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Sodium in PDB 3i6e: Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.

Enzymatic activity of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.

All present enzymatic activity of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.:
5.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi., PDB code: 3i6e was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.87 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 109.135, 135.358, 113.024, 90.00, 103.18, 90.00
R / Rfree (%) 23.5 / 26.3

Other elements in 3i6e:

The structure of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. (pdb code 3i6e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi., PDB code: 3i6e:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3i6e

Go back to Sodium Binding Sites List in 3i6e
Sodium binding site 1 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na387

b:28.3
occ:1.00
 O A:ARG239 2.4 25.4 1.0
O A:THR242 2.5 27.6 1.0
O A:HOH579 2.5 34.4 1.0
O A:HOH427 2.6 31.9 1.0
O A:HOH406 2.7 23.2 1.0
O A:HOH419 2.7 28.0 1.0
C A:ARG239 3.6 28.0 1.0
C A:THR242 3.7 30.2 1.0
O A:HOH401 3.8 30.9 1.0
CG A:ARG239 4.0 27.0 1.0
O A:HOH559 4.1 32.7 1.0
CA A:ASP243 4.2 28.0 1.0
OD1 A:ASP243 4.3 31.8 1.0
OD2 A:ASP268 4.3 24.5 1.0
NH1 A:ARG239 4.4 38.5 1.0
CA A:GLY240 4.4 28.9 1.0
N A:ASP243 4.4 27.4 1.0
N A:GLY240 4.5 27.5 1.0
OD1 A:ASP268 4.5 24.3 1.0
CA A:ARG239 4.5 27.2 1.0
N A:THR242 4.5 30.9 1.0
C A:GLY240 4.7 29.4 1.0
CA A:THR242 4.8 30.9 1.0
O A:VAL244 4.8 26.4 1.0
C A:ASP243 4.8 27.3 1.0
CG A:ASP268 4.8 23.0 1.0
CB A:ARG239 4.9 28.5 1.0
N A:LEU241 5.0 30.6 1.0

Sodium binding site 2 out of 8 in 3i6e

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Sodium binding site 2 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na387

b:25.0
occ:1.00
 O B:ARG239 2.5 25.4 1.0
O B:THR242 2.5 26.1 1.0
O B:HOH417 2.5 27.6 1.0
O B:HOH413 2.6 24.9 1.0
O B:HOH439 2.7 31.1 1.0
O B:HOH390 2.7 26.5 1.0
C B:ARG239 3.6 25.1 1.0
C B:THR242 3.7 27.7 1.0
O B:HOH430 4.0 30.8 1.0
O B:HOH919 4.0 34.2 1.0
O B:HOH438 4.1 25.2 1.0
CG B:ARG239 4.1 26.5 1.0
CA B:ASP243 4.2 24.9 1.0
OD1 B:ASP243 4.3 27.2 1.0
OD2 B:ASP268 4.3 22.6 1.0
CA B:GLY240 4.4 27.1 1.0
N B:ASP243 4.4 25.5 1.0
NH1 B:ARG239 4.4 37.6 1.0
N B:THR242 4.5 28.2 1.0
OD1 B:ASP268 4.5 23.1 1.0
N B:GLY240 4.5 24.8 1.0
CA B:ARG239 4.6 25.7 1.0
C B:GLY240 4.7 28.3 1.0
CA B:THR242 4.7 28.5 1.0
C B:ASP243 4.8 24.0 1.0
CG B:ASP268 4.8 24.0 1.0
O B:VAL244 4.8 24.3 1.0
CB B:ARG239 5.0 24.4 1.0
N B:LEU241 5.0 26.8 1.0

Sodium binding site 3 out of 8 in 3i6e

Go back to Sodium Binding Sites List in 3i6e
Sodium binding site 3 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na387

b:31.6
occ:1.00
 O C:THR242 2.4 28.2 1.0
O C:ARG239 2.4 28.9 1.0
O C:HOH400 2.6 24.6 1.0
O C:HOH464 2.6 32.5 1.0
O C:HOH412 2.7 29.8 1.0
O C:HOH932 2.7 36.2 1.0
C C:ARG239 3.6 29.0 1.0
C C:THR242 3.6 32.5 1.0
O C:HOH394 3.8 29.6 1.0
O C:HOH395 4.1 30.9 1.0
CA C:ASP243 4.1 30.4 1.0
CG C:ARG239 4.1 29.4 1.0
OD1 C:ASP243 4.2 31.3 1.0
CA C:GLY240 4.3 29.3 1.0
N C:ASP243 4.3 31.1 1.0
NH1 C:ARG239 4.4 39.9 1.0
OD2 C:ASP268 4.4 26.1 1.0
N C:GLY240 4.4 28.3 1.0
N C:THR242 4.5 32.5 1.0
CA C:ARG239 4.6 28.8 1.0
OD1 C:ASP268 4.6 27.9 1.0
C C:GLY240 4.7 30.8 1.0
C C:ASP243 4.7 30.0 1.0
CA C:THR242 4.7 33.2 1.0
O C:VAL244 4.9 28.1 1.0
CG C:ASP268 4.9 26.8 1.0
CB C:ARG239 5.0 27.9 1.0
N C:LEU241 5.0 31.3 1.0

