Phosphorus in PDB 1a5u: Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate

All present enzymatic activity of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate:
2.7.1.40;

The structure of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u was solved by T.M.Larsen, M.M.Benning, I.Rayment, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.300, 216.500, 258.600, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus atom in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate (pdb code 1a5u). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:P535 b:52.9 occ:1.00 PG A:ATP535 0.0 52.9 1.0 O3G A:ATP535 1.4 17.4 1.0 O1G A:ATP535 1.4 37.8 1.0 O2G A:ATP535 1.4 31.7 1.0 O3B A:ATP535 1.8 18.8 1.0 MG A:MG536 2.7 25.1 1.0 PB A:ATP535 3.0 27.5 1.0 O3 A:OXL533 3.3 33.3 1.0 O3A A:ATP535 3.5 56.2 1.0 MG A:MG534 3.5 19.5 1.0 O2B A:ATP535 3.6 18.7 1.0 NH2 A:ARG72 3.6 38.0 1.0 ND2 A:ASN74 3.6 10.9 1.0 C1 A:OXL533 3.7 45.5 1.0 O A:HOH6743 3.7 24.8 1.0 O A:HOH6459 3.8 11.7 1.0 O1A A:ATP535 3.9 26.3 1.0 NH2 A:ARG119 4.0 38.2 1.0 PA A:ATP535 4.1 33.9 1.0 O1B A:ATP535 4.1 43.2 1.0 O1 A:OXL533 4.2 72.1 1.0 O2A A:ATP535 4.3 7.8 1.0 NA A:NA532 4.3 43.4 1.0 C2 A:OXL533 4.4 27.2 1.0 O A:HOH6003 4.4 27.7 1.0 O4 A:OXL533 4.4 42.9 1.0 O A:HOH6079 4.5 12.6 1.0 NZ A:LYS269 4.6 31.8 1.0 OD2 A:ASP295 4.6 25.4 1.0 CG A:ASN74 4.7 24.4 1.0 CZ A:ARG72 4.7 35.4 1.0 NH1 A:ARG72 4.9 56.5 1.0 OD1 A:ASN74 5.0 22.9 1.0

Phosphorus binding site 2 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:P535 b:27.5 occ:1.00 PB A:ATP535 0.0 27.5 1.0 O1B A:ATP535 1.5 43.2 1.0 O2B A:ATP535 1.5 18.7 1.0 O3B A:ATP535 1.5 18.8 1.0 O3A A:ATP535 1.6 56.2 1.0 PA A:ATP535 2.9 33.9 1.0 PG A:ATP535 3.0 52.9 1.0 O1A A:ATP535 3.2 26.3 1.0 MG A:MG536 3.3 25.1 1.0 O1G A:ATP535 3.4 37.8 1.0 O2G A:ATP535 3.4 31.7 1.0 O A:HOH6961 3.6 35.7 1.0 O3' A:ATP535 3.6 45.3 1.0 O A:HOH6358 3.7 41.2 1.0 CE1 A:HIS77 3.8 28.5 1.0 O3G A:ATP535 3.8 17.4 1.0 C5' A:ATP535 3.9 60.8 1.0 O5' A:ATP535 3.9 33.8 1.0 ND2 A:ASN74 3.9 10.9 1.0 O2A A:ATP535 3.9 7.8 1.0 C3' A:ATP535 3.9 79.9 1.0 O A:HOH6079 4.0 12.6 1.0 NH2 A:ARG119 4.0 38.2 1.0 NH1 A:ARG119 4.2 24.1 1.0 O A:HOH6459 4.4 11.7 1.0 C4' A:ATP535 4.5 95.3 1.0 ND1 A:HIS77 4.5 34.6 1.0 CZ A:ARG119 4.6 38.2 1.0 O A:HOH6003 4.7 27.7 1.0 NE2 A:HIS77 4.8 25.0 1.0

