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Magnesium in PDB 5m6z: The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation

Enzymatic activity of The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation

All present enzymatic activity of The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation:
2.7.2.3;

Protein crystallography data

The structure of The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation, PDB code: 5m6z was solved by A.Ilari, A.Fiorillo, M.Petrosino, A.Cipollone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.06 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.880, 106.121, 50.472, 90.00, 98.13, 90.00
R / Rfree (%) 18.3 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation (pdb code 5m6z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation, PDB code: 5m6z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5m6z

Go back to Magnesium Binding Sites List in 5m6z
Magnesium binding site 1 out of 2 in the The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:48.3
occ:1.00
O3A A:ADP503 2.4 65.5 1.0
O A:HOH726 2.7 43.5 1.0
O1B A:ADP503 2.8 84.6 1.0
O A:GLY212 3.1 26.4 1.0
PB A:ADP503 3.3 83.8 1.0
CA A:GLY213 3.5 34.7 1.0
PA A:ADP503 3.7 58.5 1.0
O5' A:ADP503 3.8 52.9 1.0
CA A:GLY337 3.9 19.1 1.0
C A:GLY212 3.9 24.9 1.0
CE A:LYS219 4.0 43.6 1.0
O1A A:ADP503 4.0 48.8 1.0
O2B A:ADP503 4.1 75.3 1.0
N A:GLY213 4.2 32.2 1.0
C5' A:ADP503 4.2 43.8 1.0
O A:HOH659 4.3 42.7 1.0
O3B A:ADP503 4.4 81.5 1.0
OD2 A:ASP374 4.6 30.7 1.0
NZ A:LYS219 4.6 45.4 1.0
N A:GLY337 4.8 20.3 1.0
C A:GLY213 4.8 35.9 1.0
C A:GLY337 4.9 20.1 1.0
CD A:PRO338 5.0 21.9 1.0
O2A A:ADP503 5.0 53.8 1.0

Magnesium binding site 2 out of 2 in 5m6z

Go back to Magnesium Binding Sites List in 5m6z
Magnesium binding site 2 out of 2 in the The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The X-Ray Structure of Human M189I Pgk-1 Mutant in Partially Closed Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:54.7
occ:1.00
O1A A:ADP503 2.2 48.8 1.0
OD2 A:ASP218 2.8 47.9 1.0
N A:LYS215 3.1 33.4 1.0
NZ A:LYS219 3.2 45.4 1.0
PA A:ADP503 3.4 58.5 1.0
CB A:LYS215 3.5 45.3 1.0
CG A:ASP218 3.6 42.7 1.0
OD1 A:ASP218 3.7 45.2 1.0
O2A A:ADP503 3.7 53.8 1.0
CB A:ALA214 3.7 36.1 1.0
CA A:LYS215 3.9 38.9 1.0
N A:ALA214 4.0 32.8 1.0
C A:ALA214 4.1 32.7 1.0
CA A:ALA214 4.1 32.3 1.0
O5' A:ADP503 4.4 52.9 1.0
O A:LYS215 4.5 38.8 1.0
CD A:LYS215 4.5 59.4 1.0
NZ A:LYS215 4.5 66.5 1.0
CE A:LYS219 4.5 43.6 1.0
CE A:LYS215 4.5 62.1 1.0
O3A A:ADP503 4.6 65.5 1.0
CG A:LYS215 4.6 52.4 1.0
C A:LYS215 4.6 35.9 1.0

Reference:

A.Fiorillo, M.Petrosino, A.Ilari, A.Pasquo, A.Cipollone, M.Maggi, R.Chiaraluce, V.Consalvi. The Phosphoglycerate Kinase 1 Variants Found in Carcinoma Cells Display Different Catalytic Activity and Conformational Stability Compared to the Native Enzyme. Plos One V. 13 99191 2018.
ISSN: ESSN 1932-6203
PubMed: 29995887
DOI: 10.1371/JOURNAL.PONE.0199191
Page generated: Mon Dec 14 20:50:33 2020

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