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Manganese in PDB 1f3w: Recombinant Rabbit Muscle Pyruvate Kinase

Enzymatic activity of Recombinant Rabbit Muscle Pyruvate Kinase

All present enzymatic activity of Recombinant Rabbit Muscle Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Recombinant Rabbit Muscle Pyruvate Kinase, PDB code: 1f3w was solved by J.O.Wooll, R.H.E.Friesen, M.A.White, S.J.Watowich, R.O.Fox, J.C.Lee, E.W.Czerwinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.00 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.000, 105.400, 143.500, 95.90, 92.80, 111.90
R / Rfree (%) 23.8 / 25.7

Other elements in 1f3w:

The structure of Recombinant Rabbit Muscle Pyruvate Kinase also contains other interesting chemical elements:

Potassium (K) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Recombinant Rabbit Muscle Pyruvate Kinase (pdb code 1f3w). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Recombinant Rabbit Muscle Pyruvate Kinase, PDB code: 1f3w:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1f3w

Go back to Manganese Binding Sites List in 1f3w
Manganese binding site 1 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn532

b:45.9
occ:1.00
 OE1 A:GLU271 2.1 38.1 1.0
OD2 A:ASP295 2.2 32.6 1.0
O1 A:PYR541 2.3 32.9 1.0
O3 A:PYR541 2.6 43.1 1.0
CD A:GLU271 3.1 39.8 1.0
C1 A:PYR541 3.1 38.8 1.0
C2 A:PYR541 3.2 38.9 1.0
OE2 A:GLU271 3.4 39.4 1.0
CG A:ASP295 3.5 35.2 1.0
NZ A:LYS269 3.7 25.9 1.0
CZ A:PHE243 4.1 38.1 1.0
OD1 A:ASP295 4.3 35.2 1.0
CE A:LYS269 4.3 27.9 1.0
O2 A:PYR541 4.4 38.9 1.0
CB A:ASP295 4.4 33.7 1.0
CG A:GLU271 4.5 38.3 1.0
CE2 A:PHE243 4.5 38.3 1.0
CE1 A:PHE243 4.7 36.8 1.0
C3 A:PYR541 4.8 39.5 1.0
K A:K531 4.9 44.7 1.0
N A:ASP295 5.0 30.0 1.0

Manganese binding site 2 out of 8 in 1f3w

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Manganese binding site 2 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn533

b:45.9
occ:1.00
 OE1 B:GLU271 2.1 38.1 1.0
OD2 B:ASP295 2.2 32.6 1.0
O1 B:PYR542 2.3 32.9 1.0
O3 B:PYR542 2.6 43.1 1.0
CD B:GLU271 3.1 39.8 1.0
C1 B:PYR542 3.1 38.8 1.0
C2 B:PYR542 3.2 38.9 1.0
OE2 B:GLU271 3.4 39.4 1.0
CG B:ASP295 3.5 35.2 1.0
NZ B:LYS269 3.7 25.9 1.0
CZ B:PHE243 4.1 38.1 1.0
OD1 B:ASP295 4.3 35.2 1.0
CE B:LYS269 4.3 27.9 1.0
O2 B:PYR542 4.4 38.9 1.0
CB B:ASP295 4.4 33.7 1.0
CG B:GLU271 4.5 38.3 1.0
CE2 B:PHE243 4.5 38.3 1.0
CE1 B:PHE243 4.7 36.8 1.0
C3 B:PYR542 4.8 39.5 1.0
K B:K532 4.9 44.7 1.0
N B:ASP295 5.0 30.0 1.0

Manganese binding site 3 out of 8 in 1f3w

Go back to Manganese Binding Sites List in 1f3w
Manganese binding site 3 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn532

b:45.9
occ:1.00
 OE1 C:GLU271 2.1 38.1 1.0
OD2 C:ASP295 2.2 32.6 1.0
O1 C:PYR543 2.3 32.9 1.0
O3 C:PYR543 2.6 43.1 1.0
CD C:GLU271 3.1 39.8 1.0
C1 C:PYR543 3.1 38.8 1.0
C2 C:PYR543 3.2 38.9 1.0
OE2 C:GLU271 3.4 39.4 1.0
CG C:ASP295 3.5 35.2 1.0
NZ C:LYS269 3.7 25.9 1.0
CZ C:PHE243 4.1 38.1 1.0
OD1 C:ASP295 4.3 35.2 1.0
CE C:LYS269 4.3 27.9 1.0
O2 C:PYR543 4.4 38.9 1.0
CB C:ASP295 4.4 33.7 1.0
CG C:GLU271 4.5 38.3 1.0
CE2 C:PHE243 4.5 38.3 1.0
CE1 C:PHE243 4.7 36.8 1.0
C3 C:PYR543 4.8 39.5 1.0
K C:K533 4.9 44.7 1.0
N C:ASP295 5.0 30.0 1.0

Manganese binding site 4 out of 8 in 1f3w

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Manganese binding site 4 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn532

b:45.9
occ:1.00
 OE1 D:GLU271 2.1 38.1 1.0
OD2 D:ASP295 2.2 32.6 1.0
O1 D:PYR544 2.3 32.9 1.0
O3 D:PYR544 2.6 43.1 1.0
CD D:GLU271 3.1 39.8 1.0
C1 D:PYR544 3.1 38.8 1.0
C2 D:PYR544 3.2 38.9 1.0
OE2 D:GLU271 3.4 39.4 1.0
CG D:ASP295 3.5 35.2 1.0
NZ D:LYS269 3.7 25.9 1.0
CZ D:PHE243 4.1 38.1 1.0
OD1 D:ASP295 4.3 35.2 1.0
CE D:LYS269 4.3 27.9 1.0
O2 D:PYR544 4.4 38.9 1.0
CB D:ASP295 4.4 33.7 1.0
CG D:GLU271 4.5 38.3 1.0
CE2 D:PHE243 4.5 38.3 1.0
CE1 D:PHE243 4.7 36.8 1.0
C3 D:PYR544 4.8 39.5 1.0
K D:K534 4.9 44.7 1.0
N D:ASP295 5.0 30.0 1.0

Manganese binding site 5 out of 8 in 1f3w

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Manganese binding site 5 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn532

b:45.9
occ:1.00
 OE1 E:GLU271 2.1 38.1 1.0
OD2 E:ASP295 2.2 32.6 1.0
O1 E:PYR545 2.3 32.9 1.0
O3 E:PYR545 2.6 43.1 1.0
CD E:GLU271 3.1 39.8 1.0
C1 E:PYR545 3.1 38.8 1.0
C2 E:PYR545 3.2 38.9 1.0
OE2 E:GLU271 3.4 39.4 1.0
CG E:ASP295 3.5 35.2 1.0
NZ E:LYS269 3.7 25.9 1.0
CZ E:PHE243 4.1 38.1 1.0
OD1 E:ASP295 4.3 35.2 1.0
CE E:LYS269 4.3 27.9 1.0
O2 E:PYR545 4.4 38.9 1.0
CB E:ASP295 4.4 33.7 1.0
CG E:GLU271 4.5 38.3 1.0
CE2 E:PHE243 4.5 38.3 1.0
CE1 E:PHE243 4.7 36.8 1.0
C3 E:PYR545 4.8 39.5 1.0
K E:K535 4.9 44.7 1.0
N E:ASP295 5.0 30.0 1.0

