Phosphorus 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

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Phosphorus 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 Phosphorus atom.
In total 18 binding sites of Phosphorus where determined in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase, PDB code: 1a49:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 18 in 1a49

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Phosphorus binding site 1 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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:P535

b:39.5
occ:1.00
PG A:ATP535 0.0 39.5 1.0
O3G A:ATP535 1.4 21.0 1.0
O2G A:ATP535 1.5 33.7 1.0
O1G A:ATP535 1.6 27.7 1.0
O3B A:ATP535 1.6 20.5 1.0
PB A:ATP535 2.9 31.9 1.0
MG A:MG536 2.9 24.1 1.0
O1 A:OXL533 3.4 32.9 1.0
MG A:MG534 3.5 24.7 1.0
ND2 A:ASN74 3.5 26.0 1.0
O3A A:ATP535 3.5 37.3 1.0
O2B A:ATP535 3.6 28.4 1.0
NH2 A:ARG72 3.7 30.2 1.0
NH2 A:ARG119 3.7 46.0 1.0
O A:HOH6469 3.7 22.5 1.0
O A:HOH6763 3.8 36.5 1.0
C1 A:OXL533 3.8 53.4 1.0
O A:HOH6003 3.9 11.5 1.0
O1B A:ATP535 3.9 32.0 1.0
O1A A:ATP535 4.0 27.9 1.0
PA A:ATP535 4.1 36.8 1.0
K A:K532 4.2 37.3 1.0
O3 A:OXL533 4.2 73.9 1.0
O2A A:ATP535 4.3 19.9 1.0
C2 A:OXL533 4.5 34.1 1.0
O4 A:OXL533 4.6 35.6 1.0
CG A:ASN74 4.6 28.3 1.0
NZ A:LYS269 4.7 32.2 1.0
OD2 A:ASP295 4.7 35.5 1.0
O A:HOH6079 4.7 19.5 1.0
CZ A:ARG72 4.9 29.2 1.0
CZ A:ARG119 4.9 42.6 1.0
OD1 A:ASN74 4.9 28.7 1.0

Phosphorus binding site 2 out of 18 in 1a49

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Phosphorus binding site 2 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
A:P535

b:31.9
occ:1.00
PB A:ATP535 0.0 31.9 1.0
O1B A:ATP535 1.5 32.0 1.0
O2B A:ATP535 1.5 28.4 1.0
O3B A:ATP535 1.5 20.5 1.0
O3A A:ATP535 1.6 37.3 1.0
MG A:MG536 2.8 24.1 1.0
PA A:ATP535 2.8 36.8 1.0
PG A:ATP535 2.9 39.5 1.0
O1A A:ATP535 3.1 27.9 1.0
O1G A:ATP535 3.3 27.7 1.0
O2G A:ATP535 3.5 33.7 1.0
O A:HOH6995 3.6 46.7 1.0
O3' A:ATP535 3.7 49.5 1.0
O5' A:ATP535 3.7 30.6 1.0
C5' A:ATP535 3.7 41.6 1.0
ND2 A:ASN74 3.8 26.0 1.0
CE1 A:HIS77 3.9 36.2 1.0
O A:HOH6079 3.9 19.5 1.0
O2A A:ATP535 3.9 19.9 1.0
O3G A:ATP535 3.9 21.0 1.0
O A:HOH6366 3.9 38.5 1.0
C3' A:ATP535 3.9 64.6 1.0
NH2 A:ARG119 4.1 46.0 1.0
O A:HOH6469 4.2 22.5 1.0
NH1 A:ARG119 4.2 23.9 1.0
O A:HOH6003 4.3 11.5 1.0
C4' A:ATP535 4.4 93.5 1.0
ND1 A:HIS77 4.6 41.1 1.0
CZ A:ARG119 4.7 42.6 1.0
NE2 A:HIS77 4.8 33.4 1.0

