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Potassium in PDB 8f5u: Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate

Enzymatic activity of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate

All present enzymatic activity of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate:
2.7.1.40; 2.7.10.2; 2.7.11.1;

Protein crystallography data

The structure of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate, PDB code: 8f5u was solved by T.Holyoak, A.W.Fenton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.27 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.131, 130.198, 170.282, 90, 90, 90
R / Rfree (%) 16.4 / 22

Other elements in 8f5u:

The structure of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate (pdb code 8f5u). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate, PDB code: 8f5u:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 1 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:35.9
occ:1.00
 OG1 A:THR431 2.9 30.6 1.0
OG A:SER436 3.0 27.0 1.0
O A:HOH708 3.5 38.6 1.0
N A:SER436 3.5 25.6 1.0
CB A:SER436 3.6 22.5 1.0
CB A:THR431 3.7 28.2 1.0
OG A:SER433 3.8 27.7 1.0
O A:HOH898 4.0 30.0 1.0
CA A:THR431 4.2 26.3 1.0
CA A:SER436 4.2 24.8 1.0
CB A:ARG435 4.2 33.9 1.0
N A:ARG435 4.2 23.5 1.0
C A:ARG435 4.5 25.4 1.0
O A:GLY519 4.5 36.2 1.0
CA A:PHE520 4.5 24.4 1.0
N A:GLU432 4.5 26.0 1.0
CA A:ARG435 4.5 25.7 1.0
N A:SER433 4.8 23.1 1.0
O A:LEU430 4.8 29.2 1.0
N A:GLY434 4.8 24.4 1.0
C A:THR431 4.9 24.3 1.0
C A:GLY434 4.9 23.0 1.0
CB A:SER433 5.0 23.2 1.0

Potassium binding site 2 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 2 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K606

b:27.1
occ:1.00
 OD1 A:ASP112 2.7 29.6 1.0
OD1 A:ASN74 2.7 25.3 1.0
O A:THR113 2.7 22.3 1.0
OG A:SER76 2.8 28.0 1.0
O A:HOH766 2.9 22.1 1.0
O A:HOH889 2.9 30.0 1.0
CG A:ASP112 3.6 31.2 1.0
OG A:SER242 3.6 23.6 1.0
C A:THR113 3.7 22.7 1.0
CG A:ASN74 3.8 26.0 1.0
O A:ASP112 3.9 25.5 1.0
CB A:SER76 3.9 29.0 1.0
N A:SER76 4.1 25.2 1.0
NZ A:LYS269 4.1 22.8 1.0
CA A:LYS114 4.1 23.3 1.0
C A:ASP112 4.2 27.7 1.0
N A:LYS114 4.3 23.2 1.0
NH2 A:ARG72 4.3 26.1 1.0
ND2 A:ASN74 4.3 24.6 1.0
CB A:ASP112 4.4 21.2 1.0
O A:LYS114 4.4 24.0 1.0
OD2 A:ASP112 4.4 26.0 1.0
OE2 A:GLU117 4.4 29.5 1.0
CA A:SER76 4.5 29.3 1.0
O A:HOH711 4.5 24.5 1.0
N A:THR113 4.6 23.7 1.0
C A:LYS114 4.7 23.5 1.0
N A:PHE75 4.7 23.9 1.0
CA A:THR113 4.8 22.7 1.0
CB A:SER242 4.8 21.8 1.0
CB A:ASN74 4.9 26.1 1.0
CA A:ASP112 4.9 22.7 1.0
C A:PHE75 5.0 27.8 1.0
CA A:ASN74 5.0 25.8 1.0

Potassium binding site 3 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 3 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:31.6
occ:1.00
 O B:THR113 2.7 21.6 1.0
OD1 B:ASP112 2.7 30.4 1.0
O B:HOH827 2.8 23.1 1.0
OD1 B:ASN74 2.8 31.4 1.0
OG B:SER76 2.8 33.8 1.0
O B:HOH779 2.9 33.0 1.0
C B:THR113 3.6 25.4 1.0
CG B:ASP112 3.7 30.6 1.0
OG B:SER242 3.7 32.4 1.0
CG B:ASN74 3.9 30.3 1.0
NZ B:LYS269 3.9 25.2 1.0
CB B:SER76 3.9 29.2 1.0
O B:ASP112 3.9 28.2 1.0
CA B:LYS114 4.2 26.3 1.0
N B:SER76 4.2 32.7 1.0
N B:LYS114 4.2 26.6 1.0
C B:ASP112 4.2 29.0 1.0
NH2 B:ARG72 4.4 32.0 1.0
CB B:ASP112 4.4 29.4 1.0
OD2 B:ASP112 4.4 34.1 1.0
O B:LYS114 4.5 27.8 1.0
ND2 B:ASN74 4.5 31.4 1.0
OE2 B:GLU117 4.5 36.6 1.0
O B:HOH720 4.5 26.0 1.0
N B:THR113 4.5 29.0 1.0
CA B:SER76 4.6 35.2 1.0
CA B:THR113 4.7 29.2 1.0
C B:LYS114 4.7 27.9 1.0
N B:PHE75 4.8 32.3 1.0
CB B:SER242 4.8 26.0 1.0
CA B:ASP112 4.9 26.4 1.0

