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Manganese in PDB 3n25: The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+

Enzymatic activity of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+

All present enzymatic activity of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+:
2.7.1.40;

Protein crystallography data

The structure of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+, PDB code: 3n25 was solved by A.W.Fenton, T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.59 / 2.41
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.373, 108.747, 144.256, 95.18, 93.38, 112.23
R / Rfree (%) 20.4 / 26.8

Other elements in 3n25:

The structure of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ also contains other interesting chemical elements:

Potassium (K) 8 atoms
Sodium (Na) 12 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ (pdb code 3n25). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+, PDB code: 3n25:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3n25

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Manganese binding site 1 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn640

b:17.5
occ:1.00
 O A:HOH1275 2.0 2.0 1.0
OE1 A:GLU271 2.1 2.0 1.0
OD2 A:ASP295 2.1 2.0 1.0
O3 A:PYR1000 2.1 27.2 1.0
O2 A:PYR1000 2.2 22.3 1.0
O A:HOH1225 2.2 2.0 1.0
C2 A:PYR1000 2.9 24.6 1.0
C1 A:PYR1000 2.9 24.2 1.0
CD A:GLU271 3.2 2.0 1.0
CG A:ASP295 3.2 2.0 1.0
OE2 A:GLU271 3.6 2.0 1.0
CB A:ASP295 3.7 2.0 1.0
O A:HOH765 4.0 2.0 1.0
O1 A:PYR1000 4.1 25.2 1.0
CZ A:PHE243 4.2 2.3 1.0
NZ A:LYS269 4.2 2.0 1.0
OD1 A:ASP295 4.3 2.3 1.0
C3 A:PYR1000 4.3 23.5 1.0
O1 A:GOL6301 4.3 49.5 1.0
N A:ASP295 4.4 2.0 1.0
O A:HOH1069 4.5 2.0 1.0
CG A:GLU271 4.5 2.0 1.0
CE A:LYS269 4.5 2.0 1.0
CE2 A:PHE243 4.6 3.5 1.0
CB A:GLU271 4.6 2.0 1.0
CB A:ALA292 4.7 2.0 1.0
CE1 A:PHE243 4.7 2.5 1.0
CA A:ASP295 4.7 2.0 1.0
C1 A:GOL6301 4.8 48.8 1.0

Manganese binding site 2 out of 8 in 3n25

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Manganese binding site 2 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn640

b:33.3
occ:1.00
 OE1 B:GLU271 2.0 2.0 1.0
O3 B:PYR1500 2.0 32.4 1.0
O2 B:PYR1500 2.2 34.9 1.0
OD2 B:ASP295 2.2 4.3 1.0
O B:HOH1630 2.2 7.6 1.0
O B:HOH1195 2.5 2.0 1.0
C2 B:PYR1500 2.8 33.4 1.0
C1 B:PYR1500 2.9 33.9 1.0
CD B:GLU271 3.0 2.0 1.0
CG B:ASP295 3.1 5.6 1.0
OE2 B:GLU271 3.4 2.0 1.0
CB B:ASP295 3.5 5.6 1.0
NZ B:LYS269 3.9 2.0 1.0
O1 B:PYR1500 4.1 33.8 1.0
CZ B:PHE243 4.2 2.0 1.0
OD1 B:ASP295 4.2 4.8 1.0
C3 B:PYR1500 4.2 32.3 1.0
O1 B:GOL6302 4.3 38.0 1.0
CE2 B:PHE243 4.3 2.0 1.0
CE B:LYS269 4.4 2.0 1.0
CG B:GLU271 4.4 2.0 1.0
O2 B:EDO6048 4.4 28.3 1.0
C1 B:EDO6048 4.6 28.5 1.0
N B:ASP295 4.6 5.3 1.0
CB B:ALA292 4.6 5.2 1.0
CB B:GLU271 4.7 2.0 1.0
CA B:ASP295 4.7 5.4 1.0
CE1 B:PHE243 4.8 2.0 1.0

Manganese binding site 3 out of 8 in 3n25

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Manganese binding site 3 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn640

b:15.2
occ:1.00
 O C:HOH1196 2.0 2.0 1.0
OD2 C:ASP295 2.0 2.0 1.0
OE1 C:GLU271 2.1 2.0 1.0
O C:HOH1614 2.2 2.0 1.0
O3 C:PYR1500 2.3 13.7 1.0
O2 C:PYR1500 2.5 11.6 1.0
C2 C:PYR1500 3.1 12.3 1.0
C1 C:PYR1500 3.2 12.3 1.0
CG C:ASP295 3.2 2.0 1.0
CD C:GLU271 3.2 3.2 1.0
OE2 C:GLU271 3.7 4.0 1.0
CB C:ASP295 3.9 2.0 1.0
NZ C:LYS269 4.0 2.0 1.0
O C:HOH1097 4.1 5.5 1.0
OD1 C:ASP295 4.2 2.0 1.0
O C:HOH1603 4.2 2.0 1.0
CZ C:PHE243 4.2 2.0 1.0
CE C:LYS269 4.4 2.0 1.0
O3 C:GOL6303 4.5 29.0 1.0
O1 C:PYR1500 4.5 12.6 1.0
CG C:GLU271 4.5 3.1 1.0
N C:ASP295 4.5 2.0 1.0
O C:HOH1401 4.5 2.0 1.0
C3 C:PYR1500 4.6 12.0 1.0
CE1 C:PHE243 4.7 2.0 1.0
C3 C:GOL6303 4.7 30.5 1.0
CE2 C:PHE243 4.8 2.0 1.0
CB C:GLU271 4.8 2.0 1.0
CB C:ALA292 4.8 2.0 1.0
CA C:ASP295 4.9 2.0 1.0