Phosphorus binding site 3 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:P535 b:33.9 occ:1.00 PA A:ATP535 0.0 33.9 1.0 O2A A:ATP535 1.5 7.8 1.0 O1A A:ATP535 1.5 26.3 1.0 O3A A:ATP535 1.6 56.2 1.0 O5' A:ATP535 1.7 33.8 1.0 C5' A:ATP535 2.7 60.8 1.0 PB A:ATP535 2.9 27.5 1.0 O2B A:ATP535 3.2 18.7 1.0 ND2 A:ASN74 3.3 10.9 1.0 O3B A:ATP535 3.4 18.8 1.0 O1G A:ATP535 3.4 37.8 1.0 MG A:MG536 3.4 25.1 1.0 NH1 A:ARG72 3.6 56.5 1.0 C4' A:ATP535 3.7 95.3 1.0 O A:HOH6079 3.8 12.6 1.0 C3' A:ATP535 4.0 79.9 1.0 O1B A:ATP535 4.0 43.2 1.0 PG A:ATP535 4.1 52.9 1.0 C8 A:ATP535 4.2 16.1 1.0 O4' A:ATP535 4.3 39.6 1.0 CB A:SER361 4.3 25.6 1.0 CZ A:ARG72 4.5 35.4 1.0 NH2 A:ARG72 4.5 38.0 1.0 OG A:SER361 4.5 25.7 1.0 CG A:ASN74 4.6 24.4 1.0 O3' A:ATP535 4.6 45.3 1.0 CG2 A:THR49 4.6 56.7 1.0 O3G A:ATP535 4.8 17.4 1.0 O A:HOH6358 4.8 41.2 1.0 CE1 A:HIS77 4.8 28.5 1.0 CB A:ASN74 4.9 29.0 1.0 N9 A:ATP535 4.9 18.4 1.0 ND1 A:HIS77 5.0 34.6 1.0

Phosphorus binding site 4 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ C:P1735 b:54.0 occ:1.00 PG C:ATP1735 0.0 54.0 1.0 O3G C:ATP1735 1.4 14.7 1.0 O1G C:ATP1735 1.4 46.1 1.0 O2G C:ATP1735 1.4 31.4 1.0 O3B C:ATP1735 1.7 38.1 1.0 PB C:ATP1735 2.9 38.9 1.0 O C:HOH6006 3.1 27.4 1.0 O3 C:OXL1733 3.2 72.0 1.0 MG C:MG1736 3.2 25.6 1.0 O2B C:ATP1735 3.2 24.2 1.0 MG C:MG1734 3.2 35.7 1.0 O C:HOH6647 3.5 19.7 1.0 O3A C:ATP1735 3.5 58.9 1.0 NH2 C:ARG1272 3.6 66.6 1.0 C1 C:OXL1733 3.7 29.8 1.0 ND2 C:ASN1274 3.7 31.3 1.0 O1A C:ATP1735 3.8 16.6 1.0 O4 C:OXL1733 3.9 40.0 1.0 O C:HOH6005 4.0 40.0 1.0 O1B C:ATP1735 4.1 91.7 1.0 PA C:ATP1735 4.1 34.7 1.0 C2 C:OXL1733 4.1 39.3 1.0 O1 C:OXL1733 4.4 37.3 1.0 OD2 C:ASP1495 4.4 34.9 1.0 O2A C:ATP1735 4.4 21.2 1.0 NA C:NA1732 4.5 56.0 1.0 CZ C:ARG1272 4.6 25.7 1.0 NH1 C:ARG1272 4.7 62.3 1.0 NH2 C:ARG1319 4.7 0.0 1.0 NH1 C:ARG1319 4.7 52.6 1.0 NZ C:LYS1469 4.9 76.7 1.0 CG C:ASN1274 4.9 32.3 1.0 O C:HOH6571 4.9 26.9 1.0