Phosphorus binding site 3 out of 18 in 1a49

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Phosphorus binding site 3 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
A:P535

b:36.8
occ:1.00
PA A:ATP535 0.0 36.8 1.0
O1A A:ATP535 1.5 27.9 1.0
O2A A:ATP535 1.5 19.9 1.0
O3A A:ATP535 1.5 37.3 1.0
O5' A:ATP535 1.6 30.6 1.0
C5' A:ATP535 2.6 41.6 1.0
PB A:ATP535 2.8 31.9 1.0
MG A:MG536 3.1 24.1 1.0
O2B A:ATP535 3.2 28.4 1.0
ND2 A:ASN74 3.3 26.0 1.0
O1G A:ATP535 3.4 27.7 1.0
O3B A:ATP535 3.5 20.5 1.0
NH1 A:ARG72 3.6 43.8 1.0
C4' A:ATP535 3.8 93.5 1.0
C3' A:ATP535 3.9 64.6 1.0
O A:HOH6079 3.9 19.5 1.0
O1B A:ATP535 4.0 32.0 1.0
PG A:ATP535 4.1 39.5 1.0
C8 A:ATP535 4.2 20.2 1.0
CB A:SER361 4.3 33.6 1.0
NH2 A:ARG72 4.3 30.2 1.0
O4' A:ATP535 4.3 48.0 1.0
CZ A:ARG72 4.4 29.2 1.0
CG A:ASN74 4.5 28.3 1.0
OG A:SER361 4.6 21.9 1.0
O3' A:ATP535 4.6 49.5 1.0
CG2 A:THR49 4.6 43.5 1.0
CE1 A:HIS77 4.8 36.2 1.0
O3G A:ATP535 4.8 21.0 1.0
CB A:ASN74 4.9 26.8 1.0
N9 A:ATP535 4.9 24.2 1.0
N A:GLY362 5.0 27.7 1.0
ND1 A:HIS77 5.0 41.1 1.0
CA A:SER361 5.0 48.3 1.0

Phosphorus binding site 4 out of 18 in 1a49

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Phosphorus binding site 4 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
C:P1735

b:46.4
occ:1.00
PG C:ATP1735 0.0 46.4 1.0
O3G C:ATP1735 1.4 17.0 1.0
O2G C:ATP1735 1.5 27.0 1.0
O1G C:ATP1735 1.6 29.4 1.0
O3B C:ATP1735 1.7 35.0 1.0
PB C:ATP1735 2.8 43.3 1.0
MG C:MG1736 3.2 31.8 1.0
O1 C:OXL1733 3.2 50.0 1.0
O2B C:ATP1735 3.2 37.2 1.0
MG C:MG1734 3.4 31.0 1.0
O C:HOH6006 3.5 25.4 1.0
O3A C:ATP1735 3.5 42.2 1.0
NH2 C:ARG1272 3.7 56.1 1.0
ND2 C:ASN1274 3.7 23.8 1.0
C1 C:OXL1733 3.7 34.5 1.0
O C:HOH6005 3.8 12.7 1.0
O1B C:ATP1735 3.9 45.1 1.0
O C:HOH6663 4.0 24.2 1.0
O4 C:OXL1733 4.0 37.8 1.0
O1A C:ATP1735 4.0 19.6 1.0
PA C:ATP1735 4.2 35.4 1.0
C2 C:OXL1733 4.2 29.4 1.0
OD2 C:ASP1495 4.3 43.9 1.0
K C:K1732 4.3 43.0 1.0
NH2 C:ARG1319 4.5 74.3 1.0
O3 C:OXL1733 4.5 43.8 1.0
O2A C:ATP1735 4.5 21.6 1.0
NH1 C:ARG1319 4.5 36.6 1.0
CZ C:ARG1272 4.8 36.0 1.0
CG C:ASN1274 4.9 39.1 1.0
NH1 C:ARG1272 4.9 41.7 1.0
NZ C:LYS1469 4.9 36.5 1.0