Manganese binding site 4 out of 8 in 3n25

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Manganese binding site 4 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn640

b:20.9
occ:1.00
 OD2 D:ASP295 1.8 2.6 1.0
O D:HOH1274 2.0 25.2 1.0
O3 D:PYR1500 2.1 13.8 1.0
O2 D:PYR1500 2.2 20.3 1.0
OE1 D:GLU271 2.4 5.5 1.0
C2 D:PYR1500 2.9 15.4 1.0
C1 D:PYR1500 2.9 17.4 1.0
CG D:ASP295 3.0 4.2 1.0
CD D:GLU271 3.6 4.8 1.0
CB D:ASP295 3.8 3.7 1.0
OD1 D:ASP295 4.0 4.3 1.0
O2 D:EDO6033 4.0 36.5 1.0
OE2 D:GLU271 4.0 5.6 1.0
NZ D:LYS269 4.1 7.6 1.0
C3 D:GOL6304 4.1 29.7 1.0
O3 D:GOL6304 4.1 29.5 1.0
O1 D:PYR1500 4.2 17.8 1.0
CZ D:PHE243 4.3 4.8 1.0
C3 D:PYR1500 4.3 14.6 1.0
N D:ASP295 4.4 3.7 1.0
CE D:LYS269 4.4 6.6 1.0
CE2 D:PHE243 4.7 4.1 1.0
C2 D:EDO6033 4.7 35.4 1.0
CA D:ASP295 4.7 3.8 1.0
CG D:GLU271 4.8 5.3 1.0
C1 D:EDO6033 4.8 34.0 1.0
CB D:ALA292 4.9 5.3 1.0
CB D:GLU271 4.9 5.4 1.0
CE1 D:PHE243 4.9 5.1 1.0

Manganese binding site 5 out of 8 in 3n25

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Manganese binding site 5 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn640

b:21.0
occ:1.00
 O2 E:PYR1500 1.9 13.3 1.0
O E:HOH1638 2.0 2.0 1.0
OD2 E:ASP295 2.1 2.0 1.0
OE1 E:GLU271 2.3 5.9 1.0
O3 E:PYR1500 2.4 10.7 1.0
C1 E:PYR1500 2.8 14.1 1.0
C2 E:PYR1500 2.9 12.7 1.0
CG E:ASP295 3.2 2.0 1.0
CD E:GLU271 3.4 6.5 1.0
CB E:ASP295 3.8 2.0 1.0
OE2 E:GLU271 3.8 6.2 1.0
O1 E:PYR1500 4.0 14.6 1.0
OD1 E:ASP295 4.3 2.0 1.0
O1 E:GOL6305 4.3 21.9 1.0
N E:ASP295 4.3 2.0 1.0
NZ E:LYS269 4.3 3.1 1.0
O2 E:EDO6039 4.3 33.6 1.0
CZ E:PHE243 4.4 2.2 1.0
C3 E:PYR1500 4.4 12.7 1.0
C1 E:GOL6305 4.5 21.8 1.0
C2 E:EDO6039 4.6 34.3 1.0
CE E:LYS269 4.6 2.7 1.0
CA E:ASP295 4.7 2.0 1.0
CG E:GLU271 4.7 6.1 1.0
O E:HOH1051 4.7 2.0 1.0
CE2 E:PHE243 4.8 3.5 1.0
CB E:ALA292 4.8 2.8 1.0
CB E:GLU271 4.9 5.5 1.0
CE1 E:PHE243 5.0 2.0 1.0

