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Potassium in PDB 3n25: The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+

Enzymatic activity of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+

All present enzymatic activity of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+:
2.7.1.40;

Protein crystallography data

The structure of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+, PDB code: 3n25 was solved by A.W.Fenton, T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.59 / 2.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.373, 108.747, 144.256, 95.18, 93.38, 112.23
R / Rfree (%) 20.4 / 26.8

Other elements in 3n25:

The structure of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ also contains other interesting chemical elements:

Manganese (Mn) 8 atoms
Sodium (Na) 12 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ (pdb code 3n25). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+, PDB code: 3n25:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 1 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1100

b:23.2
occ:1.00
 OD1 A:ASN74 2.7 4.0 1.0
OG A:SER76 2.7 5.0 1.0
O A:HOH765 2.8 2.0 1.0
O A:HOH1069 2.8 2.0 1.0
OD1 A:ASP112 2.8 7.0 1.0
O A:THR113 2.9 2.2 1.0
CG A:ASP112 3.7 5.5 1.0
CG A:ASN74 3.7 4.3 1.0
CB A:SER76 3.8 6.3 1.0
C A:THR113 3.9 2.2 1.0
OG A:SER242 3.9 3.1 1.0
NZ A:LYS269 4.0 2.0 1.0
O A:ASP112 4.0 4.3 1.0
N A:SER76 4.1 6.5 1.0
OE2 A:GLU117 4.3 2.4 1.0
ND2 A:ASN74 4.3 3.5 1.0
CA A:LYS114 4.3 2.0 1.0
O A:HOH1225 4.3 2.0 1.0
C A:ASP112 4.4 4.1 1.0
CB A:ASP112 4.4 4.6 1.0
OD2 A:ASP112 4.4 7.5 1.0
NH2 A:ARG72 4.4 10.9 1.0
N A:LYS114 4.5 2.0 1.0
CA A:SER76 4.5 6.8 1.0
N A:PHE75 4.6 5.4 1.0
O A:LYS114 4.7 2.0 1.0
N A:THR113 4.8 3.1 1.0
O A:HOH1275 4.8 2.0 1.0
CB A:ASN74 4.8 4.8 1.0
CA A:ASN74 4.9 5.2 1.0
C A:LYS114 4.9 2.0 1.0
CA A:THR113 4.9 2.3 1.0
C A:ASN74 4.9 5.3 1.0
C A:PHE75 5.0 6.0 1.0

Potassium binding site 2 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 2 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1700

b:38.6
occ:1.00
 OD1 B:ASN74 2.6 5.3 1.0
OD1 B:ASP112 2.7 2.0 1.0
OG B:SER76 2.8 8.4 1.0
O B:THR113 3.2 2.7 1.0
OG B:SER242 3.7 2.0 1.0
CG B:ASP112 3.8 2.0 1.0
CG B:ASN74 3.8 7.0 1.0
C B:THR113 3.8 2.2 1.0
CB B:SER76 3.9 8.9 1.0
O B:ASP112 3.9 2.0 1.0
N B:SER76 4.1 8.9 1.0
CA B:LYS114 4.1 2.8 1.0
NZ B:LYS269 4.2 2.0 1.0
O B:HOH1630 4.2 7.6 1.0
N B:LYS114 4.2 2.6 1.0
C B:ASP112 4.4 2.0 1.0
ND2 B:ASN74 4.4 5.2 1.0
OE2 B:GLU117 4.4 5.6 1.0
CA B:SER76 4.4 8.9 1.0
O B:LYS114 4.5 3.2 1.0
OD2 B:ASP112 4.5 3.5 1.0
N B:PHE75 4.6 8.2 1.0
CB B:ASP112 4.6 2.0 1.0
NH2 B:ARG72 4.7 5.8 1.0
C B:LYS114 4.7 3.1 1.0
N B:THR113 4.7 2.0 1.0
CB B:SER242 4.8 2.0 1.0
CA B:THR113 4.9 2.2 1.0
CB B:ASN74 4.9 7.8 1.0
CA B:ASN74 4.9 7.9 1.0
C B:PHE75 4.9 8.6 1.0
C B:ASN74 5.0 8.2 1.0

Potassium binding site 3 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 3 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1700

