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Sodium in PDB 1a5u: Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate

Enzymatic activity of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate

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

Protein crystallography data

The structure of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u 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 / 2.35
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 1a5u:

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

Magnesium (Mg) 14 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate (pdb code 1a5u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1a5u

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Sodium binding site 1 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na532

b:43.4
occ:1.00
O A:THR113 2.6 32.1 1.0
OG A:SER76 2.6 32.8 1.0
OD1 A:ASP112 2.8 51.4 1.0
OD1 A:ASN74 2.8 22.9 1.0
O3G A:ATP535 2.9 17.4 1.0
OG A:SER242 3.4 37.3 1.0
CB A:SER76 3.6 19.8 1.0
CG A:ASN74 3.7 24.4 1.0
C A:THR113 3.8 19.7 1.0
CG A:ASP112 3.9 38.4 1.0
ND2 A:ASN74 4.0 10.9 1.0
NZ A:LYS269 4.2 31.8 1.0
O A:HOH6743 4.2 24.8 1.0
PG A:ATP535 4.3 52.9 1.0
O A:ASP112 4.3 38.3 1.0
NH2 A:ARG119 4.3 38.2 1.0
N A:SER76 4.3 29.1 1.0
C A:ASP112 4.4 53.4 1.0
OE1 A:GLU117 4.4 38.1 1.0
CB A:SER242 4.5 32.0 1.0
O A:LYS114 4.5 57.5 1.0
CA A:LYS114 4.5 36.0 1.0
CA A:SER76 4.6 24.3 1.0
OE2 A:GLU117 4.6 92.2 1.0
OD2 A:ASP112 4.6 38.4 1.0
N A:LYS114 4.6 53.6 1.0
N A:THR113 4.6 41.4 1.0
NH2 A:ARG72 4.6 38.0 1.0
CB A:ASP112 4.7 41.4 1.0
O3B A:ATP535 4.7 18.8 1.0
CA A:THR113 4.8 28.6 1.0
O2G A:ATP535 4.9 31.7 1.0
C A:LYS114 4.9 24.2 1.0
CD A:GLU117 4.9 61.0 1.0
N A:PHE75 5.0 53.0 1.0

Sodium binding site 2 out of 8 in 1a5u

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Sodium binding site 2 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1132

b:52.5
occ:1.00
OD1 B:ASP712 2.6 25.7 1.0
OD1 B:ASN674 2.6 39.8 1.0
O B:HOH6139 2.8 30.8 1.0
O B:THR713 3.0 15.8 1.0
OG B:SER676 3.3 36.7 1.0
O B:HOH6608 3.4 79.0 1.0
C B:THR713 3.6 41.5 1.0
CG B:ASP712 3.6 25.7 1.0
O B:ASP712 3.6 29.4 1.0
CG B:ASN674 3.7 13.3 1.0
CB B:SER676 3.7 16.2 1.0
NZ B:LYS869 3.8 11.1 1.0
C B:ASP712 3.9 46.2 1.0
OG B:SER842 4.0 14.8 1.0
N B:LYS714 4.1 7.7 1.0
CB B:ASP712 4.1 27.7 1.0
N B:SER676 4.1 35.8 1.0
CA B:LYS714 4.2 31.8 1.0
NH2 B:ARG672 4.2 15.6 1.0
ND2 B:ASN674 4.3 24.8 1.0
O B:HOH6063 4.3 37.1 1.0
N B:THR713 4.3 92.5 1.0
CA B:SER676 4.4 20.2 1.0
N B:PHE675 4.5 33.1 1.0
OD2 B:ASP712 4.5 37.9 1.0
CA B:THR713 4.5 11.0 1.0
O B:LYS714 4.6 21.7 1.0
CA B:ASP712 4.6 16.2 1.0
CA B:ASN674 4.7 33.2 1.0
C B:LYS714 4.7 16.1 1.0
CB B:ASN674 4.7 10.0 1.0
C B:ASN674 4.8 47.7 1.0

