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Sodium in PDB 5ve2: Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.

Enzymatic activity of Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.

All present enzymatic activity of Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.:
4.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution., PDB code: 5ve2 was solved by M.K.Siuda, I.G.Shabalin, D.R.Cooper, H.C.Chapman, K.L.Tkaczuk, J.Bonanno, S.C.Almo, W.Minor, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.660, 160.141, 136.271, 90.00, 90.12, 90.00
R / Rfree (%) 20.5 / 25.8

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. (pdb code 5ve2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution., PDB code: 5ve2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 5ve2

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Sodium binding site 1 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:39.5
occ:1.00
 O A:ILE48 2.4 33.0 1.0
O A:ASP45 2.4 44.9 1.0
O A:HOH403 2.4 47.1 1.0
O A:HOH445 2.4 47.1 1.0
O A:SER42 2.4 40.1 1.0
O A:HOH506 2.4 63.9 1.0
C A:ASP45 3.4 46.7 1.0
C A:ILE48 3.6 38.8 1.0
C A:SER42 3.6 40.4 1.0
CA A:ASP46 4.0 47.8 1.0
OG1 A:THR93 4.1 35.8 1.0
N A:ASP46 4.1 42.2 1.0
O A:ASN43 4.1 45.1 1.0
N A:ILE48 4.2 37.8 1.0
CA A:ILE48 4.2 34.6 1.0
CB A:ILE48 4.2 31.5 1.0
C A:ASN43 4.3 51.3 1.0
C A:ASP46 4.4 40.3 1.0
CA A:ASN43 4.4 45.5 1.0
N A:ASP45 4.5 38.7 1.0
N A:ASN43 4.5 39.3 1.0
CA A:ASP45 4.5 42.0 1.0
O A:ASP46 4.6 48.7 1.0
CA A:SER42 4.6 33.5 1.0
N A:ARG49 4.6 32.8 1.0
OD1 A:ASP46 4.8 55.6 1.0
CA A:ARG49 4.9 32.1 1.0
CG2 A:ILE48 4.9 37.3 1.0
N A:HIS44 4.9 53.6 1.0
CG2 A:THR93 4.9 44.8 1.0
N A:GLN47 5.0 36.5 1.0

Sodium binding site 2 out of 12 in 5ve2

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Sodium binding site 2 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:38.6
occ:1.00
 O B:SER42 2.4 44.3 1.0
O B:ILE48 2.4 34.7 1.0
O B:HOH449 2.4 44.3 1.0
O B:ASP45 2.4 45.1 1.0
O B:HOH506 2.4 60.5 1.0
O B:HOH427 2.4 49.3 1.0
C B:ASP45 3.5 47.6 1.0
C B:ILE48 3.6 39.0 1.0
C B:SER42 3.6 46.6 1.0
O B:HOH517 4.0 45.2 1.0
CA B:ASP46 4.1 43.0 1.0
OG1 B:THR93 4.1 43.2 1.0
O B:ASN43 4.1 54.5 1.0
N B:ASP46 4.2 41.7 1.0
N B:ILE48 4.2 44.5 1.0
CA B:ILE48 4.2 36.1 1.0
C B:ASN43 4.2 46.0 1.0
CB B:ILE48 4.2 32.8 1.0
O B:HOH466 4.3 43.7 1.0
CA B:ASN43 4.4 44.7 1.0
C B:ASP46 4.4 40.4 1.0
N B:ASN43 4.4 43.5 1.0
N B:ASP45 4.4 57.0 1.0
CA B:ASP45 4.5 51.4 1.0
CA B:SER42 4.6 38.1 1.0
N B:ARG49 4.6 30.7 1.0
O B:ASP46 4.6 52.5 1.0
CA B:ARG49 4.8 32.7 1.0
N B:HIS44 4.9 63.1 1.0
CG2 B:ILE48 4.9 50.1 1.0
OD1 B:ASP46 4.9 52.1 1.0
CG2 B:THR93 4.9 42.5 1.0

