 1.0 O C:GLY311 3.5 54.8 1.0 NE C:ARG274 3.5 64.9 1.0 CZ C:ARG274 3.5 72.9 1.0 CG C:ARG274 3.7 57.2 1.0 CZ C:ARG397 3.7 38.5 1.0 O C:SER396 3.8 50.0 1.0 NH2 C:ARG397 3.9 40.7 1.0 OD2 C:ASP313 3.9 43.0 1.0 OD1 C:ASP313 4.0 41.6 1.0 CG C:ASP313 4.2 44.4 1.0 NE C:ARG397 4.3 41.0 1.0 CB C:ARG421 4.3 45.9 1.0 CG C:ARG421 4.6 46.6 1.0 CA C:ARG397 4.7 47.2 1.0 C C:GLY311 4.7 51.2 1.0 CB C:ARG274 4.7 53.8 1.0 CD C:ARG397 4.7 43.8 1.0 O C:ARG397 4.8 49.9 1.0 NH2 C:ARG274 4.8 66.1 1.0 CD C:ARG421 4.8 48.1 1.0 C C:SER396 4.9 38.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Escherichia Coli Pyruvate Kinase II


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 Escherichia Coli Pyruvate Kinase II within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:31.8 occ:1.00 OG1 C:THR386 3.0 49.3 1.0 OG1 C:THR391 3.1 49.4 1.0 OE2 C:GLU362 3.4 58.2 1.0 OG1 C:THR471 3.4 50.9 1.0 OG C:SER388 3.6 38.9 1.0 N C:GLU387 3.7 49.3 1.0 CB C:THR386 3.9 44.1 1.0 N C:THR471 3.9 47.0 1.0 CB C:THR471 4.0 47.0 1.0 CA C:THR386 4.0 39.4 1.0 N C:SER388 4.1 48.6 1.0 C C:THR386 4.3 45.8 1.0 CB C:THR391 4.3 39.5 1.0 N C:THR391 4.4 39.4 1.0 CD C:GLU362 4.6 58.3 1.0 CA C:THR471 4.6 49.7 1.0 CA C:GLU387 4.6 47.8 1.0 O C:HOH608 4.7 39.1 1.0 CB C:GLU387 4.7 51.7 1.0 N C:ARG390 4.7 41.3 1.0 CA C:SER470 4.7 49.0 1.0 N C:GLY389 4.8 41.9 1.0 CB C:SER388 4.8 42.6 1.0 CB C:ARG390 4.8 47.8 1.0 C C:SER470 4.8 49.3 1.0 C C:GLU387 4.9 48.2 1.0 CB C:SER470 4.9 56.9 1.0 CA C:SER388 4.9 42.8 1.0 NH1 C:ARG390 5.0 56.4 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Escherichia Coli Pyruvate Kinase II


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 Escherichia Coli Pyruvate Kinase II within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:51.0 occ:1.00 OG1 D:THR386 2.6 57.6 1.0 OE1 D:GLU362 3.1 79.0 1.0 OG1 D:THR391 3.2 52.3 1.0 OG1 D:THR471 3.3 63.7 1.0 OG D:SER388 3.5 55.0 1.0 CB D:THR386 3.7 56.5 1.0 CB D:THR471 4.0 53.4 1.0 CD D:GLU362 4.0 79.7 1.0 CA D:THR386 4.1 53.5 1.0 N D:THR391 4.1 57.7 1.0 CB D:THR391 4.2 48.9 1.0 N D:THR471 4.2 52.9 1.0 N D:GLU387 4.4 57.3 1.0 NH2 D:ARG390 4.4 78.7 1.0 N D:SER388 4.5 58.2 1.0 OE2 D:GLU362 4.5 80.4 1.0 CB D:ARG390 4.5 57.4 1.0 N D:ARG390 4.5 54.9 1.0 CB D:SER388 4.6 54.1 1.0 CZ D:ARG390 4.6 81.0 1.0 C D:THR386 4.7 59.9 1.0 NE D:ARG390 4.8 79.5 1.0 CA D:THR471 4.8 53.1 1.0 CA D:THR391 4.8 51.9 1.0 N D:GLY389 4.8 52.0 1.0 CA D:ARG390 4.9 48.2 1.0

C.H.Zhao, Y.P.Zhang, Y.Li. Crystal Structure of Escherichia Coli Pyruvate Kinase II To Be Published.