Manganese binding site 6 out of 8 in 1f3w

Go back to Manganese Binding Sites List in 1f3w
Manganese binding site 6 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn532

b:45.9
occ:1.00
 OE1 F:GLU271 2.1 38.1 1.0
OD2 F:ASP295 2.2 32.6 1.0
O1 F:PYR546 2.3 32.9 1.0
O3 F:PYR546 2.6 43.1 1.0
CD F:GLU271 3.1 39.8 1.0
C1 F:PYR546 3.1 38.8 1.0
C2 F:PYR546 3.2 38.9 1.0
OE2 F:GLU271 3.4 39.4 1.0
CG F:ASP295 3.5 35.2 1.0
NZ F:LYS269 3.7 25.9 1.0
CZ F:PHE243 4.1 38.1 1.0
OD1 F:ASP295 4.3 35.2 1.0
CE F:LYS269 4.3 27.9 1.0
O2 F:PYR546 4.4 38.9 1.0
CB F:ASP295 4.4 33.7 1.0
CG F:GLU271 4.5 38.3 1.0
CE2 F:PHE243 4.5 38.3 1.0
CE1 F:PHE243 4.7 36.8 1.0
C3 F:PYR546 4.8 39.5 1.0
K F:K536 4.9 44.7 1.0
N F:ASP295 5.0 30.0 1.0

Manganese binding site 7 out of 8 in 1f3w

Go back to Manganese Binding Sites List in 1f3w
Manganese binding site 7 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn532

b:45.9
occ:1.00
 OE1 G:GLU271 2.1 38.1 1.0
OD2 G:ASP295 2.2 32.6 1.0
O1 G:PYR547 2.3 32.9 1.0
O3 G:PYR547 2.6 43.1 1.0
CD G:GLU271 3.1 39.8 1.0
C1 G:PYR547 3.1 38.8 1.0
C2 G:PYR547 3.2 38.9 1.0
OE2 G:GLU271 3.4 39.4 1.0
CG G:ASP295 3.5 35.2 1.0
NZ G:LYS269 3.7 25.9 1.0
CZ G:PHE243 4.1 38.1 1.0
OD1 G:ASP295 4.3 35.2 1.0
CE G:LYS269 4.3 27.9 1.0
O2 G:PYR547 4.4 38.9 1.0
CB G:ASP295 4.4 33.7 1.0
CG G:GLU271 4.5 38.3 1.0
CE2 G:PHE243 4.5 38.3 1.0
CE1 G:PHE243 4.7 36.8 1.0
C3 G:PYR547 4.8 39.5 1.0
K G:K537 4.9 44.7 1.0
N G:ASP295 5.0 30.0 1.0

Manganese binding site 8 out of 8 in 1f3w

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Manganese binding site 8 out of 8 in the Recombinant Rabbit Muscle Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Recombinant Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn532

b:45.9
occ:1.00
 OE1 H:GLU271 2.1 38.1 1.0
OD2 H:ASP295 2.2 32.6 1.0
O1 H:PYR548 2.3 32.9 1.0
O3 H:PYR548 2.6 43.1 1.0
CD H:GLU271 3.1 39.8 1.0
C1 H:PYR548 3.1 38.8 1.0
C2 H:PYR548 3.2 38.9 1.0
OE2 H:GLU271 3.4 39.4 1.0
CG H:ASP295 3.5 35.2 1.0
NZ H:LYS269 3.7 25.9 1.0
CZ H:PHE243 4.1 38.1 1.0
OD1 H:ASP295 4.3 35.2 1.0
CE H:LYS269 4.3 27.9 1.0
O2 H:PYR548 4.4 38.9 1.0
CB H:ASP295 4.4 33.7 1.0
CG H:GLU271 4.5 38.3 1.0
CE2 H:PHE243 4.5 38.3 1.0
CE1 H:PHE243 4.7 36.8 1.0
C3 H:PYR548 4.8 39.5 1.0
K H:K538 4.9 44.7 1.0
N H:ASP295 5.0 30.0 1.0

Reference:

J.O.Wooll, R.H.Friesen, M.A.White, S.J.Watowich, R.O.Fox, J.C.Lee, E.W.Czerwinski. Structural and Functional Linkages Between Subunit Interfaces in Mammalian Pyruvate Kinase. J.Mol.Biol. V. 312 525 2001.
ISSN: ISSN 0022-2836
PubMed: 11563914
DOI: 10.1006/JMBI.2001.4978
Page generated: Sat Oct 5 10:15:16 2024

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