Sodium binding site 3 out of 12 in 5ve2

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Sodium binding site 3 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:40.5
occ:1.00
 O C:ILE48 2.4 35.4 1.0
O C:ASP45 2.4 36.8 1.0
O C:HOH435 2.4 37.5 1.0
O C:SER42 2.4 40.9 1.0
C C:ASP45 3.4 50.6 1.0
C C:ILE48 3.5 32.7 1.0
C C:SER42 3.6 46.5 1.0
CA C:ASP46 4.0 45.7 1.0
OG1 C:THR93 4.1 32.5 1.0
N C:ASP46 4.1 46.4 1.0
N C:ILE48 4.2 40.5 1.0
O C:ASN43 4.2 41.2 1.0
CA C:ILE48 4.2 38.6 1.0
CB C:ILE48 4.2 42.1 1.0
C C:ASN43 4.3 48.2 1.0
C C:ASP46 4.4 44.6 1.0
CA C:ASN43 4.4 46.6 1.0
N C:ASP45 4.5 44.9 1.0
N C:ASN43 4.5 36.1 1.0
CA C:ASP45 4.5 41.2 1.0
O C:ASP46 4.6 40.6 1.0
N C:ARG49 4.6 33.3 1.0
CA C:SER42 4.6 41.6 1.0
CA C:ARG49 4.8 35.6 1.0
CG2 C:ILE48 4.9 38.5 1.0
OD1 C:ASP46 4.9 67.6 1.0
CG2 C:THR93 4.9 39.4 1.0
N C:HIS44 4.9 42.9 1.0
N C:GLN47 5.0 41.5 1.0

Sodium binding site 4 out of 12 in 5ve2

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Sodium binding site 4 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:38.8
occ:1.00
 O D:ILE48 2.4 34.6 1.0
O D:SER42 2.4 40.3 1.0
O D:HOH461 2.4 42.8 1.0
O D:ASP45 2.4 42.1 1.0
C D:ASP45 3.5 54.7 1.0
C D:ILE48 3.6 34.6 1.0
C D:SER42 3.6 57.0 1.0
O D:HOH537 3.7 51.0 1.0
CA D:ASP46 4.1 44.0 1.0
OG1 D:THR93 4.1 34.5 1.0
O D:ASN43 4.1 54.6 1.0
N D:ASP46 4.2 44.4 1.0
N D:ILE48 4.2 45.2 1.0
CA D:ILE48 4.2 35.4 1.0
CB D:ILE48 4.2 34.5 1.0
C D:ASN43 4.3 43.4 1.0
O D:HOH497 4.3 43.5 1.0
C D:ASP46 4.4 41.2 1.0
CA D:ASN43 4.4 41.8 1.0
N D:ASP45 4.4 63.1 1.0
N D:ASN43 4.5 41.5 1.0
CA D:ASP45 4.5 50.4 1.0
CA D:SER42 4.6 45.8 1.0
N D:ARG49 4.6 31.7 1.0
O D:ASP46 4.6 39.7 1.0
CA D:ARG49 4.8 36.0 1.0
CG2 D:ILE48 4.9 39.9 1.0
N D:HIS44 4.9 47.1 1.0
CG2 D:THR93 4.9 43.2 1.0

Sodium binding site 5 out of 12 in 5ve2

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Sodium binding site 5 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:36.9
occ:1.00
 O E:ILE48 2.4 31.2 1.0
O E:HOH407 2.4 38.5 1.0
O E:HOH402 2.4 46.6 1.0
O E:SER42 2.4 36.3 1.0
O E:ASP45 2.4 41.5 1.0
C E:ASP45 3.5 40.0 1.0
C E:ILE48 3.5 35.7 1.0
C E:SER42 3.6 35.6 1.0
CA E:ASP46 4.1 44.5 1.0
OG1 E:THR93 4.1 36.3 1.0
N E:ASP46 4.1 40.3 1.0
O E:ASN43 4.2 43.0 1.0
N E:ILE48 4.2 44.4 1.0
CA E:ILE48 4.2 40.1 1.0
CB E:ILE48 4.2 37.5 1.0
C E:ASN43 4.3 42.7 1.0
CA E:ASN43 4.4 48.0 1.0
C E:ASP46 4.4 37.8 1.0
N E:ASP45 4.5 37.4 1.0
N E:ASN43 4.5 34.8 1.0
O E:HOH549 4.5 50.7 1.0
CA E:ASP45 4.5 42.8 1.0
N E:ARG49 4.6 31.0 1.0
CA E:SER42 4.6 41.1 1.0
O E:ASP46 4.7 44.1 1.0
CA E:ARG49 4.8 37.0 1.0
OD1 E:ASP46 4.9 54.4 1.0
CG2 E:ILE48 4.9 33.8 1.0
CG2 E:THR93 4.9 41.0 1.0
N E:HIS44 4.9 47.4 1.0