Sodium binding site 3 out of 8 in 1a5u

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Sodium binding site 3 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1732

b:56.0
occ:1.00
O C:THR1313 2.5 30.3 1.0
OD1 C:ASN1274 2.8 49.1 1.0
OG C:SER1276 2.8 52.6 1.0
OD1 C:ASP1312 3.0 33.8 1.0
O3G C:ATP1735 3.2 14.7 1.0
OG C:SER1442 3.4 33.2 1.0
CG C:ASN1274 3.6 32.3 1.0
C C:THR1313 3.6 0.0 1.0
CB C:SER1276 3.7 19.5 1.0
ND2 C:ASN1274 3.8 31.3 1.0
CG C:ASP1312 3.9 53.5 1.0
NZ C:LYS1469 4.0 76.7 1.0
O C:LYS1314 4.2 47.3 1.0
CB C:SER1442 4.2 10.9 1.0
N C:SER1276 4.3 29.0 1.0
CA C:LYS1314 4.3 15.6 1.0
NH2 C:ARG1272 4.3 66.6 1.0
N C:LYS1314 4.4 29.8 1.0
OD2 C:ASP1312 4.4 26.5 1.0
OE1 C:GLU1317 4.5 72.3 1.0
C C:ASP1312 4.5 57.6 1.0
PG C:ATP1735 4.5 54.0 1.0
N C:THR1313 4.5 31.0 1.0
NH1 C:ARG1319 4.6 52.6 1.0
CA C:SER1276 4.6 44.3 1.0
O C:ASP1312 4.6 37.5 1.0
CA C:THR1313 4.7 29.4 1.0
C C:LYS1314 4.7 28.4 1.0
CB C:ASP1312 4.7 20.5 1.0
OE2 C:GLU1317 4.8 65.5 1.0
N C:PHE1275 4.9 20.0 1.0
O3B C:ATP1735 5.0 38.1 1.0
CB C:ASN1274 5.0 37.3 1.0

Sodium binding site 4 out of 8 in 1a5u

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Sodium binding site 4 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2332

b:27.3
occ:1.00
OD1 D:ASP1912 2.5 26.2 1.0
OG D:SER1876 2.6 23.8 1.0
O D:HOH7433 2.6 30.8 1.0
OD1 D:ASN1874 2.7 30.8 1.0
O3G D:ATP2335 2.7 32.8 1.0
O D:THR1913 2.8 39.6 1.0
CG D:ASN1874 3.4 20.9 1.0
ND2 D:ASN1874 3.5 22.6 1.0
OG D:SER2042 3.5 23.2 1.0
CB D:SER1876 3.6 24.0 1.0
CG D:ASP1912 3.8 17.1 1.0
C D:THR1913 3.9 20.3 1.0
O D:HOH6430 4.0 18.1 1.0
PG D:ATP2335 4.1 17.7 1.0
NZ D:LYS2069 4.1 18.9 1.0
N D:SER1876 4.4 39.7 1.0
OD2 D:ASP1912 4.4 27.6 1.0
CA D:LYS1914 4.4 13.8 1.0
NH1 D:ARG1919 4.5 25.3 1.0
O D:ASP1912 4.5 11.4 1.0
OE1 D:GLU1917 4.5 24.8 1.0
CA D:SER1876 4.5 14.9 1.0
CB D:SER2042 4.5 10.8 1.0
N D:LYS1914 4.6 23.7 1.0
C D:ASP1912 4.7 20.5 1.0
CB D:ASP1912 4.7 23.0 1.0
OE2 D:GLU1917 4.7 24.7 1.0
O2G D:ATP2335 4.7 14.9 1.0
NH2 D:ARG1872 4.7 23.5 1.0
O3B D:ATP2335 4.7 18.5 1.0
CB D:ASN1874 4.7 5.8 1.0
O1G D:ATP2335 4.8 31.3 1.0
O D:LYS1914 4.8 18.3 1.0
N D:THR1913 4.8 27.8 1.0
CA D:THR1913 4.9 15.3 1.0
CD D:GLU1917 5.0 27.6 1.0

