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Potassium in PDB 6v75: Crystal Structure of Human PKM2 in Complex with L-Aspartate

Enzymatic activity of Crystal Structure of Human PKM2 in Complex with L-Aspartate

All present enzymatic activity of Crystal Structure of Human PKM2 in Complex with L-Aspartate:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of Human PKM2 in Complex with L-Aspartate, PDB code: 6v75 was solved by S.Nandi, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.52 / 2.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.523, 157.955, 93.031, 90.00, 101.08, 90.00
R / Rfree (%) 24.6 / 28.4

Other elements in 6v75:

The structure of Crystal Structure of Human PKM2 in Complex with L-Aspartate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Human PKM2 in Complex with L-Aspartate (pdb code 6v75). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Human PKM2 in Complex with L-Aspartate, PDB code: 6v75:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6v75

Go back to Potassium Binding Sites List in 6v75
Potassium binding site 1 out of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:65.8
occ:1.00
O C:THR114 2.8 60.8 1.0
OD1 C:ASN75 2.9 44.7 1.0
OD1 C:ASP113 3.1 53.8 1.0
OG C:SER77 3.2 60.5 1.0
CG C:ASP113 3.8 55.2 1.0
C C:THR114 3.8 58.4 1.0
CG C:ASN75 3.9 44.3 1.0
NZ C:LYS270 4.0 44.6 1.0
OG C:SER243 4.1 47.0 1.0
CB C:SER77 4.1 55.4 1.0
CA C:LYS115 4.2 58.9 1.0
ND2 C:ASN75 4.2 43.6 1.0
N C:LYS115 4.4 53.5 1.0
OD2 C:ASP113 4.4 51.3 1.0
O2 C:OXL609 4.5 64.6 1.0
OE2 C:GLU118 4.5 66.7 1.0
O C:LYS115 4.5 51.1 1.0
CB C:ASP113 4.6 53.9 1.0
NH2 C:ARG73 4.6 48.1 1.0
N C:SER77 4.7 55.5 1.0
C C:LYS115 4.8 57.1 1.0
N C:THR114 4.8 50.7 1.0
C C:ASP113 4.8 48.5 1.0
O C:ASP113 4.9 49.5 1.0
CA C:THR114 4.9 49.9 1.0
CA C:SER77 5.0 56.9 1.0
MG C:MG608 5.0 57.4 1.0

Potassium binding site 2 out of 6 in 6v75

Go back to Potassium Binding Sites List in 6v75
Potassium binding site 2 out of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:82.4
occ:1.00
CD C:ARG106 3.3 51.2 1.0
O C:LEU104 3.6 53.0 1.0
CD2 C:PHE98 4.1 54.9 1.0
CG C:ARG106 4.2 49.5 1.0
CG C:PHE98 4.3 54.8 1.0
CE2 C:PHE98 4.5 57.4 1.0
CB C:PHE98 4.6 56.3 1.0
C C:LEU104 4.7 60.1 1.0
CD1 C:PHE98 4.8 55.0 1.0
CG2 C:ILE65 4.9 48.9 1.0
CB C:ARG106 4.9 40.5 1.0
N C:ARG106 5.0 59.7 1.0

Potassium binding site 3 out of 6 in 6v75

Go back to Potassium Binding Sites List in 6v75
Potassium binding site 3 out of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:63.0
occ:1.00
O A:THR114 2.7 55.4 1.0
OG A:SER77 2.8 62.8 1.0
OD1 A:ASN75 2.9 52.9 1.0
OD1 A:ASP113 3.2 67.3 1.0
OG A:SER243 3.5 61.1 1.0
C A:THR114 3.9 55.0 1.0
CB A:SER77 3.9 67.2 1.0
O A:LYS115 3.9 68.7 1.0
OE2 A:GLU118 3.9 62.1 1.0
CG A:ASN75 4.0 55.7 1.0
CG A:ASP113 4.1 69.0 1.0
CA A:LYS115 4.1 62.7 1.0
C A:LYS115 4.4 62.7 1.0
CB A:SER243 4.4 65.0 1.0
ND2 A:ASN75 4.5 64.6 1.0
N A:LYS115 4.5 57.0 1.0
N A:SER77 4.6 63.8 1.0
O A:ASP113 4.6 58.5 1.0
CA A:SER77 4.7 70.0 1.0
CB A:ASP113 4.8 63.5 1.0
C A:ASP113 4.8 58.7 1.0
OD2 A:ASP113 4.9 63.2 1.0
N A:THR114 5.0 55.9 1.0