Phosphorus binding site 5 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ C:P1735 b:38.9 occ:1.00 PB C:ATP1735 0.0 38.9 1.0 O1B C:ATP1735 1.5 91.7 1.0 O2B C:ATP1735 1.5 24.2 1.0 O3B C:ATP1735 1.5 38.1 1.0 O3A C:ATP1735 1.6 58.9 1.0 PG C:ATP1735 2.9 54.0 1.0 PA C:ATP1735 2.9 34.7 1.0 MG C:MG1736 3.2 25.6 1.0 O1G C:ATP1735 3.2 46.1 1.0 O3' C:ATP1735 3.3 57.9 1.0 O1A C:ATP1735 3.3 16.6 1.0 NH2 C:ARG1319 3.4 0.0 1.0 NE2 C:HIS1277 3.5 33.6 1.0 O2G C:ATP1735 3.6 31.4 1.0 O3G C:ATP1735 3.8 14.7 1.0 O C:HOH6851 3.8 25.4 1.0 C3' C:ATP1735 3.9 32.5 1.0 O C:HOH6006 3.9 27.4 1.0 O5' C:ATP1735 3.9 27.2 1.0 O2A C:ATP1735 4.0 21.2 1.0 O C:HOH6005 4.0 40.0 1.0 C5' C:ATP1735 4.0 35.6 1.0 ND2 C:ASN1274 4.1 31.3 1.0 CZ C:ARG1319 4.4 52.9 1.0 CD2 C:HIS1277 4.4 50.2 1.0 CE1 C:HIS1277 4.5 35.0 1.0 C4' C:ATP1735 4.5 18.0 1.0 O C:HOH6571 4.6 26.9 1.0 NH1 C:ARG1319 4.7 52.6 1.0 O C:HOH6647 4.8 19.7 1.0

Phosphorus binding site 6 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ C:P1735 b:34.7 occ:1.00 PA C:ATP1735 0.0 34.7 1.0 O2A C:ATP1735 1.5 21.2 1.0 O1A C:ATP1735 1.5 16.6 1.0 O3A C:ATP1735 1.6 58.9 1.0 O5' C:ATP1735 1.7 27.2 1.0 C5' C:ATP1735 2.7 35.6 1.0 PB C:ATP1735 2.9 38.9 1.0 MG C:MG1736 3.1 25.6 1.0 O1G C:ATP1735 3.4 46.1 1.0 O2B C:ATP1735 3.4 24.2 1.0 O3B C:ATP1735 3.5 38.1 1.0 ND2 C:ASN1274 3.6 31.3 1.0 C3' C:ATP1735 3.6 32.5 1.0 C4' C:ATP1735 3.7 18.0 1.0 C8 C:ATP1735 3.9 43.7 1.0 O4' C:ATP1735 4.0 18.0 1.0 O1B C:ATP1735 4.1 91.7 1.0 PG C:ATP1735 4.1 54.0 1.0 NH1 C:ARG1272 4.1 62.3 1.0 O3' C:ATP1735 4.1 57.9 1.0 NE2 C:HIS1277 4.2 33.6 1.0 O C:HOH6647 4.3 19.7 1.0 CD2 C:HIS1277 4.4 50.2 1.0 CB C:SER1561 4.5 36.9 1.0 CG2 C:THR1249 4.6 21.2 1.0 O C:HOH6571 4.6 26.9 1.0 O3G C:ATP1735 4.7 14.7 1.0 N9 C:ATP1735 4.7 20.6 1.0 CG C:ASN1274 4.7 32.3 1.0 NH2 C:ARG1272 4.8 66.6 1.0 N7 C:ATP1735 4.8 24.4 1.0 O C:HOH6006 4.8 27.4 1.0 CZ C:ARG1272 4.8 25.7 1.0 C1' C:ATP1735 4.8 23.7 1.0 OG C:SER1561 4.9 31.0 1.0 C2' C:ATP1735 4.9 59.0 1.0 O C:HOH6734 4.9 35.1 1.0 CB C:ASN1274 5.0 37.3 1.0 O C:HOH6851 5.0 25.4 1.0