Sodium binding site 6 out of 12 in 5ve2

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Sodium binding site 6 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:33.2
occ:1.00
 O F:ILE48 2.4 27.6 1.0
O F:HOH412 2.4 31.3 1.0
O F:HOH417 2.4 55.7 1.0
O F:ASP45 2.4 35.8 1.0
O F:SER42 2.4 36.1 1.0
C F:ASP45 3.5 40.4 1.0
C F:ILE48 3.5 35.7 1.0
C F:SER42 3.6 38.1 1.0
O F:HOH518 3.7 43.9 1.0
O F:HOH466 4.0 50.3 1.0
CA F:ASP46 4.1 39.3 1.0
OG1 F:THR93 4.1 36.8 1.0
N F:ASP46 4.1 36.3 1.0
O F:ASN43 4.1 43.6 1.0
N F:ILE48 4.2 46.3 1.0
CA F:ILE48 4.2 36.7 1.0
CB F:ILE48 4.2 31.0 1.0
C F:ASN43 4.3 35.8 1.0
C F:ASP46 4.4 31.4 1.0
CA F:ASN43 4.4 38.5 1.0
N F:ASP45 4.5 47.9 1.0
N F:ASN43 4.5 35.7 1.0
CA F:ASP45 4.5 45.4 1.0
N F:ARG49 4.6 31.5 1.0
CA F:SER42 4.6 36.9 1.0
O F:ASP46 4.6 41.4 1.0
CA F:ARG49 4.8 35.9 1.0
CG2 F:ILE48 4.9 33.6 1.0
CG2 F:THR93 4.9 40.4 1.0
N F:HIS44 4.9 55.3 1.0
OD1 F:ASP46 4.9 54.2 1.0
N F:GLN47 5.0 36.2 1.0

Sodium binding site 7 out of 12 in 5ve2

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Sodium binding site 7 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na301

b:29.9
occ:1.00
 O G:ILE48 2.4 32.1 1.0
O G:SER42 2.4 38.0 1.0
O G:ASP45 2.4 37.5 1.0
O G:HOH426 2.4 54.7 1.0
O G:HOH412 2.4 32.6 1.0
C G:ASP45 3.4 49.5 1.0
C G:ILE48 3.5 40.9 1.0
C G:SER42 3.6 46.6 1.0
CA G:ASP46 4.1 42.2 1.0
OG1 G:THR93 4.1 40.8 1.0
N G:ASP46 4.1 45.9 1.0
O G:ASN43 4.2 67.8 1.0
N G:ILE48 4.2 41.7 1.0
CA G:ILE48 4.2 34.9 1.0
CB G:ILE48 4.2 39.9 1.0
C G:ASN43 4.3 39.2 1.0
O G:HOH477 4.3 54.0 1.0
C G:ASP46 4.4 39.6 1.0
CA G:ASN43 4.4 37.0 1.0
N G:ASP45 4.4 53.7 1.0
N G:ASN43 4.4 40.0 1.0
CA G:ASP45 4.5 48.2 1.0
CA G:SER42 4.6 46.8 1.0
N G:ARG49 4.6 35.1 1.0
O G:ASP46 4.6 40.9 1.0
CA G:ARG49 4.8 35.8 1.0
CG2 G:ILE48 4.9 45.2 1.0
CG2 G:THR93 4.9 43.0 1.0
N G:HIS44 4.9 57.5 1.0
N G:GLN47 5.0 38.2 1.0

Sodium binding site 8 out of 12 in 5ve2

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Sodium binding site 8 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


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 Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:38.2
occ:1.00
 O H:ILE48 2.4 37.6 1.0
O H:ASP45 2.4 43.6 1.0
O H:SER42 2.4 34.1 1.0
O H:HOH414 2.4 53.5 1.0
O H:HOH406 2.4 37.4 1.0
C H:ASP45 3.4 51.6 1.0
C H:ILE48 3.5 36.4 1.0
C H:SER42 3.6 44.4 1.0
CA H:ASP46 4.0 48.6 1.0
OG1 H:THR93 4.1 38.9 1.0
N H:ASP46 4.1 52.9 1.0
N H:ILE48 4.2 39.5 1.0
O H:ASN43 4.2 46.4 1.0
CA H:ILE48 4.2 38.2 1.0
CB H:ILE48 4.2 35.8 1.0
O H:HOH527 4.2 60.1 1.0
C H:ASN43 4.3 46.8 1.0
C H:ASP46 4.4 43.2 1.0
CA H:ASN43 4.4 48.3 1.0
N H:ASP45 4.4 44.6 1.0
N H:ASN43 4.5 35.9 1.0
CA H:ASP45 4.5 42.3 1.0
N H:ARG49 4.6 36.6 1.0
CA H:SER42 4.6 43.7 1.0
O H:ASP46 4.6 45.6 1.0
CA H:ARG49 4.8 29.9 1.0
CG2 H:ILE48 4.9 41.4 1.0
OD1 H:ASP46 4.9 80.0 1.0
CG2 H:THR93 4.9 39.4 1.0
N H:HIS44 4.9 55.8 1.0
N H:GLN47 5.0 40.3 1.0