Sodium binding site 5 out of 8 in 1a5u

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Sodium binding site 5 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na3532

b:29.6
occ:1.00
O E:HOH7689 2.3 31.1 1.0
OD1 E:ASP3112 2.5 21.5 1.0
O E:THR3113 2.6 33.9 1.0
OD1 E:ASN3074 2.6 33.9 1.0
O3G E:ATP3535 2.9 27.8 1.0
OG E:SER3076 3.0 18.2 1.0
OG E:SER3242 3.4 8.3 1.0
CB E:SER3076 3.5 7.6 1.0
CG E:ASN3074 3.6 17.3 1.0
CG E:ASP3112 3.7 22.2 1.0
C E:THR3113 3.7 42.5 1.0
ND2 E:ASN3074 4.0 15.4 1.0
O E:ASP3112 4.1 12.9 1.0
NH2 E:ARG3119 4.1 29.4 1.0
N E:SER3076 4.2 23.4 1.0
O E:HOH6954 4.2 30.3 1.0
NZ E:LYS3269 4.2 5.4 1.0
CA E:LYS3114 4.2 16.6 1.0
PG E:ATP3535 4.3 22.2 1.0
OD2 E:ASP3112 4.3 27.0 1.0
CB E:SER3242 4.4 1.0 1.0
CA E:SER3076 4.4 25.7 1.0
N E:LYS3114 4.4 37.8 1.0
C E:ASP3112 4.4 34.3 1.0
O E:LYS3114 4.6 20.9 1.0
OE2 E:GLU3117 4.6 12.7 1.0
CB E:ASP3112 4.6 5.0 1.0
NH2 E:ARG3072 4.7 20.8 1.0
N E:THR3113 4.7 32.6 1.0
OE1 E:GLU3117 4.8 30.3 1.0
C E:LYS3114 4.8 29.0 1.0
CA E:THR3113 4.8 16.1 1.0
O3B E:ATP3535 4.9 48.8 1.0
CB E:ASN3074 4.9 23.9 1.0
N E:PHE3075 5.0 33.3 1.0
O2G E:ATP3535 5.0 6.9 1.0

Sodium binding site 6 out of 8 in 1a5u

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Sodium binding site 6 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na4132

b:40.0
occ:1.00
O3G F:ATP4135 2.4 28.8 1.0
OD1 F:ASN3674 2.6 33.3 1.0
O F:HOH6481 2.8 28.5 1.0
OG F:SER3676 2.8 30.3 1.0
OD1 F:ASP3712 3.0 25.8 1.0
O F:THR3713 3.0 32.4 1.0
CG F:ASN3674 3.4 40.5 1.0
CB F:SER3676 3.5 8.3 1.0
ND2 F:ASN3674 3.5 26.8 1.0
OG F:SER3842 3.6 22.0 1.0
PG F:ATP4135 3.7 52.6 1.0
NZ F:LYS3869 3.9 29.1 1.0
O F:HOH6450 3.9 20.4 1.0
C F:THR3713 3.9 21.9 1.0
CG F:ASP3712 4.0 82.6 1.0
O3B F:ATP4135 4.2 38.8 1.0
N F:SER3676 4.4 31.4 1.0
O2G F:ATP4135 4.4 20.2 1.0
NH2 F:ARG3672 4.4 34.0 1.0
CA F:LYS3714 4.5 37.5 1.0
CA F:SER3676 4.5 25.0 1.0
O F:ASP3712 4.5 43.7 1.0
N F:LYS3714 4.6 43.6 1.0
OD2 F:ASP3712 4.6 25.6 1.0
O F:LYS3714 4.6 54.0 1.0
C F:ASP3712 4.6 29.1 1.0
OE2 F:GLU3717 4.7 0.0 1.0
O1G F:ATP4135 4.7 54.9 1.0
CB F:ASP3712 4.7 15.5 1.0
CB F:ASN3674 4.8 43.5 1.0
N F:THR3713 4.8 26.6 1.0
CB F:SER3842 4.8 45.6 1.0
CD F:GLU3717 4.9 52.1 1.0
NH2 F:ARG3719 4.9 0.0 1.0
OE1 F:GLU3717 4.9 56.3 1.0
O3 F:OXL4133 5.0 42.2 1.0
CA F:THR3713 5.0 25.3 1.0
C F:LYS3714 5.0 17.4 1.0