Phosphorus binding site 7 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ D:P2335 b:17.7 occ:1.00 PG D:ATP2335 0.0 17.7 1.0 O3G D:ATP2335 1.4 32.8 1.0 O1G D:ATP2335 1.4 31.3 1.0 O2G D:ATP2335 1.4 14.9 1.0 O3B D:ATP2335 1.7 18.5 1.0 MG D:MG2336 2.9 24.4 1.0 PB D:ATP2335 3.0 27.7 1.0 O3 D:OXL2333 3.1 15.1 1.0 O2B D:ATP2335 3.2 33.3 1.0 O D:HOH6045 3.2 11.2 1.0 MG D:MG2334 3.3 23.9 1.0 O D:HOH6004 3.3 29.9 1.0 ND2 D:ASN1874 3.4 22.6 1.0 NH2 D:ARG1872 3.6 23.5 1.0 C1 D:OXL2333 3.7 32.5 1.0 O3A D:ATP2335 3.8 7.9 1.0 O D:HOH6430 3.8 18.1 1.0 O1A D:ATP2335 4.0 12.8 1.0 O D:HOH6378 4.0 22.6 1.0 NA D:NA2332 4.1 27.3 1.0 O1B D:ATP2335 4.1 9.7 1.0 O4 D:OXL2333 4.2 23.6 1.0 NH1 D:ARG1919 4.2 25.3 1.0 PA D:ATP2335 4.2 23.4 1.0 OD2 D:ASP2095 4.3 11.6 1.0 C2 D:OXL2333 4.3 19.0 1.0 O1 D:OXL2333 4.4 12.4 1.0 NZ D:LYS2069 4.5 18.9 1.0 CG D:ASN1874 4.6 20.9 1.0 NH2 D:ARG1919 4.7 32.0 1.0 O2A D:ATP2335 4.7 12.5 1.0 O D:HOH7433 4.8 30.8 1.0 CZ D:ARG1872 4.8 18.1 1.0 O D:HOH7302 4.9 22.6 1.0 CZ D:ARG1919 5.0 44.1 1.0 O D:HOH6453 5.0 23.5 1.0 OD1 D:ASN1874 5.0 30.8 1.0

Phosphorus binding site 8 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ D:P2335 b:27.7 occ:1.00 PB D:ATP2335 0.0 27.7 1.0 O1B D:ATP2335 1.5 9.7 1.0 O2B D:ATP2335 1.5 33.3 1.0 O3B D:ATP2335 1.5 18.5 1.0 O3A D:ATP2335 1.6 7.9 1.0 PA D:ATP2335 2.9 23.4 1.0 PG D:ATP2335 3.0 17.7 1.0 MG D:MG2336 3.0 24.4 1.0 O D:HOH6453 3.2 23.5 1.0 O1A D:ATP2335 3.2 12.8 1.0 O1G D:ATP2335 3.2 31.3 1.0 NH2 D:ARG1919 3.4 32.0 1.0 O3G D:ATP2335 3.6 32.8 1.0 NE2 D:HIS1877 3.6 17.0 1.0 O3' D:ATP2335 3.7 13.8 1.0 O2G D:ATP2335 3.7 14.9 1.0 O5' D:ATP2335 3.8 20.6 1.0 O D:HOH6004 3.8 29.9 1.0 C5' D:ATP2335 3.8 40.4 1.0 C3' D:ATP2335 3.9 17.4 1.0 ND2 D:ASN1874 3.9 22.6 1.0 O D:HOH6045 3.9 11.2 1.0 O D:HOH6138 4.0 16.8 1.0 O2A D:ATP2335 4.0 12.5 1.0 CD2 D:HIS1877 4.2 1.1 1.0 O D:HOH7302 4.3 22.6 1.0 CZ D:ARG1919 4.4 44.1 1.0 C4' D:ATP2335 4.4 27.7 1.0 NH1 D:ARG1919 4.5 25.3 1.0 O D:HOH6378 4.7 22.6 1.0 CE1 D:HIS1877 4.8 21.2 1.0