b:20.3
occ:1.00
 OD1 C:ASP112 2.5 2.0 1.0
O C:THR113 2.7 2.0 1.0
OG C:SER76 2.8 5.0 1.0
OD1 C:ASN74 2.9 5.5 1.0
O C:HOH1097 3.0 5.5 1.0
OG C:SER242 3.6 3.4 1.0
C C:THR113 3.6 2.0 1.0
CG C:ASP112 3.7 2.0 1.0
CG C:ASN74 3.9 3.7 1.0
NZ C:LYS269 3.9 2.0 1.0
O C:ASP112 4.0 2.0 1.0
CB C:SER76 4.0 4.0 1.0
O C:HOH1614 4.1 2.0 1.0
CA C:LYS114 4.1 2.3 1.0
N C:SER76 4.2 3.6 1.0
N C:LYS114 4.2 2.0 1.0
NH2 C:ARG72 4.3 7.7 1.0
C C:ASP112 4.3 2.0 1.0
OD2 C:ASP112 4.4 2.0 1.0
ND2 C:ASN74 4.5 2.8 1.0
OE2 C:GLU117 4.5 2.0 1.0
N C:PHE75 4.5 3.2 1.0
O C:LYS114 4.6 3.1 1.0
N C:THR113 4.6 2.0 1.0
CA C:SER76 4.6 3.9 1.0
CB C:ASP112 4.6 2.0 1.0
CA C:THR113 4.7 2.0 1.0
CB C:SER242 4.7 2.9 1.0
C C:LYS114 4.7 2.6 1.0
O C:HOH1196 4.9 2.0 1.0
CA C:ASN74 5.0 3.4 1.0
C C:PHE75 5.0 3.6 1.0

Potassium binding site 4 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 4 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1700

b:22.2
occ:1.00
 OD1 D:ASP112 2.6 2.5 1.0
OD1 D:ASN74 2.7 3.6 1.0
OG D:SER76 2.8 3.5 1.0
O D:THR113 3.2 2.0 1.0
O D:HOH818 3.5 3.1 1.0
CG D:ASP112 3.7 2.0 1.0
OG D:SER242 3.7 3.7 1.0
CG D:ASN74 3.7 2.1 1.0
NZ D:LYS269 3.7 7.6 1.0
CB D:SER76 4.0 2.8 1.0
NH2 D:ARG72 4.1 2.0 1.0
C D:THR113 4.1 2.0 1.0
ND2 D:ASN74 4.2 2.7 1.0
O D:HOH1274 4.3 25.2 1.0
O D:ASP112 4.4 2.0 1.0
OD2 D:ASP112 4.4 2.0 1.0
N D:SER76 4.5 2.0 1.0
OE2 D:GLU117 4.5 3.7 1.0
CB D:ASP112 4.5 2.0 1.0
CA D:LYS114 4.5 2.0 1.0
C D:ASP112 4.6 2.0 1.0
O D:LYS114 4.7 2.0 1.0
N D:LYS114 4.7 2.0 1.0
CA D:SER76 4.8 2.6 1.0
CB D:SER242 4.8 4.2 1.0
O3 D:PYR1500 4.9 13.8 1.0
N D:THR113 4.9 2.0 1.0
CB D:ASN74 4.9 2.0 1.0
N D:PHE75 5.0 2.0 1.0

Potassium binding site 5 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 5 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1700

b:25.3
occ:1.00
 OD1 E:ASN74 2.6 2.9 1.0
OD1 E:ASP112 2.7 5.1 1.0
O E:HOH1051 2.8 2.0 1.0
O E:THR113 3.0 2.0 1.0
OG E:SER76 3.0 2.0 1.0
CG E:ASP112 3.7 2.4 1.0
CG E:ASN74 3.7 2.5 1.0
OG E:SER242 3.7 5.0 1.0
C E:THR113 3.8 2.0 1.0
CB E:SER76 3.9 2.0 1.0
NZ E:LYS269 3.9 3.1 1.0
O E:ASP112 4.0 2.0 1.0
CA E:LYS114 4.3 2.0 1.0
ND2 E:ASN74 4.3 2.5 1.0
N E:SER76 4.3 2.0 1.0
C E:ASP112 4.3 2.0 1.0
N E:LYS114 4.3 2.0 1.0
CB E:ASP112 4.4 2.0 1.0
NH2 E:ARG72 4.4 2.0 1.0
OD2 E:ASP112 4.4 3.0 1.0
O E:LYS114 4.5 2.0 1.0
N E:THR113 4.6 2.0 1.0
O E:HOH1638 4.6 2.0 1.0
CA E:SER76 4.6 2.0 1.0
OE2 E:GLU117 4.7 8.4 1.0
N E:PHE75 4.8 2.0 1.0
CA E:THR113 4.8 2.0 1.0
C E:LYS114 4.8 2.0 1.0
CB E:ASN74 4.9 2.3 1.0
CB E:SER242 4.9 3.9 1.0
CA E:ASN74 4.9 2.2 1.0
CA E:ASP112 5.0 2.0 1.0

Potassium binding site 6 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 6 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K1700

