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Potassium in PDB 1a49: Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase

Enzymatic activity of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase

All present enzymatic activity of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase, PDB code: 1a49 was solved by T.M.Larsen, M.M.Benning, I.Rayment, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.300, 216.500, 258.600, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1a49:

The structure of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase also contains other interesting chemical elements:

Magnesium (Mg) 14 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase (pdb code 1a49). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase, PDB code: 1a49:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 1a49

Go back to Potassium Binding Sites List in 1a49
Potassium binding site 1 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K532

b:37.3
occ:1.00
O A:THR113 2.6 33.7 1.0
OG A:SER76 2.6 24.3 1.0
OD1 A:ASN74 2.8 28.7 1.0
O3G A:ATP535 2.8 21.0 1.0
OD1 A:ASP112 2.9 32.7 1.0
OG A:SER242 3.3 35.8 1.0
CB A:SER76 3.6 35.2 1.0
CG A:ASN74 3.7 28.3 1.0
C A:THR113 3.7 30.8 1.0
ND2 A:ASN74 3.9 26.0 1.0
CG A:ASP112 4.0 62.6 1.0
O A:ASP112 4.2 29.1 1.0
N A:SER76 4.2 35.8 1.0
PG A:ATP535 4.2 39.5 1.0
NZ A:LYS269 4.2 32.2 1.0
NH2 A:ARG119 4.2 46.0 1.0
O A:HOH6763 4.3 36.5 1.0
O A:LYS114 4.4 58.0 1.0
CB A:SER242 4.4 30.7 1.0
C A:ASP112 4.4 88.3 1.0
CA A:LYS114 4.4 29.1 1.0
CA A:SER76 4.5 17.0 1.0
N A:LYS114 4.5 30.6 1.0
OE2 A:GLU117 4.5 60.3 1.0
OE1 A:GLU117 4.6 60.5 1.0
NH2 A:ARG72 4.7 30.2 1.0
N A:THR113 4.7 32.2 1.0
OD2 A:ASP112 4.7 37.1 1.0
CB A:ASP112 4.7 47.4 1.0
CA A:THR113 4.8 38.1 1.0
O3B A:ATP535 4.8 20.5 1.0
C A:LYS114 4.8 42.1 1.0
CD A:GLU117 4.9 45.4 1.0
N A:PHE75 4.9 61.9 1.0

Potassium binding site 2 out of 8 in 1a49

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Potassium binding site 2 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1132

b:31.8
occ:1.00
OD1 B:ASN674 2.6 39.5 1.0
OD1 B:ASP712 2.6 21.9 1.0
O B:THR713 2.8 20.4 1.0
O B:HOH6141 2.8 32.1 1.0
OG B:SER676 3.1 28.1 1.0
O B:HOH6624 3.2 52.4 1.0
C B:THR713 3.5 30.5 1.0
O B:ASP712 3.5 38.3 1.0
CG B:ASN674 3.6 23.9 1.0
NZ B:LYS869 3.7 15.6 1.0
OG B:SER842 3.8 22.5 1.0
CG B:ASP712 3.8 39.0 1.0
CB B:SER676 3.8 19.6 1.0
C B:ASP712 3.9 35.7 1.0
CA B:LYS714 4.0 32.0 1.0
N B:LYS714 4.1 24.0 1.0
N B:SER676 4.1 30.2 1.0
ND2 B:ASN674 4.1 22.4 1.0
N B:THR713 4.3 44.6 1.0
NH2 B:ARG672 4.3 19.6 1.0
CB B:ASP712 4.4 25.9 1.0
CA B:SER676 4.4 31.6 1.0
CA B:THR713 4.4 17.3 1.0
O B:LYS714 4.5 22.1 1.0
N B:PHE675 4.6 33.6 1.0
OD2 B:ASP712 4.6 29.0 1.0
C B:LYS714 4.6 18.9 1.0
CB B:ASN674 4.7 18.2 1.0
CA B:ASP712 4.7 19.3 1.0
O B:HOH6063 4.7 33.6 1.0
CA B:ASN674 4.8 27.1 1.0
C B:ASN674 4.9 35.6 1.0
C B:PHE675 5.0 46.9 1.0