Manganese binding site 6 out of 8 in 3n25

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Manganese binding site 6 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn640

b:18.4
occ:1.00
 OD2 F:ASP295 2.0 2.0 1.0
O2 F:PYR1500 2.2 7.6 1.0
O3 F:PYR1500 2.2 7.7 1.0
O F:HOH1624 2.2 7.5 1.0
OE1 F:GLU271 2.2 10.8 1.0
O F:HOH1199 2.3 5.8 1.0
C1 F:PYR1500 2.9 6.0 1.0
C2 F:PYR1500 3.0 7.4 1.0
CG F:ASP295 3.1 2.3 1.0
CD F:GLU271 3.2 8.5 1.0
OE2 F:GLU271 3.7 8.0 1.0
CB F:ASP295 3.7 2.0 1.0
O1 F:PYR1500 4.2 9.1 1.0
OD1 F:ASP295 4.2 2.0 1.0
O1 F:GOL6306 4.2 38.3 1.0
NZ F:LYS269 4.2 2.0 1.0
N F:ASP295 4.4 2.2 1.0
C3 F:PYR1500 4.4 7.7 1.0
CZ F:PHE243 4.5 4.5 1.0
CG F:GLU271 4.5 5.8 1.0
CE F:LYS269 4.6 2.0 1.0
CB F:ALA292 4.6 3.1 1.0
O F:HOH1656 4.7 2.0 1.0
CA F:ASP295 4.7 2.0 1.0
C1 F:GOL6306 4.7 39.9 1.0
CB F:GLU271 4.7 4.4 1.0
CE2 F:PHE243 4.8 3.7 1.0

Manganese binding site 7 out of 8 in 3n25

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Manganese binding site 7 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn640

b:26.7
occ:1.00
 OD2 G:ASP295 1.9 2.6 1.0
O3 G:PYR1500 2.1 22.6 1.0
OE1 G:GLU271 2.2 5.6 1.0
O2 G:PYR1500 2.2 22.2 1.0
O G:HOH1408 2.2 2.0 1.0
C2 G:PYR1500 2.9 23.2 1.0
C1 G:PYR1500 2.9 24.1 1.0
O G:HOH1201 3.0 2.0 1.0
CG G:ASP295 3.0 3.8 1.0
CD G:GLU271 3.3 5.6 1.0
OE2 G:GLU271 3.7 5.2 1.0
CB G:ASP295 3.7 3.5 1.0
OD1 G:ASP295 4.0 5.1 1.0
CE2 G:PHE243 4.1 2.0 1.0
O1 G:PYR1500 4.2 25.6 1.0
NZ G:LYS269 4.2 2.0 1.0
O G:HOH651 4.3 2.0 1.0
C3 G:PYR1500 4.3 21.4 1.0
CZ G:PHE243 4.3 2.0 1.0
CB G:ALA292 4.5 2.0 1.0
CG G:GLU271 4.5 4.5 1.0
N G:ASP295 4.6 3.3 1.0
CE G:LYS269 4.6 2.0 1.0
O G:HOH1409 4.6 2.0 1.0
CB G:GLU271 4.7 3.8 1.0
O3 G:GOL6307 4.7 46.1 1.0
CA G:ASP295 4.7 3.6 1.0
CD2 G:PHE243 5.0 2.0 1.0

Manganese binding site 8 out of 8 in 3n25

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Manganese binding site 8 out of 8 in the The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Structure of Muscle Pyruvate Kinase in Complex with Proline, Pyruvate, and MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn640

b:16.2
occ:1.00
 O H:HOH1202 1.8 2.0 1.0
O2 H:PYR1500 2.0 18.6 1.0
OD2 H:ASP295 2.1 2.0 1.0
OE1 H:GLU271 2.1 2.0 1.0
O3 H:PYR1500 2.2 17.3 1.0
O H:HOH1607 2.2 2.0 1.0
C1 H:PYR1500 2.7 19.0 1.0
C2 H:PYR1500 2.8 18.6 1.0
CD H:GLU271 3.2 2.0 1.0
CG H:ASP295 3.2 2.0 1.0
OE2 H:GLU271 3.6 2.0 1.0
CB H:ASP295 3.8 2.0 1.0
CZ H:PHE243 3.9 2.0 1.0
O3 H:GOL6308 3.9 22.1 1.0
O1 H:PYR1500 4.0 17.6 1.0
C3 H:GOL6308 4.2 24.6 1.0
NZ H:LYS269 4.3 2.0 1.0
OD1 H:ASP295 4.3 2.0 1.0
C3 H:PYR1500 4.3 18.4 1.0
CE1 H:PHE243 4.4 2.0 1.0
CE2 H:PHE243 4.4 2.0 1.0
CE H:LYS269 4.5 2.0 1.0
O H:HOH1418 4.5 2.0 1.0
CG H:GLU271 4.5 2.0 1.0
N H:ASP295 4.6 2.0 1.0
O H:HOH1064 4.6 2.0 1.0
CB H:GLU271 4.7 2.0 1.0
CB H:ALA292 4.8 2.0 1.0
CA H:ASP295 4.8 2.0 1.0

Reference:

A.W.Fenton, T.A.Johnson, T.Holyoak. The Pyruvate Kinase Model System, A Cautionary Tale For the Use of Osmolyte Perturbations to Support Conformational Equilibria in Allostery. Protein Sci. V. 19 1796 2010.
ISSN: ISSN 0961-8368
PubMed: 20629175
DOI: 10.1002/PRO.450
Page generated: Sat Oct 5 17:15:07 2024

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