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Manganese in PDB 1f3x: S402P Mutant of Rabbit Muscle Pyruvate Kinase

Enzymatic activity of S402P Mutant of Rabbit Muscle Pyruvate Kinase

All present enzymatic activity of S402P Mutant of Rabbit Muscle Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of S402P Mutant of Rabbit Muscle Pyruvate Kinase, PDB code: 1f3x 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) 36.00 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.138, 108.707, 144.387, 95.26, 93.47, 112.24
R / Rfree (%) 24.1 / 27

Other elements in 1f3x:

The structure of S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase (pdb code 1f3x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the S402P Mutant of Rabbit Muscle Pyruvate Kinase, PDB code: 1f3x:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1f3x

Go back to Manganese Binding Sites List in 1f3x
Manganese binding site 1 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn532

b:33.5
occ:1.00
 OD2 A:ASP295 2.2 21.5 1.0
O1 A:PYR541 2.3 28.4 1.0
OE2 A:GLU271 2.4 28.8 1.0
O3 A:PYR541 2.7 32.3 1.0
C1 A:PYR541 3.2 29.4 1.0
C2 A:PYR541 3.3 29.2 1.0
CD A:GLU271 3.3 27.8 1.0
CG A:ASP295 3.4 26.4 1.0
OE1 A:GLU271 3.5 31.4 1.0
NZ A:LYS269 3.9 16.1 1.0
OG A:SER242 4.2 39.9 1.0
CZ A:PHE243 4.2 18.2 1.0
OD1 A:ASP295 4.2 28.3 1.0
CB A:ASP295 4.2 22.4 1.0
CE A:LYS269 4.3 20.8 1.0
CE2 A:PHE243 4.3 17.3 1.0
O2 A:PYR541 4.4 22.9 1.0
CG A:GLU271 4.7 23.1 1.0
N A:ASP295 4.8 19.5 1.0
C3 A:PYR541 4.8 27.9 1.0
CB A:ALA292 4.9 27.1 1.0
CE1 A:PHE243 5.0 18.7 1.0

Manganese binding site 2 out of 8 in 1f3x

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Manganese binding site 2 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn533

b:33.4
occ:1.00
 OE2 B:GLU271 2.3 30.0 1.0
O1 B:PYR542 2.4 22.1 1.0
OD2 B:ASP295 2.4 30.0 1.0
O B:HOH941 2.5 18.0 1.0
O3 B:PYR542 2.7 20.0 1.0
CD B:GLU271 3.0 33.7 1.0
OE1 B:GLU271 3.1 31.9 1.0
C1 B:PYR542 3.2 21.5 1.0
C2 B:PYR542 3.3 20.9 1.0
NZ B:LYS269 3.6 29.3 1.0
CG B:ASP295 3.6 27.3 1.0
O B:HOH1034 3.8 18.0 1.0
CE B:LYS269 4.0 31.9 1.0
CZ B:PHE243 4.1 21.2 1.0
CE2 B:PHE243 4.2 19.6 1.0
O2 B:PYR542 4.4 22.9 1.0
CB B:ASP295 4.4 25.0 1.0
CG B:GLU271 4.5 33.9 1.0
OD1 B:ASP295 4.5 28.4 1.0
CE1 B:PHE243 4.7 20.4 1.0
OG B:SER242 4.8 30.2 1.0
CB B:ALA292 4.8 17.4 1.0
C3 B:PYR542 4.8 19.4 1.0
CB B:GLU271 5.0 35.6 1.0
N B:ASP295 5.0 21.4 1.0

