Atomistry » Magnesium » PDB 8hh5-8hrv » 8hmu
Atomistry »
  Magnesium »
    PDB 8hh5-8hrv »
      8hmu »

Magnesium in PDB 8hmu: Crystal Structure of PKM2 Mutant R516C

Enzymatic activity of Crystal Structure of PKM2 Mutant R516C

All present enzymatic activity of Crystal Structure of PKM2 Mutant R516C:
2.7.1.40; 2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of PKM2 Mutant R516C, PDB code: 8hmu was solved by S.Upadhyay, A.Kumar, A.K.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.92 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.4, 138.512, 155.614, 90, 90, 90
R / Rfree (%) 23.7 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PKM2 Mutant R516C (pdb code 8hmu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of PKM2 Mutant R516C, PDB code: 8hmu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 1 out of 7 in the Crystal Structure of PKM2 Mutant R516C


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 PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:40.9
occ:1.00
 OE2 A:GLU272 1.9 44.9 1.0
O1 A:OXL602 1.9 47.8 1.0
O2 A:OXL602 2.1 44.6 1.0
OD2 A:ASP296 2.1 45.2 1.0
C1 A:OXL602 2.7 48.3 1.0
C2 A:OXL602 2.8 49.1 1.0
CD A:GLU272 3.1 44.3 1.0
CG A:ASP296 3.3 47.5 1.0
O3 A:OXL602 3.8 49.2 1.0
NZ A:LYS270 3.9 43.5 1.0
OE1 A:GLU272 4.0 42.8 1.0
CB A:ASP296 4.0 43.3 1.0
O4 A:OXL602 4.0 47.0 1.0
CG A:GLU272 4.0 43.9 1.0
OD1 A:ASP296 4.3 48.8 1.0
N A:ASP296 4.4 45.8 1.0
CZ A:PHE244 4.5 51.7 1.0
CE A:LYS270 4.5 45.3 1.0
CE1 A:PHE244 4.8 48.1 1.0
CB A:ALA293 4.8 40.5 1.0
CA A:ASP296 4.8 45.2 1.0
O A:HOH759 5.0 50.7 1.0

Magnesium binding site 2 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 2 out of 7 in the Crystal Structure of PKM2 Mutant R516C


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 PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:41.1
occ:1.00
 OD1 A:ASP113 2.5 42.4 1.0
OD1 A:ASN75 2.7 43.0 1.0
O A:THR114 2.9 49.7 1.0
OG A:SER77 2.9 46.6 1.0
CG A:ASP113 3.5 43.2 1.0
OG A:SER243 3.6 42.0 1.0
CG A:ASN75 3.8 44.8 1.0
C A:THR114 3.8 49.0 1.0
CB A:SER77 4.0 51.0 1.0
NZ A:LYS270 4.0 43.5 1.0
O A:ASP113 4.1 42.5 1.0
CA A:LYS115 4.2 49.1 1.0
O A:LYS115 4.2 49.5 1.0
ND2 A:ASN75 4.3 54.7 1.0
CB A:ASP113 4.3 43.6 1.0
OD2 A:ASP113 4.3 42.7 1.0
NH2 A:ARG73 4.3 40.5 1.0
C A:ASP113 4.3 43.9 1.0
N A:LYS115 4.4 46.2 1.0
N A:SER77 4.4 48.2 1.0
C A:LYS115 4.6 47.8 1.0
O1 A:OXL602 4.7 47.8 1.0
CB A:SER243 4.7 44.6 1.0
OE2 A:GLU118 4.7 53.2 1.0
N A:THR114 4.7 48.2 1.0
CA A:SER77 4.8 48.2 1.0
CA A:THR114 4.9 47.8 1.0
CA A:ASP113 4.9 44.5 1.0
CB A:ASN75 5.0 39.5 1.0
N A:PHE76 5.0 46.0 1.0

Magnesium binding site 3 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 3 out of 7 in the Crystal Structure of PKM2 Mutant R516C


