Sodium in PDB 8dop: Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)

Enzymatic activity of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)

All present enzymatic activity of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form):
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form), PDB code: 8dop was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.021, 71.159, 93.183, 108.39, 102.23, 89.99
R / Rfree (%) 18.8 / 24.6

Other elements in 8dop:

The structure of Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) also contains other interesting chemical elements:

Iodine (I) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) (pdb code 8dop). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form), PDB code: 8dop:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 8dop

Go back to Sodium Binding Sites List in 8dop
Sodium binding site 1 out of 6 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:38.8
occ:1.00
 N A:THR120 3.6 37.5 1.0
OG1 A:THR120 3.6 54.0 1.0
CA A:LEU119 3.9 29.8 1.0
CD2 A:LEU119 4.0 26.6 1.0
CG1 A:VAL156 4.0 36.6 1.0
CG A:PRO178 4.2 34.6 1.0
CG2 A:THR120 4.2 56.0 1.0
O A:HOH451 4.3 33.8 1.0
C A:LEU119 4.3 29.2 1.0
CE A:LYS62 4.3 26.8 1.0
CB A:THR120 4.4 46.3 1.0
CB A:LEU119 4.5 23.2 1.0
I A:IOD302 4.6 86.8 0.6
CA A:THR120 4.6 32.6 1.0
CG2 B:ILE66 4.7 32.4 1.0
CG1 A:VAL116 4.7 28.7 1.0
CG A:LEU119 4.8 21.4 1.0
O A:VAL118 4.8 29.1 1.0
NZ A:LYS62 5.0 24.2 1.0

Sodium binding site 2 out of 6 in 8dop

Go back to Sodium Binding Sites List in 8dop
Sodium binding site 2 out of 6 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:47.7
occ:1.00
 O B:HOH430 3.1 51.3 1.0
CG2 B:THR120 3.6 50.2 1.0
N B:THR120 3.8 41.5 1.0
CD2 B:LEU119 3.8 43.2 1.0
CG B:PRO178 3.9 48.5 1.0
CG1 B:VAL156 4.2 39.6 1.0
OG1 B:THR120 4.2 54.5 1.0
CE B:LYS62 4.2 31.5 1.0
CA B:LEU119 4.2 38.0 1.0
CB B:PRO178 4.2 49.4 1.0
CB B:THR120 4.4 51.4 1.0
C B:LEU119 4.5 39.7 1.0
I B:IOD301 4.6 69.1 0.6
CB B:LEU119 4.7 39.3 1.0
CA B:THR120 4.8 45.8 1.0
NZ B:LYS62 4.8 31.4 1.0
O B:HOH422 4.8 33.9 1.0
CG2 A:ILE66 4.8 41.2 1.0
CG B:LEU119 4.9 39.3 1.0
CG1 B:VAL116 5.0 27.8 1.0

Sodium binding site 3 out of 6 in 8dop

Go back to Sodium Binding Sites List in 8dop
Sodium binding site 3 out of 6 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:39.6
occ:1.00
 N C:THR120 3.7 38.4 1.0
CA C:LEU119 3.8 39.7 1.0
CG2 C:THR120 3.9 43.1 1.0
CD2 C:LEU119 4.0 37.9 1.0
O C:HOH435 4.1 31.0 1.0
CE C:LYS62 4.1 28.8 1.0
CG1 C:VAL156 4.1 44.7 1.0
C C:LEU119 4.3 37.4 1.0
CB C:LEU119 4.4 42.1 1.0
CB C:PRO178 4.4 53.5 1.0
CG C:PRO178 4.4 48.5 1.0
O C:VAL118 4.5 43.3 1.0
OG1 C:THR120 4.5 50.6 1.0
I C:IOD302 4.5 118.2 0.8
CG1 C:VAL116 4.6 38.2 1.0
CB C:THR120 4.7 44.8 1.0
CG C:LEU119 4.8 33.5 1.0
N C:LEU119 4.8 41.6 1.0
CA C:THR120 4.8 44.2 1.0
NZ C:LYS62 4.9 28.2 1.0
CG2 C:VAL116 4.9 36.9 1.0