Manganese binding site 3 out of 8 in 1f3x

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Manganese binding site 3 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn532

b:34.4
occ:1.00
 OD2 C:ASP295 2.2 26.4 1.0
O1 C:PYR543 2.3 31.3 1.0
OE2 C:GLU271 2.4 28.7 1.0
O3 C:PYR543 2.6 33.8 1.0
C1 C:PYR543 3.1 30.9 1.0
C2 C:PYR543 3.2 32.1 1.0
CD C:GLU271 3.2 30.7 1.0
CG C:ASP295 3.4 28.2 1.0
OE1 C:GLU271 3.4 29.3 1.0
O C:HOH978 3.4 18.0 1.0
NZ C:LYS269 3.9 23.1 1.0
CZ C:PHE243 4.1 25.5 1.0
CB C:ASP295 4.2 25.4 1.0
CE2 C:PHE243 4.2 27.4 1.0
OD1 C:ASP295 4.2 30.9 1.0
CE C:LYS269 4.3 23.3 1.0
O2 C:PYR543 4.4 29.7 1.0
CG C:GLU271 4.7 27.2 1.0
C3 C:PYR543 4.8 34.8 1.0
N C:ASP295 4.8 18.9 1.0
CB C:ALA292 4.9 16.2 1.0
CE1 C:PHE243 4.9 25.6 1.0

Manganese binding site 4 out of 8 in 1f3x

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Manganese binding site 4 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn532

b:52.1
occ:1.00
 OD2 D:ASP295 2.3 35.1 1.0
O1 D:PYR544 2.4 44.5 1.0
OE2 D:GLU271 2.4 49.2 1.0
O3 D:PYR544 2.6 45.7 1.0
CD D:GLU271 3.2 51.1 1.0
C1 D:PYR544 3.2 45.5 1.0
C2 D:PYR544 3.2 44.7 1.0
OE1 D:GLU271 3.3 51.0 1.0
CG D:ASP295 3.5 35.8 1.0
NZ D:LYS269 3.5 47.0 1.0
CE D:LYS269 4.1 49.1 1.0
CZ D:PHE243 4.2 41.8 1.0
CE2 D:PHE243 4.2 42.8 1.0
CB D:ASP295 4.3 35.1 1.0
OD1 D:ASP295 4.4 38.3 1.0
O2 D:PYR544 4.4 45.7 1.0
OG D:SER242 4.6 43.0 1.0
CG D:GLU271 4.6 49.5 1.0
C3 D:PYR544 4.8 44.7 1.0
CB D:ALA292 4.9 39.4 1.0
CE1 D:PHE243 4.9 42.5 1.0
N D:ASP295 5.0 34.3 1.0

Manganese binding site 5 out of 8 in 1f3x

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Manganese binding site 5 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn532

b:33.5
occ:1.00
 OD2 E:ASP295 2.1 21.5 1.0
O1 E:PYR545 2.3 28.4 1.0
OE2 E:GLU271 2.3 28.8 1.0
O3 E:PYR545 2.6 32.3 1.0
C1 E:PYR545 3.1 29.4 1.0
C2 E:PYR545 3.2 29.2 1.0
CD E:GLU271 3.3 27.8 1.0
CG E:ASP295 3.3 26.4 1.0
OE1 E:GLU271 3.5 31.4 1.0
NZ E:LYS269 4.0 16.1 1.0
CB E:ASP295 4.2 22.4 1.0
OD1 E:ASP295 4.2 28.3 1.0
CZ E:PHE243 4.3 18.2 1.0
OG E:SER242 4.3 39.9 1.0
O2 E:PYR545 4.3 22.9 1.0
CE E:LYS269 4.3 20.8 1.0
CE2 E:PHE243 4.4 17.3 1.0
N E:ASP295 4.6 19.5 1.0
CG E:GLU271 4.7 23.1 1.0
C3 E:PYR545 4.7 27.9 1.0
CB E:ALA292 4.8 27.1 1.0

