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Calcium in PDB 5j04: Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate

Enzymatic activity of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate

All present enzymatic activity of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate:
4.2.1.11;

Protein crystallography data

The structure of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate, PDB code: 5j04 was solved by J.M.Gonzalez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.55 / 2.30
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 164.230, 164.230, 72.680, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 24.6

Other elements in 5j04:

The structure of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate (pdb code 5j04). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate, PDB code: 5j04:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5j04

Go back to Calcium Binding Sites List in 5j04
Calcium binding site 1 out of 6 in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:45.3
occ:1.00
 O A:HOH694 2.2 50.1 1.0
O A:HOH644 2.4 33.0 1.0
O1P A:PEP501 2.4 36.4 1.0
O A:ALA46 2.5 27.4 1.0
O A:HOH678 2.6 37.5 1.0
O A:HOH606 2.9 26.4 1.0
P A:PEP501 3.7 31.6 1.0
C A:ALA46 3.7 33.7 1.0
O3P A:PEP501 4.0 29.4 1.0
NH2 A:ARG368 4.1 20.3 1.0
OD1 A:ASP315 4.1 25.4 1.0
O2 A:PEP501 4.2 36.6 1.0
O A:HOH616 4.3 19.1 1.0
N A:THR48 4.4 37.2 1.0
C A:SER47 4.4 31.7 1.0
NZ A:LYS339 4.5 30.0 1.0
CA A:ALA46 4.5 31.0 1.0
CB A:THR48 4.5 35.4 1.0
N A:ALA46 4.5 30.3 1.0
CB A:ALA46 4.6 30.2 1.0
O A:SER47 4.7 28.0 1.0
N A:SER47 4.7 36.0 1.0
CA A:THR48 4.7 39.0 1.0
CA A:SER47 4.8 33.9 1.0
O2P A:PEP501 4.9 29.0 1.0
OD2 A:ASP314 4.9 23.4 1.0
OE1 A:GLU52 5.0 29.6 1.0

Calcium binding site 2 out of 6 in 5j04

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Calcium binding site 2 out of 6 in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:58.4
occ:1.00
 O A:HOH703 2.2 51.7 1.0
O A:ASN162 2.5 34.9 1.0
O A:HOH654 2.5 39.9 1.0
O A:HOH698 2.7 49.2 1.0
C A:ASN162 3.7 40.2 1.0
N A:ASN162 4.0 41.8 1.0
O A:GLY157 4.0 41.6 1.0
O A:ALA160 4.5 47.8 1.0
CA A:ASN162 4.5 42.4 1.0
OD1 A:ASN162 4.6 42.4 1.0
N A:ASN163 4.7 44.2 1.0
O A:VAL164 4.8 29.4 1.0
CA A:ASN163 4.8 45.6 1.0
C A:GLY157 4.8 36.8 1.0
C A:ASP161 4.9 48.0 1.0

Calcium binding site 3 out of 6 in 5j04

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Calcium binding site 3 out of 6 in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:53.9
occ:1.00
 O A:HOH675 2.8 30.5 1.0
CD A:PRO237 3.6 25.0 1.0
CG A:PRO237 3.9 25.5 1.0
CB A:PRO237 4.5 24.2 1.0
N A:PRO237 4.5 23.0 1.0
O A:PRO237 4.8 26.6 1.0

Calcium binding site 4 out of 6 in 5j04

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Calcium binding site 4 out of 6 in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:59.7
occ:1.00
 O A:HOH684 2.4 35.4 1.0
O A:THR48 2.6 37.1 1.0
OE1 A:GLU292 2.7 45.9 1.0
OE2 A:GLU292 2.7 52.5 1.0
OG1 A:THR48 2.9 34.6 1.0
CD A:GLU292 3.0 43.8 1.0
C A:THR48 3.5 37.6 1.0
CA A:THR48 3.8 39.0 1.0
CB A:THR48 3.9 35.4 1.0
CG A:GLU292 4.5 39.9 1.0
OD2 A:ASP315 4.5 26.9 1.0
CG A:ASP315 4.7 26.7 1.0
N A:GLY49 4.7 46.3 1.0
CB A:SER250 4.8 24.3 1.0
OG A:SER250 4.9 24.4 1.0
CB A:ASP315 5.0 27.7 1.0

Calcium binding site 5 out of 6 in 5j04

Go back to Calcium Binding Sites List in 5j04
Calcium binding site 5 out of 6 in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:58.5
occ:1.00
 O B:HOH677 2.2 44.5 1.0
O B:HOH668 2.3 43.0 1.0
O B:HOH659 2.4 43.0 1.0
O B:ALA46 2.4 59.0 1.0
O B:HOH624 2.7 45.4 1.0
O2P B:PEP501 2.8 47.1 1.0
C B:ALA46 3.6 64.9 1.0
O3P B:PEP501 3.7 44.5 1.0
P B:PEP501 3.8 45.6 1.0
NH2 B:ARG368 3.9 21.0 1.0
OD1 B:ASP315 4.3 40.7 1.0
N B:THR48 4.3 63.8 1.0
C B:SER47 4.4 63.4 1.0
O B:HOH616 4.4 30.0 1.0
CA B:ALA46 4.5 65.5 1.0
N B:ALA46 4.5 65.8 1.0
NZ B:LYS339 4.5 31.1 1.0
CB B:THR48 4.6 62.9 1.0
N B:SER47 4.6 67.3 1.0
CB B:ALA46 4.7 63.2 1.0
O B:SER47 4.7 62.3 1.0
CA B:SER47 4.7 67.0 1.0
CA B:THR48 4.8 64.3 1.0
O1P B:PEP501 4.8 40.0 1.0
O2' B:PEP501 4.8 54.9 1.0
OE1 B:GLU52 4.9 54.9 1.0
O B:HOH613 4.9 33.4 1.0
CZ B:ARG368 5.0 21.1 1.0
O2 B:PEP501 5.0 51.5 1.0

Calcium binding site 6 out of 6 in 5j04

Go back to Calcium Binding Sites List in 5j04
Calcium binding site 6 out of 6 in the Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Enolase From Synechococcus Elongatus, Complex with Phosphoenolpyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:62.5
occ:0.80
 O B:THR48 2.1 63.8 1.0
OE1 B:GLU292 2.6 54.3 1.0
C B:THR48 3.2 63.4 1.0
OG1 B:THR48 3.3 55.8 1.0
CD B:GLU292 3.4 51.1 1.0
OE2 B:GLU292 3.9 51.8 1.0
N B:GLY49 4.0 69.7 1.0
CA B:GLY49 4.1 72.8 1.0
CA B:THR48 4.2 64.3 1.0
CB B:THR48 4.2 62.9 1.0
N B:THR50 4.4 80.1 1.0
CG B:GLU292 4.5 43.7 1.0
CG2 B:THR48 4.6 60.5 1.0
C B:GLY49 4.7 75.5 1.0
OG1 B:THR50 4.9 81.3 1.0

Reference:

J.M.Gonzalez, R.Marti-Arbona, C.J.Unkefer. Crystal Structure of Enolase From Synechococcus Elongatus To Be Published.
Page generated: Sun Jul 14 20:44:52 2024

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