Sodium binding site 7 out of 8 in 1a5u

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Sodium binding site 7 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na4732

b:31.2
occ:1.00
O G:HOH7008 2.2 28.3 1.0
OD1 G:ASN4274 2.5 21.1 1.0
OD1 G:ASP4312 2.6 24.4 1.0
OG G:SER4276 2.8 30.3 1.0
O3G G:ATP4735 2.8 22.6 1.0
O G:THR4313 2.8 25.0 1.0
CB G:SER4276 3.4 29.6 1.0
CG G:ASN4274 3.4 38.3 1.0
OG G:SER4442 3.6 31.7 1.0
ND2 G:ASN4274 3.7 16.1 1.0
CG G:ASP4312 3.7 23.0 1.0
O G:HOH6654 3.8 32.1 1.0
C G:THR4313 3.8 45.0 1.0
NH2 G:ARG4319 4.0 0.0 1.0
PG G:ATP4735 4.1 32.1 1.0
NZ G:LYS4469 4.1 26.2 1.0
OE1 G:GLU4317 4.2 58.2 1.0
N G:SER4276 4.2 31.2 1.0
CA G:SER4276 4.3 26.7 1.0
CA G:LYS4314 4.4 16.6 1.0
OD2 G:ASP4312 4.4 31.5 1.0
O2G G:ATP4735 4.5 3.0 1.0
NH2 G:ARG4272 4.5 15.4 1.0
N G:LYS4314 4.5 45.3 1.0
CB G:SER4442 4.5 19.7 1.0
O G:LYS4314 4.6 36.1 1.0
OE2 G:GLU4317 4.6 30.1 1.0
CB G:ASP4312 4.6 12.3 1.0
C G:ASP4312 4.7 42.1 1.0
O G:ASP4312 4.7 25.4 1.0
CD G:GLU4317 4.7 31.9 1.0
N G:THR4313 4.7 41.9 1.0
CB G:ASN4274 4.8 10.2 1.0
O3 G:OXL4733 4.8 55.8 1.0
CA G:THR4313 4.8 23.3 1.0
O3B G:ATP4735 4.9 30.6 1.0
C G:LYS4314 4.9 40.3 1.0
O1G G:ATP4735 5.0 35.7 1.0

Sodium binding site 8 out of 8 in 1a5u

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Sodium binding site 8 out of 8 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na5332

b:57.1
occ:1.00
OD1 H:ASN4874 2.6 22.4 1.0
OG H:SER4876 2.9 41.0 1.0
OD1 H:ASP4912 3.0 21.3 1.0
O H:HOH6813 3.1 42.2 1.0
O H:THR4913 3.2 31.9 1.0
CG H:ASN4874 3.5 15.8 1.0
O H:HOH6932 3.6 39.7 1.0
CG H:ASP4912 3.8 27.7 1.0
NZ H:LYS5069 3.9 19.7 1.0
C H:THR4913 3.9 5.8 1.0
NH2 H:ARG4872 3.9 31.1 1.0
O H:ASP4912 4.0 31.5 1.0
ND2 H:ASN4874 4.0 25.9 1.0
OG H:SER5042 4.1 28.5 1.0
CB H:SER4876 4.1 16.8 1.0
O H:HOH7233 4.2 44.9 1.0
C H:ASP4912 4.3 23.7 1.0
N H:SER4876 4.3 26.9 1.0
CB H:ASP4912 4.4 1.0 1.0
CA H:LYS4914 4.4 19.2 1.0
N H:LYS4914 4.5 66.9 1.0
OD2 H:ASP4912 4.5 39.8 1.0
CB H:ASN4874 4.7 20.2 1.0
CA H:ASN4874 4.7 9.9 1.0
N H:PHE4875 4.7 32.4 1.0
CA H:SER4876 4.7 18.0 1.0
N H:THR4913 4.8 29.7 1.0
O H:HOH7232 4.8 30.4 1.0
O H:LYS4914 4.8 16.3 1.0
O3 H:OXL5333 4.8 65.3 1.0
O H:HOH6478 4.9 32.6 1.0
CA H:THR4913 4.9 34.5 1.0
CA H:ASP4912 4.9 10.5 1.0
CZ H:ARG4872 5.0 38.1 1.0
C H:ASN4874 5.0 14.9 1.0
C H:LYS4914 5.0 24.9 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: Tue Dec 15 05:21:44 2020

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