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Magnesium 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:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate, PDB code: 1a5u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 1a5u

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Magnesium binding site 1 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg534

b:19.5
occ:1.00
O A:HOH6743 1.8 24.8 1.0
OD2 A:ASP295 2.0 25.4 1.0
O3 A:OXL533 2.0 33.3 1.0
O4 A:OXL533 2.1 42.9 1.0
OE1 A:GLU271 2.2 20.8 1.0
O2G A:ATP535 2.5 31.7 1.0
C1 A:OXL533 2.8 45.5 1.0
C2 A:OXL533 2.9 27.2 1.0
CG A:ASP295 2.9 69.9 1.0
CD A:GLU271 3.3 25.6 1.0
CB A:ASP295 3.3 24.3 1.0
PG A:ATP535 3.5 52.9 1.0
O3G A:ATP535 3.8 17.4 1.0
O A:HOH6003 3.8 27.7 1.0
OE2 A:GLU271 3.9 23.9 1.0
O1 A:OXL533 4.1 72.1 1.0
O2 A:OXL533 4.1 40.2 1.0
NZ A:LYS269 4.1 31.8 1.0
O A:HOH6459 4.2 11.7 1.0
OD1 A:ASP295 4.2 48.2 1.0
N A:ASP295 4.3 1.9 1.0
O1G A:ATP535 4.3 37.8 1.0
CA A:ASP295 4.4 44.3 1.0
CZ A:PHE243 4.5 34.5 1.0
CE2 A:PHE243 4.5 48.1 1.0
CG A:GLU271 4.5 13.3 1.0
CB A:GLU271 4.6 12.8 1.0
CB A:ALA292 4.6 38.6 1.0
MG A:MG536 4.9 25.1 1.0
CE A:LYS269 4.9 14.8 1.0
O3B A:ATP535 4.9 18.8 1.0
OG A:SER242 5.0 37.3 1.0

Magnesium binding site 2 out of 14 in 1a5u

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Magnesium binding site 2 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg536

b:25.1
occ:1.00
O1G A:ATP535 1.9 37.8 1.0
O A:HOH6079 2.0 12.6 1.0
O1A A:ATP535 2.3 26.3 1.0
O A:HOH6459 2.3 11.7 1.0
PG A:ATP535 2.7 52.9 1.0
O2B A:ATP535 2.8 18.7 1.0
O2G A:ATP535 3.1 31.7 1.0
PB A:ATP535 3.3 27.5 1.0
O3B A:ATP535 3.3 18.8 1.0
PA A:ATP535 3.4 33.9 1.0
O3A A:ATP535 3.7 56.2 1.0
C1 A:OXL533 3.8 45.5 1.0
O1 A:OXL533 3.9 72.1 1.0
OG1 A:THR327 3.9 37.4 1.0
C2 A:OXL533 3.9 27.2 1.0
O A:HOH6598 4.0 30.6 1.0
O3G A:ATP535 4.0 17.4 1.0
O2 A:OXL533 4.1 40.2 1.0
O2A A:ATP535 4.2 7.8 1.0
O3 A:OXL533 4.2 33.3 1.0
OG A:SER361 4.3 25.7 1.0
OD2 A:ASP177 4.3 27.7 1.0
NH2 A:ARG72 4.3 38.0 1.0
NH1 A:ARG72 4.4 56.5 1.0
O4 A:OXL533 4.4 42.9 1.0
O A:HOH6358 4.5 41.2 1.0
CB A:SER361 4.6 25.6 1.0
O5' A:ATP535 4.7 33.8 1.0
O1B A:ATP535 4.7 43.2 1.0
CG2 A:THR327 4.8 21.2 1.0
MG A:MG534 4.9 19.5 1.0
CZ A:ARG72 4.9 35.4 1.0
C5' A:ATP535 4.9 60.8 1.0
CB A:THR327 4.9 18.8 1.0

Magnesium binding site 3 out of 14 in 1a5u

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Magnesium binding site 3 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg1134

b:26.2
occ:1.00
O B:HOH6992 2.0 39.4 1.0
OD2 B:ASP895 2.2 21.4 1.0
O3 B:OXL1133 2.3 33.6 1.0
OE1 B:GLU871 2.4 56.7 1.0
O4 B:OXL1133 2.7 21.8 1.0
C1 B:OXL1133 3.2 30.0 1.0
CG B:ASP895 3.3 0.0 1.0
C2 B:OXL1133 3.4 35.0 1.0
CD B:GLU871 3.5 20.7 1.0
OE2 B:GLU871 3.9 34.8 1.0
O B:HOH6139 4.0 30.8 1.0
O B:HOH6608 4.0 79.0 1.0
CB B:ASP895 4.2 18.1 1.0
NZ B:LYS869 4.2 11.1 1.0
OD1 B:ASP895 4.4 33.3 1.0
O B:HOH6417 4.4 86.4 1.0
O1 B:OXL1133 4.4 34.8 1.0
CE B:LYS869 4.6 18.8 1.0
O2 B:OXL1133 4.6 34.2 1.0
CG B:GLU871 4.8 26.1 1.0
O B:HOH6840 4.9 35.8 1.0
N B:ASP895 4.9 28.8 1.0

