Atomistry » Magnesium » PDB 5m3f-5mdl » 5m3u
Atomistry »
  Magnesium »
    PDB 5m3f-5mdl »
      5m3u »

Magnesium in PDB 5m3u: The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant

Enzymatic activity of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant

All present enzymatic activity of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant:
2.7.2.3;

Protein crystallography data

The structure of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant, PDB code: 5m3u was solved by A.Ilari, A.Fiorillo, A.Cipollone, M.Petrosino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.650, 106.031, 50.097, 90.00, 98.71, 90.00
R / Rfree (%) 19.2 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant (pdb code 5m3u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant, PDB code: 5m3u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5m3u

Go back to Magnesium Binding Sites List in 5m3u
Magnesium binding site 1 out of 3 in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant


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 V216F Phosphoglycerate Kinase 1 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:36.7
occ:1.00
O1A A:ADP501 2.0 33.9 1.0
O A:HOH601 2.0 38.9 1.0
O A:HOH728 2.3 45.2 1.0
OD2 A:ASP374 2.3 41.2 1.0
O2B A:ADP501 2.4 41.9 1.0
PA A:ADP501 3.4 31.3 1.0
CG A:ASP374 3.4 38.8 1.0
PB A:ADP501 3.7 41.4 1.0
O3A A:ADP501 3.8 33.2 1.0
O A:HOH703 3.8 45.2 1.0
O5' A:ADP501 4.2 28.4 1.0
CB A:ASP374 4.2 38.6 1.0
OD1 A:ASP374 4.3 38.9 1.0
O A:HOH721 4.3 32.5 1.0
C5' A:ADP501 4.3 24.9 1.0
O2A A:ADP501 4.5 36.3 1.0
N A:ASP374 4.5 40.9 1.0
O3B A:ADP501 4.6 39.5 1.0
O1B A:ADP501 4.8 42.0 1.0

Magnesium binding site 2 out of 3 in 5m3u

Go back to Magnesium Binding Sites List in 5m3u
Magnesium binding site 2 out of 3 in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant


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 V216F Phosphoglycerate Kinase 1 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:42.3
occ:1.00
O A:HOH664 2.0 34.0 1.0
O A:LEU413 2.6 24.3 1.0
NZ A:LYS5 2.8 44.1 1.0
O A:ASP411 2.9 24.3 1.0
OD1 A:ASN415 3.3 35.0 1.0
CG A:ASN415 3.7 41.0 1.0
C A:LEU413 3.9 26.9 1.0
ND2 A:ASN415 3.9 44.9 1.0
C A:ASP411 4.0 23.3 1.0
N A:ASN415 4.2 30.1 1.0
CE A:LYS5 4.3 40.7 1.0
C A:SER414 4.4 30.4 1.0
CB A:ASN415 4.5 37.5 1.0
CA A:SER414 4.6 28.0 1.0
O A:HOH686 4.6 37.1 1.0
C A:ALA412 4.7 23.3 1.0
N A:SER414 4.7 25.8 1.0
N A:LEU413 4.7 23.4 1.0
CA A:ASN415 4.8 36.4 1.0
O A:ALA412 4.9 22.4 1.0
CD A:LYS5 4.9 36.2 1.0
CA A:ASP411 4.9 22.9 1.0
CA A:LEU413 4.9 23.6 1.0
N A:ALA412 4.9 20.1 1.0
O A:SER414 5.0 28.1 1.0

Magnesium binding site 3 out of 3 in 5m3u

Go back to Magnesium Binding Sites List in 5m3u
Magnesium binding site 3 out of 3 in the The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The X-Ray Structure of Human V216F Phosphoglycerate Kinase 1 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:46.7
occ:1.00
O2 A:3PG502 2.2 69.6 1.0
C1 A:3PG502 3.4 62.7 1.0
N A:GLY395 3.5 28.2 1.0
O A:HOH656 3.6 32.2 1.0
CA A:GLY395 3.7 30.0 1.0
N A:GLY396 3.9 24.3 1.0
O1 A:3PG502 4.2 62.5 1.0
C A:GLY395 4.3 28.0 1.0
C2 A:3PG502 4.5 59.0 1.0
C A:GLY394 4.7 25.5 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 20:50:15 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy