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Potassium in PDB 3srf: Human M1 Pyruvate Kinase

Enzymatic activity of Human M1 Pyruvate Kinase

All present enzymatic activity of Human M1 Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Human M1 Pyruvate Kinase, PDB code: 3srf was solved by H.P.Morgan, F.O'reilly, R.Palmer, I.W.Mcnae, M.W.Nowicki, M.A.Wear, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 238.003, 192.222, 109.060, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 28

Other elements in 3srf:

The structure of Human M1 Pyruvate Kinase also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human M1 Pyruvate Kinase (pdb code 3srf). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Human M1 Pyruvate Kinase, PDB code: 3srf:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 3srf

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Potassium binding site 1 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K532

b:58.1
occ:1.00
 OD1 C:ASP112 2.9 36.6 1.0
OG C:SER76 2.9 31.2 1.0
O C:THR113 3.1 36.6 1.0
NZ C:LYS269 3.3 25.4 1.0
OD1 C:ASN74 3.4 29.2 1.0
OG C:SER242 3.4 34.0 1.0
CG C:ASP112 4.0 36.1 1.0
O C:ASP112 4.0 35.8 1.0
C C:THR113 4.0 36.4 1.0
NH2 C:ARG72 4.1 29.3 1.0
O C:LYS114 4.3 36.6 1.0
CA C:LYS114 4.3 36.6 1.0
CB C:SER76 4.3 31.0 1.0
C C:ASP112 4.6 35.7 1.0
CB C:SER242 4.6 34.1 1.0
N C:LYS114 4.6 36.5 1.0
CG C:ASN74 4.6 29.9 1.0
C C:LYS114 4.7 36.6 1.0
OD2 C:ASP112 4.8 36.3 1.0
CE C:LYS269 4.8 26.7 1.0
CB C:ASP112 4.8 35.7 1.0
OE1 C:GLU117 4.8 40.0 1.0
N C:SER76 4.9 30.8 1.0

Potassium binding site 2 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 2 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K532

b:37.7
occ:1.00
 O A:HOH594 2.6 13.5 1.0
OD1 A:ASN74 2.7 31.2 1.0
O A:HOH551 2.8 25.9 1.0
OG A:SER76 3.0 33.0 1.0
O A:THR113 3.1 33.1 1.0
OD1 A:ASP112 3.4 32.6 1.0
CG A:ASN74 3.8 30.9 1.0
OG A:SER242 3.9 32.0 1.0
NZ A:LYS269 4.0 24.8 1.0
NH2 A:ARG72 4.0 26.3 1.0
CG A:ASP112 4.0 32.4 1.0
C A:THR113 4.2 33.1 1.0
ND2 A:ASN74 4.2 31.1 1.0
CB A:SER76 4.4 33.0 1.0
O A:LYS114 4.4 34.3 1.0
CA A:LYS114 4.4 34.0 1.0
O A:ASP112 4.5 32.3 1.0
OD2 A:ASP112 4.5 32.5 1.0
N A:LYS114 4.7 33.6 1.0
CB A:ASP112 4.8 32.0 1.0
C A:LYS114 4.8 34.4 1.0
O3 A:PYR534 4.8 39.6 1.0
C A:ASP112 4.8 32.2 1.0
OE1 A:GLU117 4.8 41.5 1.0
N A:SER76 4.9 32.8 1.0
O A:HOH598 4.9 27.3 1.0
CB A:SER242 4.9 32.4 1.0