Magnesium binding site 4 out of 14 in 1a5u

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Magnesium binding site 4 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg1734

b:35.7
occ:1.00
O4 C:OXL1733 2.0 40.0 1.0
O3 C:OXL1733 2.0 72.0 1.0
OD2 C:ASP1495 2.2 34.9 1.0
OE1 C:GLU1471 2.2 33.8 1.0
O2G C:ATP1735 2.4 31.4 1.0
C2 C:OXL1733 2.7 39.3 1.0
C1 C:OXL1733 2.7 29.8 1.0
CD C:GLU1471 3.2 29.0 1.0
PG C:ATP1735 3.2 54.0 1.0
O3G C:ATP1735 3.3 14.7 1.0
CG C:ASP1495 3.3 15.7 1.0
OE2 C:GLU1471 3.5 25.4 1.0
NZ C:LYS1469 3.6 76.7 1.0
O1 C:OXL1733 4.0 37.3 1.0
O2 C:OXL1733 4.0 29.6 1.0
O1G C:ATP1735 4.0 46.1 1.0
CB C:ASP1495 4.2 22.1 1.0
CE C:LYS1469 4.3 28.6 1.0
OD1 C:ASP1495 4.3 30.0 1.0
O C:HOH6006 4.5 27.4 1.0
CE2 C:PHE1443 4.5 23.0 1.0
CB C:ALA1492 4.6 14.0 1.0
CG C:GLU1471 4.6 13.9 1.0
O C:HOH6005 4.6 40.0 1.0
O3B C:ATP1735 4.7 38.1 1.0
N C:ASP1495 4.9 19.1 1.0
CB C:GLU1471 4.9 27.2 1.0
NH2 C:ARG1272 4.9 66.6 1.0
CZ C:PHE1443 4.9 39.5 1.0
O C:HOH6647 5.0 19.7 1.0

Magnesium binding site 5 out of 14 in 1a5u

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Magnesium binding site 5 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg1736

b:25.6
occ:1.00
O C:HOH6006 1.9 27.4 1.0
O1A C:ATP1735 1.9 16.6 1.0
O C:HOH6571 2.0 26.9 1.0
O C:HOH6647 2.1 19.7 1.0
O1G C:ATP1735 2.2 46.1 1.0
O2B C:ATP1735 2.3 24.2 1.0
PA C:ATP1735 3.1 34.7 1.0
PB C:ATP1735 3.2 38.9 1.0
PG C:ATP1735 3.2 54.0 1.0
O3A C:ATP1735 3.4 58.9 1.0
O3B C:ATP1735 3.5 38.1 1.0
O2G C:ATP1735 3.8 31.4 1.0
O C:HOH6851 3.9 25.4 1.0
O C:HOH6734 3.9 35.1 1.0
O C:HOH7372 4.0 33.1 1.0
O2A C:ATP1735 4.1 21.2 1.0
CB C:SER1561 4.1 36.9 1.0
O5' C:ATP1735 4.1 27.2 1.0
C5' C:ATP1735 4.2 35.6 1.0
OG C:SER1561 4.2 31.0 1.0
OG1 C:THR1527 4.4 44.2 1.0
OD2 C:ASP1377 4.4 54.1 1.0
O3G C:ATP1735 4.4 14.7 1.0
NH1 C:ARG1272 4.4 62.3 1.0
O1B C:ATP1735 4.5 91.7 1.0
C1 C:OXL1733 4.6 29.8 1.0
O1 C:OXL1733 4.6 37.3 1.0
CG2 C:THR1527 4.7 41.4 1.0
C2 C:OXL1733 4.7 39.3 1.0
O3 C:OXL1733 4.9 72.0 1.0
NH2 C:ARG1272 4.9 66.6 1.0
O2 C:OXL1733 4.9 29.6 1.0

Magnesium binding site 6 out of 14 in 1a5u

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Magnesium binding site 6 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg2334

b:23.9
occ:1.00
OD2 D:ASP2095 2.0 11.6 1.0
O3 D:OXL2333 2.0 15.1 1.0
O D:HOH6430 2.0 18.1 1.0
O4 D:OXL2333 2.1 23.6 1.0
OE1 D:GLU2071 2.2 37.2 1.0
O2G D:ATP2335 2.3 14.9 1.0
C1 D:OXL2333 2.7 32.5 1.0
C2 D:OXL2333 2.8 19.0 1.0
CG D:ASP2095 3.0 6.4 1.0
PG D:ATP2335 3.3 17.7 1.0
CD D:GLU2071 3.4 25.7 1.0
CB D:ASP2095 3.6 24.9 1.0
O D:HOH6004 3.7 29.9 1.0
O3G D:ATP2335 3.8 32.8 1.0
NZ D:LYS2069 3.9 18.9 1.0
O D:HOH6045 3.9 11.2 1.0
OE2 D:GLU2071 3.9 32.0 1.0
O2 D:OXL2333 4.0 17.5 1.0
O1 D:OXL2333 4.0 12.4 1.0
O1G D:ATP2335 4.0 31.3 1.0
OD1 D:ASP2095 4.2 28.6 1.0
N D:ASP2095 4.3 39.4 1.0
CE D:LYS2069 4.4 30.7 1.0
CA D:ASP2095 4.6 20.4 1.0
CB D:ALA2092 4.6 9.7 1.0
O3B D:ATP2335 4.6 18.5 1.0
O D:HOH7433 4.6 30.8 1.0
CG D:GLU2071 4.7 34.6 1.0
CE1 D:PHE2043 4.7 39.3 1.0
O D:HOH6382 4.8 32.8 1.0
MG D:MG2336 4.9 24.4 1.0
CB D:GLU2071 4.9 15.8 1.0

Magnesium binding site 7 out of 14 in 1a5u

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Magnesium binding site 7 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
D:Mg2336

b:24.4
occ:1.00
O D:HOH6378 1.8 22.6 1.0
O D:HOH6045 1.9 11.2 1.0
O1A D:ATP2335 2.1 12.8 1.0
O2B D:ATP2335 2.1 33.3 1.0
O D:HOH7302 2.1 22.6 1.0
O1G D:ATP2335 2.1 31.3 1.0
PG D:ATP2335 2.9 17.7 1.0
PB D:ATP2335 3.0 27.7 1.0
O3B D:ATP2335 3.1 18.5 1.0
PA D:ATP2335 3.2 23.4 1.0
O2G D:ATP2335 3.4 14.9 1.0
O3A D:ATP2335 3.4 7.9 1.0
OD2 D:ASP1977 4.0 26.4 1.0
C1 D:OXL2333 4.0 32.5 1.0
C2 D:OXL2333 4.1 19.0 1.0
O3G D:ATP2335 4.1 32.8 1.0
O2A D:ATP2335 4.2 12.5 1.0
NH2 D:ARG1872 4.2 23.5 1.0
OG D:SER2161 4.2 28.4 1.0
O1 D:OXL2333 4.3 12.4 1.0
O1B D:ATP2335 4.3 9.7 1.0
O3 D:OXL2333 4.4 15.1 1.0
O D:HOH6004 4.4 29.9 1.0
OG1 D:THR2127 4.4 12.0 1.0
CB D:SER2161 4.4 23.1 1.0
O5' D:ATP2335 4.4 20.6 1.0
O4 D:OXL2333 4.4 23.6 1.0
O2 D:OXL2333 4.4 17.5 1.0
O D:HOH6606 4.5 29.6 1.0
C5' D:ATP2335 4.5 40.4 1.0
NH1 D:ARG1872 4.7 72.3 1.0
O D:HOH6087 4.7 16.1 1.0
O D:HOH6138 4.7 16.8 1.0
CG2 D:THR2127 4.9 11.2 1.0
MG D:MG2334 4.9 23.9 1.0
CZ D:ARG1872 4.9 18.1 1.0
ND2 D:ASN1874 4.9 22.6 1.0

Magnesium binding site 8 out of 14 in 1a5u

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Magnesium binding site 8 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
E:Mg3534

b:19.2
occ:1.00
OD2 E:ASP3295 2.0 19.6 1.0
O E:HOH6954 2.1 30.3 1.0
O3 E:OXL3533 2.1 38.5 1.0
O4 E:OXL3533 2.1 34.2 1.0
OE1 E:GLU3271 2.2 26.3 1.0
O2G E:ATP3535 2.3 6.9 1.0
C2 E:OXL3533 2.8 19.2 1.0
C1 E:OXL3533 2.8 21.9 1.0
CG E:ASP3295 3.0 49.3 1.0
CD E:GLU3271 3.1 5.9 1.0
PG E:ATP3535 3.3 22.2 1.0
OE2 E:GLU3271 3.4 57.2 1.0
O3G E:ATP3535 3.5 27.8 1.0
CB E:ASP3295 3.6 30.8 1.0
O1G E:ATP3535 3.8 23.1 1.0
O E:HOH6156 3.9 18.4 1.0
O2 E:OXL3533 4.0 19.8 1.0
O1 E:OXL3533 4.0 21.4 1.0
OD1 E:ASP3295 4.2 35.6 1.0
NZ E:LYS3269 4.2 5.4 1.0
O E:HOH6341 4.2 40.5 1.0
N E:ASP3295 4.5 13.2 1.0
CG E:GLU3271 4.5 29.7 1.0
O E:HOH7689 4.5 31.1 1.0
CB E:ALA3292 4.5 13.9 1.0
CE E:LYS3269 4.5 25.3 1.0
CE2 E:PHE3243 4.6 18.0 1.0
CZ E:PHE3243 4.7 25.3 1.0
CA E:ASP3295 4.7 9.0 1.0
O3B E:ATP3535 4.7 48.8 1.0
CB E:GLU3271 4.8 8.0 1.0

Magnesium binding site 9 out of 14 in 1a5u

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Magnesium binding site 9 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3536

b:26.2
occ:1.00
O E:HOH6341 1.8 40.5 1.0
O E:HOH7379 2.0 22.3 1.0
O1A E:ATP3535 2.0 11.0 1.0
O1G E:ATP3535 2.1 23.1 1.0
O2B E:ATP3535 2.2 22.5 1.0
O E:HOH6159 2.3 14.6 1.0
PG E:ATP3535 3.1 22.2 1.0
PB E:ATP3535 3.1 23.0 1.0
PA E:ATP3535 3.1 26.9 1.0
O3B E:ATP3535 3.3 48.8 1.0
O3A E:ATP3535 3.4 19.1 1.0
O2G E:ATP3535 3.5 6.9 1.0
O E:HOH6310 3.9 21.8 1.0
C1 E:OXL3533 4.0 21.9 1.0
OG E:SER3361 4.1 15.2 1.0
O2A E:ATP3535 4.1 14.9 1.0
O1 E:OXL3533 4.1 21.4 1.0
OD2 E:ASP3177 4.1 21.4 1.0
O3G E:ATP3535 4.3 27.8 1.0
CB E:SER3361 4.3 36.3 1.0
O5' E:ATP3535 4.3 23.8 1.0
O3 E:OXL3533 4.3 38.5 1.0
C2 E:OXL3533 4.4 19.2 1.0
C5' E:ATP3535 4.4 5.3 1.0
O1B E:ATP3535 4.4 22.1 1.0
OG1 E:THR3327 4.5 34.9 1.0
NH2 E:ARG3072 4.5 20.8 1.0
O E:HOH7696 4.5 52.7 1.0
O E:HOH6156 4.6 18.4 1.0
O E:HOH6271 4.6 22.9 1.0
O2 E:OXL3533 4.7 19.8 1.0
CG2 E:THR3327 4.7 25.6 1.0
NH1 E:ARG3072 4.8 12.2 1.0
O4 E:OXL3533 4.8 34.2 1.0

Magnesium binding site 10 out of 14 in 1a5u

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Magnesium binding site 10 out of 14 in the Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pyruvate Kinase Complex with Bis Mg-Atp-Na-Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg4134

b:18.1
occ:1.00
OD2 F:ASP3895 2.0 38.2 1.0
O F:HOH6450 2.0 20.4 1.0
OE1 F:GLU3871 2.1 31.1 1.0
O2G F:ATP4135 2.1 20.2 1.0
O3 F:OXL4133 2.1 42.2 1.0
O4 F:OXL4133 2.2 25.1 1.0
C2 F:OXL4133 2.9 36.7 1.0
C1 F:OXL4133 2.9 29.2 1.0
CG F:ASP3895 3.1 19.2 1.0
CD F:GLU3871 3.1 18.6 1.0
PG F:ATP4135 3.3 52.6 1.0
OE2 F:GLU3871 3.5 25.7 1.0
O3G F:ATP4135 3.6 28.8 1.0
O1G F:ATP4135 3.8 54.9 1.0
CB F:ASP3895 3.8 17.4 1.0
NZ F:LYS3869 3.9 29.1 1.0
O F:HOH7013 4.0 16.8 1.0
O2 F:OXL4133 4.1 31.4 1.0
O1 F:OXL4133 4.1 23.9 1.0
OD1 F:ASP3895 4.1 43.2 1.0
O F:HOH6481 4.2 28.5 1.0
CE F:LYS3869 4.2 23.1 1.0
CZ F:PHE3843 4.4 31.2 1.0
CG F:GLU3871 4.5 14.0 1.0
N F:ASP3895 4.5 10.1 1.0
CE1 F:PHE3843 4.7 9.4 1.0
CB F:ALA3892 4.7 26.1 1.0
O3B F:ATP4135 4.7 38.8 1.0
CB F:GLU3871 4.7 10.5 1.0
CA F:ASP3895 4.8 29.1 1.0
OG F:SER3842 4.8 22.0 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 Dec 14 03:26:38 2020

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