Sodium binding site 4 out of 6 in 8dop

Go back to Sodium Binding Sites List in 8dop
Sodium binding site 4 out of 6 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:43.0
occ:1.00
 N D:THR120 3.5 36.1 1.0
CG2 D:THR120 3.7 46.5 1.0
OG1 D:THR120 3.7 59.2 1.0
CD2 D:LEU119 3.9 22.9 1.0
CA D:LEU119 3.9 30.0 1.0
CG D:PRO178 4.0 36.2 1.0
CB D:PRO178 4.2 38.7 1.0
CB D:THR120 4.2 42.3 1.0
C D:LEU119 4.2 35.6 1.0
CE D:LYS62 4.3 24.8 1.0
CG1 D:VAL156 4.3 31.1 1.0
CB D:LEU119 4.4 30.0 1.0
CG2 C:ILE66 4.4 28.8 1.0
CA D:THR120 4.4 39.0 1.0
O D:HOH450 4.6 35.3 1.0
CG D:LEU119 4.7 21.2 1.0
O D:VAL118 4.8 36.5 1.0
I D:IOD301 4.8 81.7 0.6
CG1 D:VAL116 4.9 34.6 1.0
NZ D:LYS62 4.9 28.2 1.0

Sodium binding site 5 out of 6 in 8dop

Go back to Sodium Binding Sites List in 8dop
Sodium binding site 5 out of 6 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:47.5
occ:1.00
 N E:THR120 3.7 45.3 1.0
CG2 E:THR120 3.7 56.3 1.0
OG1 E:THR120 4.0 55.9 1.0
CA E:LEU119 4.1 44.5 1.0
CG1 E:VAL156 4.1 34.1 1.0
CD2 E:LEU119 4.1 34.7 1.0
CE E:LYS62 4.2 35.2 1.0
O E:HOH418 4.2 42.1 1.0
CB E:THR120 4.3 59.3 1.0
CG1 E:VAL116 4.4 33.9 1.0
C E:LEU119 4.4 45.1 1.0
O E:HOH424 4.5 33.0 1.0
CA E:THR120 4.6 47.7 1.0
CG E:PRO178 4.7 40.6 1.0
CB E:LEU119 4.7 34.0 1.0
O E:VAL118 4.7 42.3 1.0
CB E:VAL156 4.8 31.5 1.0
I E:IOD302 4.9 48.8 0.6
NZ E:LYS62 5.0 33.0 1.0

Sodium binding site 6 out of 6 in 8dop

Go back to Sodium Binding Sites List in 8dop
Sodium binding site 6 out of 6 in the Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form)


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 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:51.4
occ:1.00
 OG1 H:THR120 3.7 54.6 1.0
CD2 H:LEU119 3.9 35.8 1.0
N H:THR120 4.0 39.3 1.0
CG2 H:THR120 4.1 59.1 1.0
CE H:LYS62 4.1 41.6 1.0
O H:HOH422 4.1 32.4 1.0
CG1 H:VAL156 4.1 35.1 1.0
CG H:PRO178 4.3 45.0 1.0
CB H:THR120 4.4 53.8 1.0
NZ H:LYS62 4.4 32.5 1.0
CA H:LEU119 4.6 38.9 1.0
I H:IOD302 4.6 62.2 0.6
CG2 G:ILE66 4.7 39.0 1.0
CG1 H:VAL116 4.7 45.0 1.0
C H:LEU119 4.8 40.9 1.0
CA H:THR120 4.9 46.7 1.0

Reference:

S.Lovell, L.Liu, S.Seibold, K.P.Battaile. Crystal Structure of 2,3-Diketo-5-Methylthiopentyl-1-Phosphate Enolase-Phosphatase From Klebsiella Aerogenes (P1 Form) To Be Published.
Page generated: Fri Apr 7 18:45:03 2023

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