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Magnesium in PDB 6p0y: Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp

Enzymatic activity of Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp

All present enzymatic activity of Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp:
2.7.1.40;

Protein crystallography data

The structure of Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp, PDB code: 6p0y was solved by N.Schormann, D.Chattopadhyay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.03 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.465, 105.305, 83.453, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26.8

Other elements in 6p0y:

The structure of Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp (pdb code 6p0y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp, PDB code: 6p0y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6p0y

Go back to Magnesium Binding Sites List in 6p0y
Magnesium binding site 1 out of 2 in the Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:39.8
occ:1.00
O A:HOH789 2.3 36.9 1.0
O2A A:ADP601 2.4 49.2 1.0
O3B A:ADP601 2.5 50.3 1.0
O A:HOH760 2.6 40.0 1.0
OD2 A:ASP170 3.4 73.1 1.0
PB A:ADP601 3.4 50.6 1.0
PA A:ADP601 3.5 48.8 1.0
O A:HOH753 3.5 30.8 1.0
O3A A:ADP601 3.6 50.8 1.0
O2B A:ADP601 3.7 50.9 1.0
OD1 A:ASP170 4.1 72.5 1.0
O5' A:ADP601 4.1 49.9 1.0
CG A:ASP170 4.1 73.8 1.0
OG A:SER362 4.3 34.7 1.0
O A:HOH777 4.5 23.5 1.0
CB A:SER362 4.6 34.5 1.0
O1A A:ADP601 4.8 49.6 1.0
O1B A:ADP601 4.8 49.6 1.0
NH2 A:ARG74 5.0 34.3 1.0

Magnesium binding site 2 out of 2 in 6p0y

Go back to Magnesium Binding Sites List in 6p0y
Magnesium binding site 2 out of 2 in the Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryptosporidium Parvum Pyruvate Kinase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:49.0
occ:1.00
O B:HOH709 2.0 38.5 1.0
O2B B:ADP601 2.3 39.9 1.0
O B:HOH774 2.5 34.7 1.0
O1A B:ADP601 2.5 44.9 1.0
PB B:ADP601 3.7 40.3 1.0
OD2 B:ASP170 3.7 68.0 1.0
PA B:ADP601 3.8 43.5 1.0
O B:HOH746 3.9 29.6 1.0
O B:HOH775 4.0 41.8 1.0
O3A B:ADP601 4.0 42.3 1.0
O B:HOH793 4.1 31.0 1.0
OG B:SER362 4.5 32.1 1.0
O5' B:ADP601 4.6 44.2 1.0
O3B B:ADP601 4.6 40.6 1.0
O1B B:ADP601 4.7 38.1 1.0
CG B:ASP170 4.7 68.8 1.0
CB B:SER362 4.8 32.3 1.0
O2A B:ADP601 4.9 42.8 1.0

Reference:

N.Schormann, K.L.Hayden, P.Lee, S.Banerjee, D.Chattopadhyay. An Overview of Structure, Function, and Regulation of Pyruvate Kinases. Protein Sci. V. 28 1771 2019.
ISSN: ESSN 1469-896X
PubMed: 31342570
DOI: 10.1002/PRO.3691
Page generated: Tue Oct 1 13:46:03 2024

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