Potassium binding site 3 out of 8 in 1a49

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Potassium binding site 3 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1732

b:43.0
occ:1.00
O C:THR1313 2.7 34.2 1.0
OD1 C:ASN1274 2.7 46.5 1.0
OG C:SER1276 2.9 32.7 1.0
O3G C:ATP1735 3.0 17.0 1.0
OD1 C:ASP1312 3.0 36.6 1.0
O C:HOH7921 3.0 47.1 1.0
OG C:SER1442 3.4 42.8 1.0
CG C:ASN1274 3.5 39.1 1.0
CB C:SER1276 3.6 40.0 1.0
ND2 C:ASN1274 3.7 23.8 1.0
C C:THR1313 3.8 85.8 1.0
CG C:ASP1312 4.0 42.1 1.0
NZ C:LYS1469 4.1 36.5 1.0
N C:SER1276 4.2 51.9 1.0
NH2 C:ARG1272 4.2 56.1 1.0
O C:LYS1314 4.3 45.7 1.0
PG C:ATP1735 4.3 46.4 1.0
O C:ASP1312 4.4 35.5 1.0
CB C:SER1442 4.4 22.3 1.0
CA C:LYS1314 4.4 14.9 1.0
CA C:SER1276 4.5 28.7 1.0
NH1 C:ARG1319 4.5 36.6 1.0
C C:ASP1312 4.5 55.8 1.0
OE1 C:GLU1317 4.5 82.3 1.0
OD2 C:ASP1312 4.6 32.9 1.0
N C:LYS1314 4.6 44.2 1.0
N C:THR1313 4.7 40.5 1.0
CB C:ASP1312 4.7 50.6 1.0
C C:LYS1314 4.8 35.3 1.0
CA C:THR1313 4.8 33.4 1.0
CB C:ASN1274 4.9 44.2 1.0
MG C:MG1734 4.9 31.0 1.0
OE2 C:GLU1317 4.9 51.5 1.0
N C:PHE1275 5.0 38.3 1.0

Potassium binding site 4 out of 8 in 1a49

Go back to Potassium Binding Sites List in 1a49
Potassium binding site 4 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K2332

b:23.8
occ:1.00
OD1 D:ASP1912 2.6 24.3 1.0
OG D:SER1876 2.7 27.7 1.0
OD1 D:ASN1874 2.7 28.2 1.0
O D:HOH7499 2.7 26.4 1.0
O D:THR1913 2.8 33.3 1.0
O3G D:ATP2335 2.8 31.2 1.0
OG D:SER2042 3.4 18.9 1.0
CG D:ASN1874 3.5 22.3 1.0
ND2 D:ASN1874 3.6 24.9 1.0
CB D:SER1876 3.6 17.0 1.0
CG D:ASP1912 3.8 55.2 1.0
C D:THR1913 3.8 37.4 1.0
O D:HOH6439 3.9 21.3 1.0
NZ D:LYS2069 3.9 23.0 1.0
PG D:ATP2335 4.2 26.7 1.0
O D:ASP1912 4.4 14.3 1.0
N D:SER1876 4.4 29.6 1.0
OD2 D:ASP1912 4.4 30.0 1.0
CA D:LYS1914 4.5 10.5 1.0
CB D:SER2042 4.5 24.2 1.0
NH1 D:ARG1919 4.5 24.8 1.0
N D:LYS1914 4.5 22.5 1.0
OE1 D:GLU1917 4.5 31.9 1.0
C D:ASP1912 4.6 20.8 1.0
CA D:SER1876 4.6 8.9 1.0
CB D:ASP1912 4.7 27.1 1.0
N D:THR1913 4.7 22.7 1.0
NH2 D:ARG1872 4.7 25.4 1.0
O D:LYS1914 4.8 26.4 1.0
CB D:ASN1874 4.8 13.9 1.0
CA D:THR1913 4.8 17.8 1.0
O3B D:ATP2335 4.9 26.7 1.0
OE2 D:GLU1917 4.9 30.4 1.0
O2G D:ATP2335 4.9 15.4 1.0
O1G D:ATP2335 4.9 17.4 1.0