Sodium binding site 4 out of 8 in 3i6e

Go back to Sodium Binding Sites List in 3i6e
Sodium binding site 4 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na387

b:31.7
occ:1.00
 O D:ARG239 2.5 27.2 1.0
O D:THR242 2.5 28.8 1.0
O D:HOH402 2.6 25.7 1.0
O D:HOH772 2.6 34.7 1.0
O D:HOH619 2.6 32.2 1.0
O D:HOH582 2.7 30.6 1.0
C D:ARG239 3.6 27.6 1.0
C D:THR242 3.7 32.1 1.0
O D:HOH414 3.7 32.3 1.0
CG D:ARG239 4.1 27.3 1.0
O D:HOH470 4.1 34.5 1.0
CA D:ASP243 4.2 30.0 1.0
O D:HOH540 4.2 31.1 1.0
OD1 D:ASP243 4.3 33.6 1.0
OD2 D:ASP268 4.4 24.6 1.0
CA D:GLY240 4.4 29.4 1.0
N D:ASP243 4.4 29.7 1.0
N D:GLY240 4.5 25.4 1.0
OD1 D:ASP268 4.5 25.2 1.0
NH1 D:ARG239 4.5 38.5 1.0
N D:THR242 4.5 32.4 1.0
CA D:ARG239 4.6 26.8 1.0
C D:GLY240 4.7 30.3 1.0
C D:ASP243 4.7 29.8 1.0
CA D:THR242 4.8 33.2 1.0
O D:VAL244 4.8 29.1 1.0
CG D:ASP268 4.9 25.9 1.0
CB D:ARG239 5.0 27.8 1.0

Sodium binding site 5 out of 8 in 3i6e

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Sodium binding site 5 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na387

b:27.5
occ:1.00
 O E:ARG239 2.4 23.2 1.0
O E:THR242 2.5 26.1 1.0
O E:HOH398 2.6 24.9 1.0
O E:HOH607 2.6 31.3 1.0
O E:HOH402 2.6 27.9 1.0
O E:HOH397 2.7 29.6 1.0
C E:ARG239 3.6 26.1 1.0
C E:THR242 3.7 29.2 1.0
O E:HOH407 3.8 26.0 1.0
O E:HOH427 4.0 28.9 1.0
O E:HOH798 4.0 36.5 1.0
CG E:ARG239 4.1 28.0 1.0
CA E:ASP243 4.1 28.6 1.0
CA E:GLY240 4.3 27.2 1.0
OD1 E:ASP243 4.3 28.1 1.0
N E:ASP243 4.4 27.1 1.0
N E:GLY240 4.4 25.7 1.0
OD2 E:ASP268 4.4 24.8 1.0
NH1 E:ARG239 4.4 38.8 1.0
OD1 E:ASP268 4.5 26.6 1.0
N E:THR242 4.5 30.9 1.0
CA E:ARG239 4.5 25.8 1.0
C E:GLY240 4.7 28.7 1.0
C E:ASP243 4.7 28.1 1.0
CA E:THR242 4.8 30.1 1.0
O E:VAL244 4.8 25.0 1.0
CG E:ASP268 4.9 23.8 1.0
CB E:ARG239 5.0 25.3 1.0