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 PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg609

b:63.5
occ:1.00
 OE2 B:GLU272 1.9 55.4 1.0
O3 B:OXL602 1.9 62.4 1.0
OD2 B:ASP296 2.0 61.7 1.0
O B:HOH746 2.4 62.7 1.0
O4 B:OXL602 2.7 57.2 1.0
C1 B:OXL602 2.9 59.6 1.0
CD B:GLU272 3.0 62.5 1.0
CG B:ASP296 3.2 61.8 1.0
C2 B:OXL602 3.3 57.1 1.0
OE1 B:GLU272 3.5 61.7 1.0
CB B:ASP296 3.9 58.1 1.0
O1 B:OXL602 4.1 57.2 1.0
NZ B:LYS270 4.1 55.0 1.0
OD1 B:ASP296 4.1 65.3 1.0
CG B:GLU272 4.2 61.8 1.0
CE1 B:PHE244 4.3 66.5 1.0
CZ B:PHE244 4.3 68.9 1.0
O2 B:OXL602 4.5 53.5 1.0
CE B:LYS270 4.6 57.0 1.0
N B:ASP296 4.6 55.8 1.0
CA B:ASP296 4.9 59.4 1.0

Magnesium binding site 4 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 4 out of 7 in the Crystal Structure of PKM2 Mutant R516C


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 PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg608

b:46.5
occ:1.00
 OE1 C:GLU272 1.9 51.1 1.0
OD2 C:ASP296 1.9 53.8 1.0
O1 C:OXL602 2.1 45.8 1.0
O2 C:OXL602 2.3 46.8 1.0
C1 C:OXL602 2.8 47.0 1.0
C2 C:OXL602 2.8 46.3 1.0
CD C:GLU272 3.1 51.9 1.0
CG C:ASP296 3.1 52.2 1.0
OE2 C:GLU272 3.7 51.0 1.0
CB C:ASP296 3.8 49.8 1.0
O C:HOH736 4.0 48.1 1.0
O3 C:OXL602 4.1 48.2 1.0
OD1 C:ASP296 4.1 55.8 1.0
NZ C:LYS270 4.1 44.8 1.0
CE2 C:PHE244 4.1 64.8 1.0
O4 C:OXL602 4.1 44.8 1.0
CZ C:PHE244 4.1 62.9 1.0
O C:HOH748 4.2 53.1 1.0
CG C:GLU272 4.3 50.7 1.0
N C:ASP296 4.4 44.7 1.0
CE C:LYS270 4.6 48.5 1.0
CB C:ALA293 4.7 43.4 1.0
CB C:GLU272 4.8 51.9 1.0
CA C:ASP296 4.8 48.4 1.0
CD2 C:PHE244 5.0 63.6 1.0

Magnesium binding site 5 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 5 out of 7 in the Crystal Structure of PKM2 Mutant R516C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg609

b:42.8
occ:1.00
 OD1 C:ASN75 2.5 51.1 1.0
OD1 C:ASP113 2.6 45.2 1.0
O C:HOH748 2.6 53.1 1.0
O C:THR114 2.7 48.3 1.0
OG C:SER77 2.9 53.8 1.0
O C:HOH736 3.1 48.1 1.0
CG C:ASP113 3.6 45.8 1.0
OG C:SER243 3.6 47.1 1.0
CG C:ASN75 3.6 50.3 1.0
C C:THR114 3.7 49.0 1.0
O C:ASP113 4.0 46.8 1.0
NZ C:LYS270 4.0 44.8 1.0
NH2 C:ARG73 4.0 44.3 1.0
CB C:SER77 4.1 52.8 1.0
CA C:LYS115 4.2 50.8 1.0
C C:ASP113 4.2 46.4 1.0
CB C:ASP113 4.2 44.2 1.0
N C:LYS115 4.3 50.0 1.0
N C:SER77 4.3 52.4 1.0
ND2 C:ASN75 4.3 53.0 1.0
OE2 C:GLU118 4.3 64.6 1.0
N C:THR114 4.5 49.7 1.0
O C:LYS115 4.5 56.0 1.0
OD2 C:ASP113 4.5 45.7 1.0
N C:PHE76 4.6 47.3 1.0
CA C:THR114 4.7 48.7 1.0
C C:LYS115 4.7 54.2 1.0
CA C:SER77 4.7 53.2 1.0
CB C:SER243 4.7 50.9 1.0
CB C:ASN75 4.8 45.2 1.0
CA C:ASN75 4.8 44.8 1.0
CA C:ASP113 4.8 46.4 1.0
C C:ASN75 5.0 47.9 1.0