Phosphorus binding site 5 out of 18 in 1a49

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Phosphorus binding site 5 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
C:P1735

b:43.3
occ:1.00
PB C:ATP1735 0.0 43.3 1.0
O3B C:ATP1735 1.4 35.0 1.0
O1B C:ATP1735 1.5 45.1 1.0
O2B C:ATP1735 1.5 37.2 1.0
O3A C:ATP1735 1.6 42.2 1.0
PG C:ATP1735 2.8 46.4 1.0
PA C:ATP1735 2.8 35.4 1.0
MG C:MG1736 3.1 31.8 1.0
O1A C:ATP1735 3.2 19.6 1.0
O1G C:ATP1735 3.2 29.4 1.0
NH2 C:ARG1319 3.5 74.3 1.0
O3' C:ATP1735 3.6 43.9 1.0
O2G C:ATP1735 3.7 27.0 1.0
NE2 C:HIS1277 3.7 43.7 1.0
O5' C:ATP1735 3.8 25.4 1.0
O3G C:ATP1735 3.8 17.0 1.0
O C:HOH6879 3.8 59.5 1.0
O2A C:ATP1735 3.9 21.6 1.0
C3' C:ATP1735 3.9 34.5 1.0
C5' C:ATP1735 3.9 33.5 1.0
O C:HOH6006 3.9 25.4 1.0
ND2 C:ASN1274 4.1 23.8 1.0
O C:HOH6005 4.2 12.7 1.0
O C:HOH6581 4.3 25.8 1.0
CD2 C:HIS1277 4.5 72.1 1.0
C4' C:ATP1735 4.5 25.7 1.0
CZ C:ARG1319 4.6 66.9 1.0
CE1 C:HIS1277 4.7 38.3 1.0
O C:HOH6663 4.9 24.2 1.0
NH1 C:ARG1319 4.9 36.6 1.0

Phosphorus binding site 6 out of 18 in 1a49

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Phosphorus binding site 6 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
C:P1735

b:35.4
occ:1.00
PA C:ATP1735 0.0 35.4 1.0
O2A C:ATP1735 1.5 21.6 1.0
O1A C:ATP1735 1.5 19.6 1.0
O3A C:ATP1735 1.5 42.2 1.0
O5' C:ATP1735 1.6 25.4 1.0
C5' C:ATP1735 2.6 33.5 1.0
PB C:ATP1735 2.8 43.3 1.0
MG C:MG1736 3.1 31.8 1.0
O2B C:ATP1735 3.3 37.2 1.0
O1G C:ATP1735 3.5 29.4 1.0
C4' C:ATP1735 3.7 25.7 1.0
O3B C:ATP1735 3.7 35.0 1.0
ND2 C:ASN1274 3.7 23.8 1.0
C3' C:ATP1735 3.7 34.5 1.0
O1B C:ATP1735 3.9 45.1 1.0
C8 C:ATP1735 4.1 34.9 1.0
O4' C:ATP1735 4.1 21.5 1.0
NH1 C:ARG1272 4.1 41.7 1.0
PG C:ATP1735 4.2 46.4 1.0
CB C:SER1561 4.3 29.3 1.0
O C:HOH6581 4.4 25.8 1.0
O3' C:ATP1735 4.4 43.9 1.0
O C:HOH6663 4.4 24.2 1.0
NE2 C:HIS1277 4.5 43.7 1.0
OG C:SER1561 4.6 37.5 1.0
CD2 C:HIS1277 4.6 72.1 1.0
CG2 C:THR1249 4.7 21.2 1.0
O3G C:ATP1735 4.7 17.0 1.0
NH2 C:ARG1272 4.8 56.1 1.0
O C:HOH6754 4.9 38.0 1.0
CG C:ASN1274 4.9 39.1 1.0
CZ C:ARG1272 4.9 36.0 1.0
N9 C:ATP1735 4.9 28.3 1.0
C1' C:ATP1735 4.9 31.4 1.0
N7 C:ATP1735 4.9 41.8 1.0
O C:HOH6879 5.0 59.5 1.0
O C:HOH6006 5.0 25.4 1.0
C2' C:ATP1735 5.0 54.5 1.0