Potassium binding site 4 out of 6 in 6v75

Go back to Potassium Binding Sites List in 6v75
Potassium binding site 4 out of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:69.6
occ:1.00
OD1 B:ASN75 2.9 64.8 1.0
OD1 B:ASP113 3.1 72.7 1.0
O B:THR114 3.2 65.0 1.0
OG B:SER77 3.5 73.4 1.0
CG B:ASP113 3.9 69.0 1.0
CG B:ASN75 4.0 57.7 1.0
CB B:SER77 4.0 64.3 1.0
OG B:SER243 4.1 61.6 1.0
C B:THR114 4.1 67.5 1.0
NZ B:LYS270 4.2 58.1 1.0
CA B:LYS115 4.4 68.0 1.0
ND2 B:ASN75 4.4 64.1 1.0
O B:ASP113 4.5 70.9 1.0
N B:SER77 4.5 71.4 1.0
OD2 B:ASP113 4.5 65.8 1.0
N B:LYS115 4.6 67.6 1.0
CB B:ASP113 4.6 63.3 1.0
O B:LYS115 4.6 67.5 1.0
NH2 B:ARG73 4.6 66.2 1.0
C B:ASP113 4.7 66.3 1.0
C B:LYS115 4.9 63.6 1.0
CA B:SER77 4.9 64.9 1.0

Potassium binding site 5 out of 6 in 6v75

Go back to Potassium Binding Sites List in 6v75
Potassium binding site 5 out of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K601

b:68.9
occ:1.00
OG D:SER77 2.8 71.8 1.0
OD1 D:ASP113 3.0 70.4 1.0
OD1 D:ASN75 3.2 69.9 1.0
O D:THR114 3.5 70.0 1.0
OE2 D:GLU118 3.6 74.2 1.0
CB D:SER77 4.0 74.6 1.0
CG D:ASP113 4.0 67.6 1.0
CA D:LYS115 4.0 73.4 1.0
O D:LYS115 4.1 71.5 1.0
CG D:ASN75 4.1 66.8 1.0
NZ D:LYS270 4.2 63.5 1.0
C D:THR114 4.2 71.6 1.0
ND2 D:ASN75 4.4 63.1 1.0
C D:LYS115 4.5 68.6 1.0
N D:LYS115 4.5 73.6 1.0
O D:ASP113 4.6 67.4 1.0
N D:SER77 4.6 78.6 1.0
CB D:SER243 4.7 66.5 1.0
OD2 D:ASP113 4.7 67.4 1.0
CD D:GLU118 4.8 76.5 1.0
CA D:SER77 4.8 78.1 1.0
CB D:ASP113 4.8 66.0 1.0
NH2 D:ARG73 4.9 63.4 1.0
C D:ASP113 4.9 66.6 1.0

Potassium binding site 6 out of 6 in 6v75

Go back to Potassium Binding Sites List in 6v75
Potassium binding site 6 out of 6 in the Crystal Structure of Human PKM2 in Complex with L-Aspartate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Human PKM2 in Complex with L-Aspartate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:0.7
occ:1.00
OD2 D:ASP487 3.7 98.7 1.0
CG D:ASP487 4.3 88.4 1.0
OD1 D:ASP487 4.5 79.8 1.0
CG1 D:VAL490 4.9 59.5 1.0

Reference:

S.Nandi, M.Dey. Biochemical and Structural Investigation of Pyurvate Kinase Muscle Isoform 2 Regulation By Amino Acids To Be Published.
Page generated: Mon Dec 14 02:01:16 2020

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