Potassium binding site 5 out of 8 in 1a49

Go back to Potassium Binding Sites List in 1a49
Potassium binding site 5 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K3532

b:23.7
occ:1.00
O E:HOH7785 2.6 34.9 1.0
OD1 E:ASP3112 2.6 18.0 1.0
O E:THR3113 2.7 23.6 1.0
OD1 E:ASN3074 2.7 28.1 1.0
O3G E:ATP3535 3.0 23.0 1.0
OG E:SER3076 3.0 21.1 1.0
OG E:SER3242 3.5 15.1 1.0
CB E:SER3076 3.5 14.9 1.0
CG E:ASN3074 3.6 27.9 1.0
CG E:ASP3112 3.8 31.5 1.0
C E:THR3113 3.8 62.9 1.0
ND2 E:ASN3074 3.8 16.0 1.0
NZ E:LYS3269 4.0 11.1 1.0
O E:HOH6988 4.0 27.4 1.0
N E:SER3076 4.1 29.1 1.0
NH2 E:ARG3119 4.2 29.6 1.0
O E:ASP3112 4.2 23.7 1.0
PG E:ATP3535 4.3 28.7 1.0
CA E:LYS3114 4.3 17.2 1.0
CA E:SER3076 4.4 19.4 1.0
CB E:SER3242 4.4 4.1 1.0
C E:ASP3112 4.5 53.2 1.0
OD2 E:ASP3112 4.5 29.7 1.0
N E:LYS3114 4.6 39.0 1.0
CB E:ASP3112 4.6 11.6 1.0
NH2 E:ARG3072 4.6 25.5 1.0
O E:LYS3114 4.6 17.7 1.0
OE1 E:GLU3117 4.7 43.5 1.0
N E:THR3113 4.7 27.8 1.0
OE2 E:GLU3117 4.7 24.4 1.0
CA E:THR3113 4.9 25.7 1.0
C E:LYS3114 4.9 32.5 1.0
CB E:ASN3074 4.9 31.6 1.0
O3B E:ATP3535 4.9 35.1 1.0

Potassium binding site 6 out of 8 in 1a49

Go back to Potassium Binding Sites List in 1a49
Potassium binding site 6 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K4132

b:35.7
occ:1.00
O3G F:ATP4135 2.6 27.2 1.0
OD1 F:ASN3674 2.6 37.9 1.0
OD1 F:ASP3712 2.7 35.1 1.0
O F:THR3713 2.8 21.7 1.0
O F:HOH6491 2.8 34.2 1.0
OG F:SER3676 2.9 33.6 1.0
OG F:SER3842 3.4 23.3 1.0
CG F:ASN3674 3.6 70.6 1.0
CB F:SER3676 3.6 14.2 1.0
C F:THR3713 3.7 39.3 1.0
CG F:ASP3712 3.8 74.4 1.0
ND2 F:ASN3674 3.8 40.0 1.0
PG F:ATP4135 3.9 58.4 1.0
O F:HOH6460 3.9 24.1 1.0
NZ F:LYS3869 4.0 32.9 1.0
O F:ASP3712 4.2 49.4 1.0
N F:SER3676 4.3 24.1 1.0
C F:ASP3712 4.3 26.0 1.0
CA F:LYS3714 4.4 38.0 1.0
O3B F:ATP4135 4.4 44.2 1.0
N F:LYS3714 4.4 31.2 1.0
OD2 F:ASP3712 4.4 32.9 1.0
O F:LYS3714 4.5 37.7 1.0
CA F:SER3676 4.5 27.9 1.0
N F:THR3713 4.5 41.4 1.0
NH2 F:ARG3672 4.6 41.1 1.0
CB F:SER3842 4.6 36.7 1.0
CB F:ASP3712 4.6 29.3 1.0
O2G F:ATP4135 4.7 20.6 1.0
CA F:THR3713 4.7 21.2 1.0
C F:LYS3714 4.9 34.9 1.0
OE2 F:GLU3717 4.9 73.5 1.0
O1G F:ATP4135 4.9 45.3 1.0
CB F:ASN3674 4.9 48.6 1.0