Phosphorus binding site 7 out of 18 in 1a49

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Phosphorus binding site 7 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
D:P2335

b:26.7
occ:1.00
PG D:ATP2335 0.0 26.7 1.0
O3G D:ATP2335 1.4 31.2 1.0
O1G D:ATP2335 1.4 17.4 1.0
O2G D:ATP2335 1.5 15.4 1.0
O3B D:ATP2335 1.7 26.7 1.0
PB D:ATP2335 2.9 31.0 1.0
MG D:MG2336 3.0 20.5 1.0
O2B D:ATP2335 3.1 28.9 1.0
O D:HOH6045 3.2 11.8 1.0
MG D:MG2334 3.3 19.4 1.0
O1 D:OXL2333 3.3 22.1 1.0
ND2 D:ASN1874 3.5 24.9 1.0
O D:HOH6004 3.6 5.6 1.0
O3A D:ATP2335 3.7 13.4 1.0
NH2 D:ARG1872 3.8 25.4 1.0
O D:HOH6439 3.8 21.3 1.0
C1 D:OXL2333 3.9 41.2 1.0
O D:HOH6387 4.0 20.0 1.0
O1B D:ATP2335 4.0 13.2 1.0
NH1 D:ARG1919 4.1 24.8 1.0
O1A D:ATP2335 4.1 22.7 1.0
K D:K2332 4.2 23.8 1.0
OD2 D:ASP2095 4.2 10.7 1.0
O4 D:OXL2333 4.2 25.2 1.0
PA D:ATP2335 4.2 25.7 1.0
C2 D:OXL2333 4.4 18.2 1.0
NH2 D:ARG1919 4.6 41.3 1.0
O2A D:ATP2335 4.6 17.4 1.0
CG D:ASN1874 4.7 22.3 1.0
O3 D:OXL2333 4.7 23.3 1.0
NZ D:LYS2069 4.7 23.0 1.0
CZ D:ARG1919 4.8 49.9 1.0
O D:HOH6463 4.9 22.3 1.0
O D:HOH7499 4.9 26.4 1.0
O D:HOH7364 5.0 30.9 1.0

Phosphorus binding site 8 out of 18 in 1a49

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Phosphorus binding site 8 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P 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
D:P2335

b:31.0
occ:1.00
PB D:ATP2335 0.0 31.0 1.0
O3B D:ATP2335 1.5 26.7 1.0
O2B D:ATP2335 1.5 28.9 1.0
O1B D:ATP2335 1.5 13.2 1.0
O3A D:ATP2335 1.6 13.4 1.0
PA D:ATP2335 2.9 25.7 1.0
PG D:ATP2335 2.9 26.7 1.0
MG D:MG2336 3.0 20.5 1.0
O D:HOH6463 3.2 22.3 1.0
O1G D:ATP2335 3.2 17.4 1.0
O1A D:ATP2335 3.3 22.7 1.0
NH2 D:ARG1919 3.4 41.3 1.0
NE2 D:HIS1877 3.6 21.0 1.0
O3' D:ATP2335 3.6 16.8 1.0
O2G D:ATP2335 3.7 15.4 1.0
O5' D:ATP2335 3.8 19.4 1.0
O D:HOH6140 3.8 24.0 1.0
O3G D:ATP2335 3.9 31.2 1.0
ND2 D:ASN1874 3.9 24.9 1.0
C3' D:ATP2335 3.9 17.3 1.0
C5' D:ATP2335 3.9 37.3 1.0
O2A D:ATP2335 3.9 17.4 1.0
O D:HOH6045 4.0 11.8 1.0
O D:HOH6004 4.1 5.6 1.0
CD2 D:HIS1877 4.2 12.3 1.0
O D:HOH7364 4.4 30.9 1.0
CZ D:ARG1919 4.4 49.9 1.0
NH1 D:ARG1919 4.5 24.8 1.0
C4' D:ATP2335 4.5 20.8 1.0
O D:HOH6387 4.8 20.0 1.0
CE1 D:HIS1877 4.8 34.5 1.0

