Magnesium in PDB 1xdp: Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp

All present enzymatic activity of Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp:
2.7.4.1;

The structure of Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp, PDB code: 1xdp was solved by Y.Zhu, W.Huang, S.S.Lee, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	152.000, 152.000, 150.000, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 27.4

The binding sites of Magnesium atom in the Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp (pdb code 1xdp). 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 the E.Coli Polyphosphate Kinase in Complex with Amppnp, PDB code: 1xdp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp


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 the E.Coli Polyphosphate Kinase in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:58.2 occ:1.00 O2A A:ATP701 2.8 71.4 1.0 NH1 A:ARG405 2.9 0.2 1.0 NH2 A:ARG375 3.0 80.0 1.0 MG A:MG703 3.1 79.1 1.0 CD A:ARG405 3.1 0.1 1.0 O2B A:ATP701 3.5 71.4 1.0 O1G A:ATP701 3.6 71.8 1.0 CZ A:ARG375 3.8 79.2 1.0 NH1 A:ARG375 3.8 80.0 1.0 CZ A:ARG405 3.8 0.3 1.0 NE A:ARG405 3.9 1.0 1.0 PA A:ATP701 4.0 71.1 1.0 O3A A:ATP701 4.0 71.2 1.0 C5' A:ATP701 4.1 68.1 1.0 CG A:ARG405 4.3 0.5 1.0 OE2 A:GLU48 4.3 47.5 1.0 O5' A:ATP701 4.4 69.2 1.0 CB A:ARG405 4.4 0.0 1.0 PB A:ATP701 4.5 70.8 1.0 O3' A:ATP701 4.7 67.7 1.0 C4' A:ATP701 4.8 67.3 1.0 NH2 A:ARG53 4.9 49.8 1.0 PG A:ATP701 4.9 70.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp


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 the E.Coli Polyphosphate Kinase in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:79.1 occ:1.00 O1G A:ATP701 2.1 71.8 1.0 CD A:ARG405 2.4 0.1 1.0 NE A:ARG405 2.5 1.0 1.0 NH2 A:ARG375 2.6 80.0 1.0 NH1 A:ARG405 2.6 0.2 1.0 CZ A:ARG405 2.7 0.3 1.0 MG A:MG702 3.1 58.2 1.0 CG A:ARG405 3.3 0.5 1.0 OH A:TYR374 3.3 63.9 1.0 PG A:ATP701 3.6 70.5 1.0 NH2 A:ARG405 3.7 0.1 1.0 CZ A:ARG375 3.9 79.2 1.0 CB A:ARG405 4.0 0.0 1.0 O2B A:ATP701 4.2 71.4 1.0 O3G A:ATP701 4.2 71.4 1.0 O2A A:ATP701 4.3 71.4 1.0 NH2 A:ARG621 4.3 35.7 1.0 CZ A:TYR374 4.4 63.0 1.0 CE2 A:TYR374 4.5 62.4 1.0 O2G A:ATP701 4.5 71.5 1.0 NE A:ARG375 4.7 77.5 1.0 O3B A:ATP701 4.7 69.8 1.0 NZ A:LYS433 4.8 55.4 1.0 NH1 A:ARG375 4.8 80.0 1.0 NH1 A:ARG621 4.8 34.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp


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 the E.Coli Polyphosphate Kinase in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg705 b:68.0 occ:1.00 O1G B:ATP704 1.9 63.6 1.0 O B:HOH743 3.1 15.8 1.0 NH1 B:ARG405 3.1 0.4 1.0 O B:HOH707 3.2 1.0 1.0 MG B:MG706 3.3 88.6 1.0 PG B:ATP704 3.5 63.0 1.0 CZ B:ARG405 3.9 0.7 1.0 O2A B:ATP704 4.0 68.3 1.0 NH2 B:ARG405 4.1 0.2 1.0 OD2 B:ASP612 4.2 14.1 1.0 PA B:ATP704 4.2 67.8 1.0 O2G B:ATP704 4.3 62.9 1.0 O1A B:ATP704 4.4 65.6 1.0 O3B B:ATP704 4.4 63.8 1.0 O3G B:ATP704 4.4 64.4 1.0 OD1 B:ASN539 4.7 19.1 1.0 NH2 B:ARG53 4.9 61.3 1.0 NE B:ARG405 4.9 0.1 1.0 O2B B:ATP704 4.9 66.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the E.Coli Polyphosphate Kinase in Complex with Amppnp


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 the E.Coli Polyphosphate Kinase in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg706 b:88.6 occ:1.00 O B:HOH743 1.4 15.8 1.0 NH2 B:ARG53 2.3 61.3 1.0 O2A B:ATP704 2.5 68.3 1.0 MG B:MG705 3.3 68.0 1.0 NH1 B:ARG405 3.3 0.4 1.0 PA B:ATP704 3.5 67.8 1.0 CZ B:ARG53 3.6 61.4 1.0 O1A B:ATP704 3.6 65.6 1.0 NH1 B:ARG53 4.2 63.0 1.0 O5' B:ATP704 4.3 67.5 1.0 NH2 B:ARG564 4.5 20.7 1.0 NE B:ARG53 4.5 59.8 1.0 O1G B:ATP704 4.5 63.6 1.0 CZ B:ARG405 4.5 0.7 1.0 OD1 B:ASN539 4.6 19.1 1.0 O3A B:ATP704 4.9 66.3 1.0 NH2 B:ARG405 5.0 0.2 1.0

Y.Zhu, W.Huang, S.S.Lee, W.Xu. Crystal Structure of A Polyphosphate Kinase and Its Implications For Polyphosphate Synthesis Embo Rep. V. 6 681 2005.
ISSN: ISSN 1469-221X
PubMed: 15947782
DOI: 10.1038/SJ.EMBOR.7400448