Phosphorus binding site 9 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ D:P2335 b:23.4 occ:1.00 PA D:ATP2335 0.0 23.4 1.0 O2A D:ATP2335 1.5 12.5 1.0 O1A D:ATP2335 1.5 12.8 1.0 O3A D:ATP2335 1.5 7.9 1.0 O5' D:ATP2335 1.7 20.6 1.0 C5' D:ATP2335 2.7 40.4 1.0 PB D:ATP2335 2.9 27.7 1.0 MG D:MG2336 3.2 24.4 1.0 O2B D:ATP2335 3.2 33.3 1.0 O1G D:ATP2335 3.5 31.3 1.0 NH1 D:ARG1872 3.6 72.3 1.0 ND2 D:ASN1874 3.6 22.6 1.0 O3B D:ATP2335 3.8 18.5 1.0 C4' D:ATP2335 3.8 27.7 1.0 C3' D:ATP2335 3.9 17.4 1.0 O D:HOH6378 3.9 22.6 1.0 O1B D:ATP2335 4.0 9.7 1.0 O D:HOH7302 4.1 22.6 1.0 C8 D:ATP2335 4.2 9.9 1.0 CB D:SER2161 4.2 23.1 1.0 PG D:ATP2335 4.2 17.7 1.0 O4' D:ATP2335 4.3 49.6 1.0 NH2 D:ARG1872 4.3 23.5 1.0 CZ D:ARG1872 4.4 18.1 1.0 OG D:SER2161 4.5 28.4 1.0 CG2 D:THR1849 4.5 21.0 1.0 O3' D:ATP2335 4.7 13.8 1.0 CD2 D:HIS1877 4.7 1.1 1.0 NE2 D:HIS1877 4.7 17.0 1.0 CG D:ASN1874 4.8 20.9 1.0 O3G D:ATP2335 4.8 32.8 1.0 O D:HOH6087 4.8 16.1 1.0 N9 D:ATP2335 4.9 33.9 1.0 N D:GLY2162 4.9 11.2 1.0 CB D:ASN1874 5.0 5.8 1.0 CA D:SER2161 5.0 24.1 1.0 C1' D:ATP2335 5.0 5.2 1.0

Phosphorus binding site 10 out of 18 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ E:P3535 b:22.2 occ:1.00 PG E:ATP3535 0.0 22.2 1.0 O3G E:ATP3535 1.4 27.8 1.0 O2G E:ATP3535 1.4 6.9 1.0 O1G E:ATP3535 1.5 23.1 1.0 O3B E:ATP3535 1.7 48.8 1.0 PB E:ATP3535 3.0 23.0 1.0 O3 E:OXL3533 3.0 38.5 1.0 MG E:MG3536 3.1 26.2 1.0 MG E:MG3534 3.3 19.2 1.0 O2B E:ATP3535 3.3 22.5 1.0 NH2 E:ARG3119 3.5 29.4 1.0 O E:HOH6341 3.5 40.5 1.0 O E:HOH6156 3.5 18.4 1.0 O3A E:ATP3535 3.6 19.1 1.0 C1 E:OXL3533 3.7 21.9 1.0 ND2 E:ASN3074 3.7 15.4 1.0 NH2 E:ARG3072 3.8 20.8 1.0 O1A E:ATP3535 4.0 11.0 1.0 O E:HOH6954 4.0 30.3 1.0 O1B E:ATP3535 4.1 22.1 1.0 PA E:ATP3535 4.2 26.9 1.0 OD2 E:ASP3295 4.2 19.6 1.0 NA E:NA3532 4.3 29.6 1.0 O1 E:OXL3533 4.3 21.4 1.0 O4 E:OXL3533 4.4 34.2 1.0 O E:HOH6159 4.4 14.6 1.0 C2 E:OXL3533 4.4 19.2 1.0 O2A E:ATP3535 4.6 14.9 1.0 CZ E:ARG3119 4.6 41.3 1.0 O E:HOH7689 4.6 31.1 1.0 CG E:ASN3074 4.7 17.3 1.0 NH1 E:ARG3119 4.8 18.8 1.0 OD1 E:ASN3074 4.8 33.9 1.0 NZ E:LYS3269 4.8 5.4 1.0 CZ E:ARG3072 5.0 16.7 1.0

T.M.Larsen, M.M.Benning, I.Rayment, G.H.Reed. Structure of the Bis(MG2+)-Atp-Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 A Resolution: Atp Binding Over A Barrel. Biochemistry V. 37 6247 1998.
ISSN: ISSN 0006-2960
PubMed: 9572839
DOI: 10.1021/BI980243S