Phosphorus binding site 9 out of 18 in 1a49

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Phosphorus binding site 9 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:P2335

b:25.7
occ:1.00
PA D:ATP2335 0.0 25.7 1.0
O2A D:ATP2335 1.4 17.4 1.0
O1A D:ATP2335 1.5 22.7 1.0
O3A D:ATP2335 1.5 13.4 1.0
O5' D:ATP2335 1.7 19.4 1.0
C5' D:ATP2335 2.7 37.3 1.0
PB D:ATP2335 2.9 31.0 1.0
MG D:MG2336 3.1 20.5 1.0
O2B D:ATP2335 3.3 28.9 1.0
O1G D:ATP2335 3.6 17.4 1.0
ND2 D:ASN1874 3.6 24.9 1.0
NH1 D:ARG1872 3.7 38.5 1.0
O3B D:ATP2335 3.8 26.7 1.0
C4' D:ATP2335 3.8 20.8 1.0
C3' D:ATP2335 3.9 17.3 1.0
O1B D:ATP2335 4.0 13.2 1.0
O D:HOH6387 4.0 20.0 1.0
C8 D:ATP2335 4.2 18.0 1.0
NH2 D:ARG1872 4.2 25.4 1.0
PG D:ATP2335 4.2 26.7 1.0
O D:HOH7364 4.3 30.9 1.0
CB D:SER2161 4.3 20.2 1.0
O4' D:ATP2335 4.4 38.7 1.0
CZ D:ARG1872 4.5 33.8 1.0
OG D:SER2161 4.5 27.2 1.0
O3' D:ATP2335 4.6 16.8 1.0
CG2 D:THR1849 4.6 25.7 1.0
CD2 D:HIS1877 4.7 12.3 1.0
NE2 D:HIS1877 4.7 21.0 1.0
CG D:ASN1874 4.8 22.3 1.0
O3G D:ATP2335 4.8 31.2 1.0
N9 D:ATP2335 4.9 32.4 1.0
CB D:ASN1874 5.0 13.9 1.0
O D:HOH6045 5.0 11.8 1.0

Phosphorus binding site 10 out of 18 in 1a49

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Phosphorus binding site 10 out of 18 in the Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Bis Mg-Atp-K-Oxalate Complex of Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:P3535

b:28.7
occ:1.00
PG E:ATP3535 0.0 28.7 1.0
O3G E:ATP3535 1.4 23.0 1.0
O2G E:ATP3535 1.4 11.1 1.0
O1G E:ATP3535 1.5 17.0 1.0
O3B E:ATP3535 1.7 35.1 1.0
PB E:ATP3535 3.0 19.9 1.0
O1 E:OXL3533 3.0 35.9 1.0
MG E:MG3536 3.1 25.1 1.0
O E:HOH6348 3.3 31.4 1.0
MG E:MG3534 3.3 18.2 1.0
O2B E:ATP3535 3.3 21.1 1.0
NH2 E:ARG3119 3.6 29.6 1.0
O3A E:ATP3535 3.6 22.2 1.0
O E:HOH6159 3.6 2.9 1.0
ND2 E:ASN3074 3.7 16.0 1.0
C1 E:OXL3533 3.7 35.0 1.0
NH2 E:ARG3072 3.8 25.5 1.0
O E:HOH6988 3.9 27.4 1.0
O1A E:ATP3535 4.0 18.5 1.0
O1B E:ATP3535 4.1 20.9 1.0
PA E:ATP3535 4.2 30.0 1.0
O E:HOH6162 4.3 14.4 1.0
O3 E:OXL3533 4.3 28.5 1.0
K E:K3532 4.3 23.7 1.0
O4 E:OXL3533 4.4 31.4 1.0
C2 E:OXL3533 4.4 26.0 1.0
OD2 E:ASP3295 4.4 18.5 1.0
O2A E:ATP3535 4.6 21.1 1.0
CZ E:ARG3119 4.6 75.4 1.0
NH1 E:ARG3119 4.7 19.5 1.0
CG E:ASN3074 4.7 27.9 1.0
NZ E:LYS3269 4.8 11.1 1.0
CZ E:ARG3072 5.0 28.0 1.0
OD1 E:ASN3074 5.0 28.1 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: Fri Sep 25 12:11:30 2020

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