Manganese binding site 6 out of 8 in 1f3x

Go back to Manganese Binding Sites List in 1f3x
Manganese binding site 6 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn532

b:33.4
occ:1.00
 OE2 F:GLU271 2.2 30.0 1.0
OD2 F:ASP295 2.4 30.0 1.0
O1 F:PYR546 2.4 22.1 1.0
O F:HOH1941 2.7 18.0 1.0
O3 F:PYR546 2.8 20.0 1.0
CD F:GLU271 3.0 33.7 1.0
OE1 F:GLU271 3.0 31.9 1.0
C1 F:PYR546 3.3 21.5 1.0
C2 F:PYR546 3.4 20.9 1.0
NZ F:LYS269 3.6 29.3 1.0
CG F:ASP295 3.7 27.3 1.0
O F:HOH2034 3.7 18.0 1.0
CE F:LYS269 3.9 31.9 1.0
CZ F:PHE243 4.0 21.2 1.0
CE2 F:PHE243 4.2 19.6 1.0
CG F:GLU271 4.4 33.9 1.0
CB F:ASP295 4.5 25.0 1.0
O2 F:PYR546 4.5 22.9 1.0
OD1 F:ASP295 4.6 28.4 1.0
CE1 F:PHE243 4.6 20.4 1.0
OG F:SER242 4.7 30.2 1.0
CB F:ALA292 4.8 17.4 1.0
C3 F:PYR546 4.9 19.4 1.0
CB F:GLU271 4.9 35.6 1.0
CD2 F:PHE243 5.0 20.2 1.0

Manganese binding site 7 out of 8 in 1f3x

Go back to Manganese Binding Sites List in 1f3x
Manganese binding site 7 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn532

b:34.4
occ:1.00
 OD2 G:ASP295 2.1 26.4 1.0
O1 G:PYR547 2.3 31.3 1.0
OE2 G:GLU271 2.3 28.7 1.0
O3 G:PYR547 2.6 33.8 1.0
C1 G:PYR547 3.1 30.9 1.0
CD G:GLU271 3.1 30.7 1.0
C2 G:PYR547 3.2 32.1 1.0
CG G:ASP295 3.3 28.2 1.0
OE1 G:GLU271 3.3 29.3 1.0
O G:HOH1978 3.6 18.0 1.0
NZ G:LYS269 4.0 23.1 1.0
CZ G:PHE243 4.0 25.5 1.0
CB G:ASP295 4.1 25.4 1.0
CE2 G:PHE243 4.1 27.4 1.0
OD1 G:ASP295 4.2 30.9 1.0
CE G:LYS269 4.2 23.3 1.0
O2 G:PYR547 4.3 29.7 1.0
CG G:GLU271 4.6 27.2 1.0
C3 G:PYR547 4.8 34.8 1.0
N G:ASP295 4.8 18.9 1.0
CE1 G:PHE243 4.8 25.6 1.0
CB G:ALA292 4.8 16.2 1.0
CB G:GLU271 4.9 30.4 1.0

Manganese binding site 8 out of 8 in 1f3x

Go back to Manganese Binding Sites List in 1f3x
Manganese binding site 8 out of 8 in the S402P Mutant of 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 S402P Mutant of Rabbit Muscle Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn532

b:52.1
occ:1.00
 OD2 H:ASP295 2.2 35.1 1.0
OE2 H:GLU271 2.3 49.2 1.0
O1 H:PYR548 2.4 44.5 1.0
O3 H:PYR548 2.7 45.7 1.0
CD H:GLU271 3.1 51.1 1.0
C1 H:PYR548 3.2 45.5 1.0
OE1 H:GLU271 3.2 51.0 1.0
C2 H:PYR548 3.3 44.7 1.0
CG H:ASP295 3.5 35.8 1.0
NZ H:LYS269 3.5 47.0 1.0
CZ H:PHE243 4.1 41.8 1.0
CE H:LYS269 4.1 49.1 1.0
CE2 H:PHE243 4.2 42.8 1.0
CB H:ASP295 4.3 35.1 1.0
OD1 H:ASP295 4.4 38.3 1.0
O2 H:PYR548 4.4 45.7 1.0
OG H:SER242 4.5 43.0 1.0
CG H:GLU271 4.6 49.5 1.0
C3 H:PYR548 4.8 44.7 1.0
CB H:ALA292 4.8 39.4 1.0
CE1 H:PHE243 4.9 42.5 1.0
N H:ASP295 5.0 34.3 1.0
CD2 H:PHE243 5.0 44.0 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: Tue Dec 15 03:47:44 2020

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