Potassium binding site 4 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 4 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:31.7
occ:1.00
 O B:HOH859 2.9 35.7 1.0
OG1 B:THR431 3.1 29.6 1.0
OG B:SER436 3.1 22.4 1.0
N B:SER436 3.4 23.2 1.0
CB B:SER436 3.6 20.1 1.0
CB B:THR431 3.9 34.3 1.0
OG B:SER433 4.0 28.8 1.0
CA B:SER436 4.1 18.3 1.0
N B:ARG435 4.1 23.2 1.0
CA B:THR431 4.2 25.6 1.0
CB B:ARG435 4.2 22.2 1.0
C B:ARG435 4.4 25.6 1.0
CA B:PHE520 4.4 18.4 1.0
CA B:ARG435 4.5 21.9 1.0
N B:GLU432 4.6 26.9 1.0
N B:GLY434 4.7 29.3 1.0
O B:GLY519 4.7 28.2 1.0
C B:GLY434 4.8 25.1 1.0
O B:LEU430 4.8 27.4 1.0
N B:SER433 4.9 25.2 1.0
O B:HOH897 4.9 31.1 1.0
C B:THR431 4.9 28.6 1.0
N B:THR521 5.0 19.1 1.0

Potassium binding site 5 out of 8 in 8f5u

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Potassium binding site 5 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:45.0
occ:1.00
 OD1 C:ASN74 2.7 30.5 1.0
O C:THR113 2.8 27.9 1.0
O C:HOH794 2.9 26.4 1.0
O C:HOH925 2.9 37.6 1.0
OD1 C:ASP112 3.0 37.0 1.0
OG C:SER76 3.0 34.1 1.0
C C:THR113 3.7 29.5 1.0
CG C:ASN74 3.7 28.2 1.0
CG C:ASP112 3.7 36.6 1.0
NZ C:LYS269 3.8 26.5 1.0
O C:HOH809 3.8 30.6 1.0
OG C:SER242 4.0 29.5 1.0
O C:ASP112 4.0 24.1 1.0
CB C:SER76 4.1 29.3 1.0
O C:HOH822 4.2 45.3 1.0
CA C:LYS114 4.2 34.4 1.0
ND2 C:ASN74 4.2 27.3 1.0
NH2 C:ARG72 4.2 24.7 1.0
N C:LYS114 4.2 30.6 1.0
C C:ASP112 4.2 30.5 1.0
N C:SER76 4.3 27.3 1.0
CB C:ASP112 4.3 30.7 1.0
OD2 C:ASP112 4.4 30.5 1.0
N C:THR113 4.5 25.1 1.0
O C:LYS114 4.6 32.3 1.0
CA C:THR113 4.7 29.3 1.0
CA C:SER76 4.7 30.7 1.0
C C:LYS114 4.8 29.9 1.0
O C:HOH749 4.8 29.4 1.0
N C:PHE75 4.8 27.5 1.0
CB C:ASN74 4.8 23.2 1.0
O C:HOH748 4.8 34.3 1.0
CA C:ASP112 4.9 29.4 1.0
CA C:ASN74 5.0 29.1 1.0

Potassium binding site 6 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 6 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:35.3
occ:1.00
 OG1 C:THR431 2.8 26.3 1.0
OG C:SER436 3.0 23.1 1.0
N C:SER436 3.5 17.2 1.0
O C:HOH713 3.5 26.8 1.0
CB C:SER436 3.5 23.4 1.0
CB C:THR431 3.6 27.3 1.0
OG C:SER433 3.9 29.9 1.0
CA C:SER436 4.1 21.7 1.0
CA C:THR431 4.1 26.8 1.0
N C:ARG435 4.1 22.8 1.0
O C:HOH918 4.3 29.8 1.0
NH1 C:ARG435 4.4 41.9 1.0
CB C:ARG435 4.4 30.2 1.0
O C:GLY519 4.4 33.4 1.0
C C:ARG435 4.5 24.1 1.0
CA C:PHE520 4.5 23.7 1.0
CA C:ARG435 4.6 22.0 1.0
N C:GLU432 4.6 28.2 1.0
N C:GLY434 4.7 25.2 1.0
C C:GLY434 4.8 20.7 1.0
N C:SER433 4.8 25.9 1.0
O C:LEU430 4.8 26.3 1.0
C C:THR431 4.8 24.6 1.0
O C:HOH912 4.9 37.7 1.0
N C:THR521 5.0 23.3 1.0