Potassium binding site 3 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 3 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K532

b:94.2
occ:1.00
 OD1 B:ASP112 3.0 37.1 1.0
OD1 B:ASN74 3.2 29.9 1.0
OG B:SER76 3.3 29.8 1.0
O B:THR113 3.3 37.2 1.0
NZ B:LYS269 3.4 27.3 1.0
NH2 B:ARG72 3.9 30.0 1.0
OG B:SER242 3.9 32.3 1.0
CG B:ASP112 4.1 36.7 1.0
OE1 B:GLU117 4.3 42.5 1.0
CG B:ASN74 4.3 29.9 1.0
O B:LYS114 4.3 38.1 1.0
C B:THR113 4.5 37.1 1.0
CB B:SER76 4.5 29.6 1.0
O3 B:PYR534 4.7 43.1 1.0
CA B:LYS114 4.7 37.8 1.0
ND2 B:ASN74 4.7 30.6 1.0
MG B:MG533 4.8 26.3 1.0
OD2 B:ASP112 4.8 37.0 1.0
CE B:LYS269 4.8 28.3 1.0
CB B:SER242 4.9 32.8 1.0
C B:LYS114 4.9 38.0 1.0

Potassium binding site 4 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 4 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K532

b:48.5
occ:1.00
 O D:HOH556 2.8 10.2 1.0
OG D:SER76 2.9 36.2 1.0
O D:THR113 3.2 35.9 1.0
OD1 D:ASN74 3.2 34.4 1.0
OD1 D:ASP112 3.3 36.2 1.0
NZ D:LYS269 3.6 29.4 1.0
OG D:SER242 3.7 34.1 1.0
O D:LYS114 4.0 36.5 1.0
OE1 D:GLU117 4.0 40.7 1.0
CB D:SER76 4.2 36.3 1.0
C D:THR113 4.2 35.8 1.0
O3 D:PYR534 4.2 51.6 1.0
CG D:ASP112 4.3 36.0 1.0
CG D:ASN74 4.3 33.8 1.0
CA D:LYS114 4.3 36.3 1.0
C D:LYS114 4.5 36.4 1.0
NH2 D:ARG72 4.5 35.7 1.0
MG D:MG533 4.7 51.2 1.0
ND2 D:ASN74 4.7 33.6 1.0
O D:ASP112 4.7 35.3 1.0
N D:LYS114 4.7 36.1 1.0
CB D:SER242 4.8 33.9 1.0
N D:SER76 4.9 36.0 1.0
CB D:ASP112 4.9 35.5 1.0

Potassium binding site 5 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 5 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K532

b:85.0
occ:1.00
 OD1 E:ASN74 3.1 52.0 1.0
OG E:SER76 3.2 54.8 1.0
NZ E:LYS269 3.4 52.2 1.0
O E:THR113 3.5 57.3 1.0
OD1 E:ASP112 3.7 57.2 1.0
O3 E:PYR534 3.8 63.2 1.0
O E:LYS114 3.8 58.2 1.0
OG E:SER242 3.9 57.5 1.0
NH2 E:ARG72 4.1 48.5 1.0
OE1 E:GLU117 4.1 63.5 1.0
CG E:ASN74 4.2 52.2 1.0
MG E:MG533 4.3 58.5 1.0
CB E:SER76 4.3 55.0 1.0
CG E:ASP112 4.5 56.9 1.0
C E:LYS114 4.6 58.2 1.0
CA E:LYS114 4.6 58.0 1.0
ND2 E:ASN74 4.6 52.2 1.0
C E:THR113 4.6 57.3 1.0
OD2 E:ASP112 4.8 57.4 1.0
CE E:LYS269 4.9 52.3 1.0
CB E:SER242 5.0 57.6 1.0

Potassium binding site 6 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 6 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K532