Potassium binding site 7 out of 8 in 1a49

Go back to Potassium Binding Sites List in 1a49
Potassium binding site 7 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K4732

b:28.6
occ:1.00
OD1 G:ASN4274 2.5 21.1 1.0
O G:HOH7049 2.5 30.6 1.0
OD1 G:ASP4312 2.6 34.5 1.0
O3G G:ATP4735 2.8 26.0 1.0
OG G:SER4276 2.8 27.5 1.0
O G:THR4313 2.9 25.1 1.0
CG G:ASN4274 3.3 39.5 1.0
CB G:SER4276 3.4 24.0 1.0
ND2 G:ASN4274 3.5 21.4 1.0
OG G:SER4442 3.6 18.7 1.0
O G:HOH6671 3.6 37.4 1.0
CG G:ASP4312 3.7 23.6 1.0
C G:THR4313 3.9 58.2 1.0
NZ G:LYS4469 4.1 31.3 1.0
PG G:ATP4735 4.1 30.8 1.0
NH2 G:ARG4319 4.1 94.4 1.0
N G:SER4276 4.2 28.9 1.0
OE1 G:GLU4317 4.3 40.2 1.0
CA G:SER4276 4.3 32.9 1.0
OD2 G:ASP4312 4.4 33.6 1.0
NH2 G:ARG4272 4.4 18.1 1.0
CA G:LYS4314 4.5 32.0 1.0
CB G:ASP4312 4.5 15.3 1.0
O2G G:ATP4735 4.5 7.1 1.0
N G:LYS4314 4.6 38.2 1.0
CB G:SER4442 4.6 31.6 1.0
C G:ASP4312 4.6 56.7 1.0
O G:ASP4312 4.6 21.4 1.0
N G:THR4313 4.7 36.5 1.0
O G:LYS4314 4.7 27.7 1.0
CB G:ASN4274 4.8 14.9 1.0
OE2 G:GLU4317 4.8 30.7 1.0
O1 G:OXL4733 4.8 45.0 1.0
CD G:GLU4317 4.8 20.4 1.0
O3B G:ATP4735 4.9 30.3 1.0
CA G:THR4313 4.9 28.7 1.0
O1G G:ATP4735 5.0 26.9 1.0

Potassium binding site 8 out of 8 in 1a49

Go back to Potassium Binding Sites List in 1a49
Potassium binding site 8 out of 8 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K5332

b:33.1
occ:1.00
OD1 H:ASN4874 2.7 21.8 1.0
O H:THR4913 2.8 22.2 1.0
O H:HOH6965 2.8 44.6 1.0
OD1 H:ASP4912 2.8 20.1 1.0
OG H:SER4876 2.9 33.3 1.0
O H:HOH6838 3.0 31.9 1.0
C H:THR4913 3.6 18.6 1.0
O H:ASP4912 3.6 20.2 1.0
CG H:ASN4874 3.7 32.7 1.0
CG H:ASP4912 3.8 34.3 1.0
C H:ASP4912 4.0 27.4 1.0
CB H:SER4876 4.0 20.3 1.0
NZ H:LYS5069 4.1 17.4 1.0
N H:SER4876 4.1 40.2 1.0
N H:LYS4914 4.1 54.8 1.0
CA H:LYS4914 4.1 23.0 1.0
OG H:SER5042 4.1 31.6 1.0
NH2 H:ARG4872 4.2 25.9 1.0
ND2 H:ASN4874 4.2 26.7 1.0
CB H:ASP4912 4.3 18.0 1.0
N H:THR4913 4.4 25.9 1.0
CA H:SER4876 4.5 27.5 1.0
CA H:THR4913 4.5 13.2 1.0
N H:PHE4875 4.6 30.7 1.0
OD2 H:ASP4912 4.6 39.1 1.0
CA H:ASN4874 4.7 17.1 1.0
O H:LYS4914 4.7 32.2 1.0
CA H:ASP4912 4.7 9.6 1.0
C H:LYS4914 4.8 15.3 1.0
CB H:ASN4874 4.8 18.1 1.0
C H:ASN4874 4.9 27.1 1.0
O H:HOH6488 4.9 38.9 1.0
C H:PHE4875 5.0 25.1 1.0

Reference:

T.M.Larsen, M.M.Benning, I.Rayment, G.H.Reed. Structure of the Bis(MG2+)-Atp-Oxalate Complex of the Rabbit Muscle Pyruvate Kinase at 2.1 A Resolution: Atp Binding Over A Barrel. Biochemistry V. 37 6247 1998.
ISSN: ISSN 0006-2960
PubMed: 9572839
DOI: 10.1021/BI980243S
Page generated: Mon Aug 12 04:00:30 2024

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