Sodium binding site 9 out of 12 in 5ve2

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Sodium binding site 9 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na301

b:41.7
occ:1.00
 O I:HOH445 2.4 39.0 1.0
O I:ASP45 2.4 36.0 1.0
O I:SER42 2.4 39.4 1.0
O I:ILE48 2.4 36.2 1.0
O I:HOH436 2.4 66.5 1.0
C I:ASP45 3.4 40.1 1.0
C I:ILE48 3.6 36.7 1.0
C I:SER42 3.6 44.0 1.0
O I:HOH507 3.8 39.7 1.0
O I:HOH456 4.0 55.6 1.0
CA I:ASP46 4.0 47.7 1.0
N I:ASP46 4.1 40.8 1.0
OG1 I:THR93 4.1 32.8 1.0
O I:ASN43 4.1 54.0 1.0
N I:ILE48 4.2 45.3 1.0
CA I:ILE48 4.2 39.2 1.0
CB I:ILE48 4.2 36.5 1.0
C I:ASN43 4.2 39.1 1.0
C I:ASP46 4.4 36.9 1.0
CA I:ASN43 4.4 43.9 1.0
N I:ASP45 4.4 62.6 1.0
N I:ASN43 4.5 45.7 1.0
CA I:ASP45 4.5 52.7 1.0
CA I:SER42 4.6 44.1 1.0
N I:ARG49 4.6 33.7 1.0
O I:ASP46 4.6 41.1 1.0
CA I:ARG49 4.9 35.6 1.0
CG2 I:ILE48 4.9 41.2 1.0
N I:HIS44 4.9 58.6 1.0
CG2 I:THR93 4.9 47.4 1.0
OD1 I:ASP46 4.9 85.3 1.0

Sodium binding site 10 out of 12 in 5ve2

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Sodium binding site 10 out of 12 in the Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na301

b:41.2
occ:1.00
 O J:ASP45 2.4 40.2 1.0
O J:ILE48 2.4 34.1 1.0
O J:HOH418 2.4 39.4 1.0
O J:SER42 2.4 44.8 1.0
O J:HOH458 2.4 51.4 1.0
C J:ASP45 3.4 39.9 1.0
C J:ILE48 3.5 30.4 1.0
C J:SER42 3.6 42.2 1.0
CA J:ASP46 4.1 48.8 1.0
N J:ASP46 4.1 47.4 1.0
OG1 J:THR93 4.1 35.8 1.0
O J:ASN43 4.2 49.8 1.0
N J:ILE48 4.2 45.3 1.0
CA J:ILE48 4.2 39.4 1.0
CB J:ILE48 4.2 41.6 1.0
C J:ASN43 4.3 41.7 1.0
C J:ASP46 4.4 41.3 1.0
CA J:ASN43 4.4 44.4 1.0
N J:ASP45 4.4 48.0 1.0
N J:ASN43 4.5 42.5 1.0
CA J:ASP45 4.5 49.4 1.0
CA J:SER42 4.6 42.7 1.0
N J:ARG49 4.6 31.3 1.0
O J:ASP46 4.7 39.2 1.0
CA J:ARG49 4.9 34.1 1.0
CG2 J:ILE48 4.9 47.0 1.0
CG2 J:THR93 4.9 50.5 1.0
N J:HIS44 4.9 48.6 1.0
OD1 J:ASP46 5.0 83.1 1.0
N J:GLN47 5.0 43.2 1.0

Reference:

M.K.Siuda, I.G.Shabalin, D.R.Cooper, S.C.Almo, W.Minor. Crystal Structure of Enoyl-Coa Hydratase/Isomerase From Pseudoalteromonas Atlantica T6C at 2.3 A Resolution. To Be Published.
Page generated: Tue Oct 8 00:48:03 2024

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