b:46.4
occ:1.00
 O F:HOH581 2.7 13.4 1.0
OD1 F:ASP112 2.9 34.5 1.0
OG F:SER76 2.9 34.4 1.0
OD1 F:ASN74 3.0 33.6 1.0
O F:THR113 3.1 34.2 1.0
NZ F:LYS269 3.5 27.2 1.0
OG F:SER242 3.8 32.7 1.0
CG F:ASP112 3.9 34.2 1.0
NH2 F:ARG72 4.1 35.8 1.0
CG F:ASN74 4.1 33.6 1.0
C F:THR113 4.2 34.2 1.0
CB F:SER76 4.3 34.2 1.0
O F:LYS114 4.3 33.9 1.0
OE1 F:GLU117 4.4 33.9 1.0
ND2 F:ASN74 4.5 33.8 1.0
CA F:LYS114 4.5 34.0 1.0
O F:ASP112 4.5 34.2 1.0
OD2 F:ASP112 4.6 33.6 1.0
N F:SER76 4.7 34.0 1.0
N F:LYS114 4.8 34.1 1.0
CB F:ASP112 4.8 34.4 1.0
C F:ASP112 4.8 34.3 1.0
C F:LYS114 4.8 33.9 1.0
O3 F:PYR534 4.8 39.0 1.0
CB F:SER242 4.9 32.5 1.0

Potassium binding site 7 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 7 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K532

b:60.7
occ:1.00
 OD1 G:ASP112 2.8 43.5 1.0
O G:HOH585 2.9 6.1 1.0
OD1 G:ASN74 3.0 42.9 1.0
O G:THR113 3.0 44.5 1.0
OG G:SER76 3.1 46.3 1.0
OG G:SER242 3.3 45.9 1.0
O G:HOH584 3.5 31.0 1.0
NZ G:LYS269 3.5 39.4 1.0
O G:LYS114 3.8 46.0 1.0
O G:HOH583 4.0 12.8 1.0
OE1 G:GLU117 4.0 51.4 1.0
CG G:ASP112 4.1 42.9 1.0
CG G:ASN74 4.1 43.1 1.0
C G:THR113 4.2 44.4 1.0
NH2 G:ARG72 4.3 40.5 1.0
CB G:SER76 4.4 46.2 1.0
CA G:LYS114 4.4 45.6 1.0
C G:LYS114 4.4 46.0 1.0
CB G:SER242 4.5 46.0 1.0
O3 G:PYR534 4.5 66.8 1.0
ND2 G:ASN74 4.6 43.0 1.0
N G:LYS114 4.7 45.0 1.0
OD2 G:ASP112 4.7 42.6 1.0
O G:ASP112 4.8 43.0 1.0
MG G:MG533 4.9 33.5 1.0
CE G:LYS269 5.0 39.6 1.0

Potassium binding site 8 out of 8 in 3srf

Go back to Potassium Binding Sites List in 3srf
Potassium binding site 8 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K532

b:48.2
occ:1.00
 OG H:SER76 2.8 32.9 1.0
OD1 H:ASP112 2.9 37.3 1.0
OD1 H:ASN74 3.3 32.3 1.0
O H:THR113 3.3 37.3 1.0
NZ H:LYS269 3.5 25.8 1.0
OG H:SER242 3.7 35.0 1.0
NH2 H:ARG72 3.9 32.2 1.0
CG H:ASP112 4.0 36.5 1.0
CB H:SER76 4.1 32.8 1.0
O H:LYS114 4.3 38.6 1.0
C H:THR113 4.3 37.2 1.0
CG H:ASN74 4.3 32.1 1.0
O H:ASP112 4.3 36.0 1.0
CA H:LYS114 4.4 38.2 1.0
OE1 H:GLU117 4.6 43.9 1.0
N H:SER76 4.7 32.6 1.0
OD2 H:ASP112 4.7 36.9 1.0
ND2 H:ASN74 4.8 32.9 1.0
N H:LYS114 4.8 37.7 1.0
C H:LYS114 4.8 38.5 1.0
C H:ASP112 4.8 36.1 1.0
CB H:ASP112 4.9 35.9 1.0
CB H:SER242 4.9 35.0 1.0
CA H:SER76 4.9 32.8 1.0
CE H:LYS269 5.0 27.1 1.0

Reference:

H.P.Morgan, F.O'reilly, R.Palmer, I.W.Mcnae, M.W.Nowicki, M.A.Wear, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Allosetric Regulation of M2 Pyruvate Kinase. To Be Published.
Page generated: Sun Dec 13 23:23:23 2020

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