b:17.2
occ:1.00
 O F:HOH1656 2.6 2.0 1.0
OD1 F:ASP112 2.6 2.6 1.0
O F:THR113 2.7 2.5 1.0
OG F:SER76 2.7 2.3 1.0
OD1 F:ASN74 2.8 2.0 1.0
OG F:SER242 3.6 2.0 1.0
CG F:ASP112 3.6 2.8 1.0
C F:THR113 3.7 2.0 1.0
CG F:ASN74 3.7 2.0 1.0
NZ F:LYS269 3.9 2.0 1.0
CB F:SER76 4.0 3.2 1.0
CA F:LYS114 4.1 2.3 1.0
O F:HOH1199 4.1 5.8 1.0
ND2 F:ASN74 4.1 2.0 1.0
N F:LYS114 4.3 2.1 1.0
N F:SER76 4.3 2.9 1.0
O F:ASP112 4.3 2.8 1.0
OD2 F:ASP112 4.4 2.0 1.0
NH2 F:ARG72 4.4 7.8 1.0
OE2 F:GLU117 4.4 8.0 1.0
C F:ASP112 4.4 2.4 1.0
CB F:ASP112 4.5 2.0 1.0
O F:LYS114 4.6 2.3 1.0
N F:THR113 4.6 2.2 1.0
CA F:SER76 4.6 3.2 1.0
N F:PHE75 4.7 2.6 1.0
CB F:SER242 4.7 2.0 1.0
C F:LYS114 4.8 2.6 1.0
CA F:THR113 4.8 2.1 1.0
CB F:ASN74 4.8 2.0 1.0
O F:HOH1624 4.9 7.5 1.0
CA F:ASN74 5.0 2.0 1.0

Potassium binding site 7 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 7 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K1700

b:43.0
occ:1.00
 O G:HOH1409 2.6 2.0 1.0
OD1 G:ASN74 2.7 7.2 1.0
OD1 G:ASP112 2.8 3.9 1.0
OG G:SER76 2.9 5.8 1.0
O G:THR113 3.0 2.7 1.0
O G:HOH651 3.0 2.0 1.0
OG G:SER242 3.5 2.0 1.0
NZ G:LYS269 3.7 2.0 1.0
CG G:ASP112 3.8 3.4 1.0
CG G:ASN74 3.8 6.6 1.0
C G:THR113 3.9 2.8 1.0
O G:ASP112 4.0 3.0 1.0
CB G:SER76 4.1 5.9 1.0
CA G:LYS114 4.2 2.9 1.0
OE2 G:GLU117 4.3 4.1 1.0
O G:HOH1408 4.3 2.0 1.0
NH2 G:ARG72 4.4 2.7 1.0
N G:LYS114 4.4 2.8 1.0
N G:SER76 4.4 6.0 1.0
ND2 G:ASN74 4.4 4.7 1.0
O G:LYS114 4.4 3.0 1.0
C G:ASP112 4.4 3.0 1.0
OD2 G:ASP112 4.5 3.3 1.0
CB G:ASP112 4.6 3.1 1.0
C G:LYS114 4.7 2.9 1.0
CB G:SER242 4.7 2.0 1.0
CA G:SER76 4.8 6.0 1.0
N G:PHE75 4.8 6.2 1.0
N G:THR113 4.8 3.0 1.0
O G:HOH1201 4.9 2.0 1.0
O3 G:PYR1500 4.9 22.6 1.0
CA G:THR113 5.0 2.6 1.0

Potassium binding site 8 out of 8 in 3n25

Go back to Potassium Binding Sites List in 3n25
Potassium binding site 8 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K1700

b:26.5
occ:1.00
 OD1 H:ASN74 2.7 6.2 1.0
O H:THR113 2.8 5.6 1.0
O H:HOH1064 2.9 2.0 1.0
OD1 H:ASP112 2.9 5.6 1.0
OG H:SER76 2.9 2.1 1.0
O H:HOH1418 3.0 2.0 1.0
CG H:ASN74 3.6 5.2 1.0
CG H:ASP112 3.7 5.6 1.0
C H:THR113 3.8 5.6 1.0
OG H:SER242 3.9 2.0 1.0
O H:ASP112 3.9 5.8 1.0
NZ H:LYS269 3.9 2.0 1.0
CB H:SER76 4.0 3.9 1.0
ND2 H:ASN74 4.1 4.5 1.0
N H:SER76 4.3 4.5 1.0
C H:ASP112 4.3 5.7 1.0
O H:HOH1607 4.3 2.0 1.0
OE2 H:GLU117 4.3 7.4 1.0
CA H:LYS114 4.3 5.2 1.0
CB H:ASP112 4.3 5.6 1.0
N H:LYS114 4.5 5.4 1.0
OD2 H:ASP112 4.5 5.8 1.0
O H:LYS114 4.5 4.9 1.0
NH2 H:ARG72 4.5 2.0 1.0
CA H:SER76 4.7 4.2 1.0
N H:PHE75 4.7 4.7 1.0
N H:THR113 4.7 5.5 1.0
C H:LYS114 4.8 5.0 1.0
CB H:ASN74 4.8 5.1 1.0
CA H:THR113 4.9 5.6 1.0
O H:HOH1202 4.9 2.0 1.0
CA H:ASP112 4.9 5.7 1.0
CA H:ASN74 5.0 5.2 1.0
O3 H:PYR1500 5.0 17.3 1.0

Reference:

A.W.Fenton, T.A.Johnson, T.Holyoak. The Pyruvate Kinase Model System, A Cautionary Tale For the Use of Osmolyte Perturbations to Support Conformational Equilibria in Allostery. Protein Sci. V. 19 1796 2010.
ISSN: ISSN 0961-8368
PubMed: 20629175
DOI: 10.1002/PRO.450
Page generated: Mon Aug 12 08:49:00 2024

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