Potassium binding site 7 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 7 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:44.9
occ:1.00
 O D:THR113 2.8 23.4 1.0
OD1 D:ASN74 2.9 29.4 1.0
OD1 D:ASP112 2.9 28.2 1.0
OG D:SER76 2.9 27.8 1.0
O D:HOH826 3.0 28.9 1.0
C D:THR113 3.6 24.2 1.0
CG D:ASP112 3.7 29.7 1.0
CG D:ASN74 3.7 26.7 1.0
NZ D:LYS269 3.8 25.2 1.0
O D:ASP112 3.8 25.4 1.0
CB D:SER76 4.1 30.2 1.0
C D:ASP112 4.1 26.7 1.0
N D:SER76 4.1 31.4 1.0
ND2 D:ASN74 4.2 34.4 1.0
CA D:LYS114 4.2 28.6 1.0
NH2 D:ARG72 4.2 25.7 1.0
N D:LYS114 4.2 25.3 1.0
CB D:ASP112 4.2 22.7 1.0
OG D:SER242 4.3 31.3 1.0
N D:THR113 4.4 26.4 1.0
OD2 D:ASP112 4.5 28.7 1.0
CA D:SER76 4.6 29.8 1.0
O D:LYS114 4.6 28.7 1.0
N D:PHE75 4.6 28.5 1.0
CA D:THR113 4.6 27.7 1.0
C D:LYS114 4.8 30.4 1.0
CA D:ASP112 4.8 22.8 1.0
CB D:ASN74 4.9 21.1 1.0
CA D:ASN74 4.9 27.4 1.0
O D:HOH841 5.0 28.6 1.0
O D:HOH795 5.0 38.1 1.0
C D:PHE75 5.0 29.2 1.0

Potassium binding site 8 out of 8 in 8f5u

Go back to Potassium Binding Sites List in 8f5u
Potassium binding site 8 out of 8 in the Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Rabbit Muscle Pyruvate Kinase in Complex with Magnesium, Potassium and Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K603

b:36.4
occ:1.00
 OG D:SER436 2.9 24.2 1.0
OG1 D:THR431 2.9 26.0 1.0
O D:HOH874 3.0 38.6 1.0
O D:HOH743 3.3 38.2 1.0
N D:SER436 3.4 21.3 1.0
CB D:SER436 3.6 21.8 1.0
CB D:THR431 3.8 30.3 1.0
O D:HOH904 3.9 43.5 1.0
OG D:SER433 4.0 27.7 1.0
CB D:ARG435 4.1 35.4 1.0
N D:ARG435 4.1 26.5 1.0
CA D:SER436 4.1 25.3 1.0
CA D:THR431 4.2 23.9 1.0
C D:ARG435 4.4 23.2 1.0
CA D:ARG435 4.4 28.2 1.0
CA D:PHE520 4.4 23.4 1.0
N D:GLU432 4.5 23.9 1.0
O D:GLY519 4.6 38.2 1.0
N D:GLY434 4.7 27.8 1.0
C D:GLY434 4.7 26.3 1.0
N D:SER433 4.8 29.4 1.0
C D:THR431 4.9 28.4 1.0
O D:LEU430 4.9 26.3 1.0
CB D:PHE520 4.9 28.1 1.0
NH1 D:ARG435 4.9 48.2 1.0
N D:THR521 5.0 22.1 1.0

Reference:

L.Swint-Kruse, L.L.Dougherty, B.Page, T.Wu, P.T.O'neil, C.B.Prasannan, C.Timmons, Q.Tang, D.J.Parente, S.Sreenivasan, T.Holyoak, A.W.Fenton. Pyk-Substitutionome: An Integrated Database Containing Allosteric Coupling, Ligand Affinity and Mutational, Structural, Pathological, Bioinformatic and Computational Information About Pyruvate Kinase Isozymes. Database (Oxford) V.2023 2023.
ISSN: ISSN 1758-0463
PubMed: 37171062
DOI: 10.1093/DATABASE/BAAD030
Page generated: Mon Aug 12 23:39:50 2024

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