Sodium binding site 6 out of 8 in 3i6e

Go back to Sodium Binding Sites List in 3i6e
Sodium binding site 6 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na387

b:26.5
occ:1.00
 O F:ARG239 2.4 24.4 1.0
O F:THR242 2.5 24.2 1.0
O F:HOH428 2.5 27.9 1.0
O F:HOH396 2.6 24.2 1.0
O F:HOH664 2.7 33.5 1.0
O F:HOH404 2.7 26.0 1.0
C F:ARG239 3.6 25.3 1.0
C F:THR242 3.7 26.5 1.0
O F:HOH415 3.9 31.4 1.0
O F:HOH628 4.0 30.1 1.0
CG F:ARG239 4.1 23.9 1.0
O F:HOH566 4.1 32.8 1.0
CA F:ASP243 4.2 26.4 1.0
CA F:GLY240 4.3 26.2 1.0
OD2 F:ASP268 4.4 21.2 1.0
N F:GLY240 4.4 24.9 1.0
N F:ASP243 4.4 24.1 1.0
NH1 F:ARG239 4.5 36.6 1.0
OD1 F:ASP268 4.5 23.1 1.0
OD1 F:ASP243 4.5 30.7 1.0
N F:THR242 4.5 28.7 1.0
CA F:ARG239 4.5 25.3 1.0
C F:GLY240 4.6 27.2 1.0
CA F:THR242 4.7 28.2 1.0
C F:ASP243 4.8 27.1 1.0
O F:VAL244 4.8 23.9 1.0
CG F:ASP268 4.8 22.8 1.0
N F:LEU241 5.0 28.7 1.0
CB F:ARG239 5.0 23.6 1.0

Sodium binding site 7 out of 8 in 3i6e

Go back to Sodium Binding Sites List in 3i6e
Sodium binding site 7 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na387

b:23.2
occ:1.00
 O G:THR242 2.4 23.9 1.0
O G:ARG239 2.5 20.5 1.0
O G:HOH430 2.5 24.4 1.0
O G:HOH399 2.6 24.8 1.0
O G:HOH808 2.6 32.3 1.0
O G:HOH448 2.7 26.6 1.0
C G:THR242 3.6 24.1 1.0
C G:ARG239 3.6 22.6 1.0
O G:HOH406 3.8 24.2 1.0
O G:HOH464 4.0 30.3 1.0
O G:HOH389 4.1 28.6 1.0
CA G:ASP243 4.2 23.0 1.0
CG G:ARG239 4.2 24.1 1.0
OD1 G:ASP243 4.3 24.2 1.0
OD2 G:ASP268 4.3 18.1 1.0
CA G:GLY240 4.3 24.9 1.0
N G:ASP243 4.4 23.1 1.0
N G:GLY240 4.5 22.0 1.0
N G:THR242 4.5 24.8 1.0
OD1 G:ASP268 4.5 19.7 1.0
NH1 G:ARG239 4.6 34.7 1.0
CA G:ARG239 4.6 23.0 1.0
C G:GLY240 4.6 24.9 1.0
CA G:THR242 4.7 25.1 1.0
O G:VAL244 4.8 18.6 1.0
C G:ASP243 4.8 22.8 1.0
CG G:ASP268 4.9 22.0 1.0
N G:LEU241 4.9 24.1 1.0

Sodium binding site 8 out of 8 in 3i6e

Go back to Sodium Binding Sites List in 3i6e
Sodium binding site 8 out of 8 in the Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na387

b:28.4
occ:1.00
 O H:THR242 2.4 27.4 1.0
O H:ARG239 2.5 26.7 1.0
O H:HOH396 2.6 30.3 1.0
O H:HOH736 2.6 31.4 1.0
O H:HOH392 2.7 28.5 1.0
O H:HOH643 2.7 36.8 1.0
C H:ARG239 3.6 26.5 1.0
C H:THR242 3.6 30.8 1.0
O H:HOH496 3.8 30.4 1.0
O H:HOH644 4.1 31.7 1.0
CA H:ASP243 4.1 28.2 1.0
CG H:ARG239 4.1 25.5 1.0
OD1 H:ASP243 4.3 28.2 1.0
N H:ASP243 4.4 27.9 1.0
OD2 H:ASP268 4.4 23.6 1.0
CA H:GLY240 4.4 28.5 1.0
N H:GLY240 4.5 27.1 1.0
N H:THR242 4.5 32.4 1.0
CA H:ARG239 4.6 26.1 1.0
OD1 H:ASP268 4.6 27.5 1.0
NH1 H:ARG239 4.6 38.0 1.0
C H:GLY240 4.7 30.4 1.0
CA H:THR242 4.7 31.1 1.0
C H:ASP243 4.7 27.9 1.0
O H:VAL244 4.8 27.0 1.0
CG H:ASP268 4.9 26.3 1.0
CB H:ARG239 5.0 25.7 1.0
O H:GLY240 5.0 31.4 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, J.A.Gerlt, S.C.Almo. Crystal Structure of Muconate Lactonizing Enzyme From Ruegeria Pomeroyi. To Be Published.
Page generated: Mon Oct 7 10:36:17 2024

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