Magnesium binding site 6 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 6 out of 7 in the Crystal Structure of PKM2 Mutant R516C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg609

b:40.4
occ:1.00
 O3 D:OXL602 1.8 37.2 1.0
OE1 D:GLU272 1.9 47.3 1.0
OD2 D:ASP296 1.9 38.9 1.0
CD D:GLU272 2.8 47.2 1.0
C1 D:OXL602 2.8 39.8 1.0
O2 D:OXL602 3.0 38.0 1.0
OE2 D:GLU272 3.0 46.8 1.0
CG D:ASP296 3.1 39.4 1.0
CZ D:PHE244 3.4 46.1 1.0
C2 D:OXL602 3.5 40.3 1.0
NZ D:LYS270 3.8 39.6 1.0
CB D:ASP296 3.8 39.6 1.0
CE2 D:PHE244 3.9 46.8 1.0
O1 D:OXL602 3.9 36.3 1.0
CE1 D:PHE244 4.0 40.2 1.0
OD1 D:ASP296 4.0 34.5 1.0
CG D:GLU272 4.2 40.5 1.0
O D:HOH775 4.3 37.0 1.0
CB D:GLU272 4.6 42.3 1.0
CE D:LYS270 4.6 40.2 1.0
O4 D:OXL602 4.7 38.3 1.0
CD2 D:PHE244 4.7 44.6 1.0
N D:ASP296 4.7 37.4 1.0
OG D:SER243 4.8 41.3 1.0
CD1 D:PHE244 4.8 41.6 1.0
CA D:ASP296 4.9 41.5 1.0

Magnesium binding site 7 out of 7 in 8hmu

Go back to Magnesium Binding Sites List in 8hmu
Magnesium binding site 7 out of 7 in the Crystal Structure of PKM2 Mutant R516C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of PKM2 Mutant R516C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg610

b:37.9
occ:1.00
 O D:HOH775 2.4 37.0 1.0
O D:THR114 2.4 42.9 1.0
OD1 D:ASP113 2.6 42.8 1.0
OD1 D:ASN75 2.7 40.4 1.0
OG D:SER77 2.7 48.5 1.0
C D:THR114 3.5 42.2 1.0
OG D:SER243 3.5 41.3 1.0
CG D:ASP113 3.6 41.6 1.0
CG D:ASN75 3.8 40.7 1.0
NZ D:LYS270 3.9 39.6 1.0
CB D:SER77 4.0 48.4 1.0
NH2 D:ARG73 4.1 36.4 1.0
O D:ASP113 4.1 41.2 1.0
CA D:LYS115 4.2 46.4 1.0
C D:ASP113 4.2 41.5 1.0
N D:LYS115 4.3 47.7 1.0
O D:LYS115 4.3 47.8 1.0
N D:THR114 4.3 45.9 1.0
N D:SER77 4.3 45.4 1.0
CB D:ASP113 4.3 40.0 1.0
ND2 D:ASN75 4.4 41.2 1.0
OD2 D:ASP113 4.4 40.8 1.0
OE2 D:GLU118 4.5 56.1 1.0
CA D:THR114 4.6 42.9 1.0
C D:LYS115 4.6 46.6 1.0
CB D:SER243 4.6 40.9 1.0
CA D:SER77 4.7 46.1 1.0
N D:PHE76 4.8 46.2 1.0
CA D:ASP113 4.9 38.6 1.0
CB D:ASN75 4.9 40.1 1.0
CA D:ASN75 5.0 42.1 1.0

Reference:

S.Upadhyay, A.Kumar, A.K.Patel. Structural and Mechanistic Insights Into Cancer Patient-Derived Mutations in Pyruvate Kinase Muscle Isoform 2 To Be Published.
Page generated: Fri Oct 4 08:07:11 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy