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Sodium in PDB 3hjz: The Structure of An Aldolase From Prochlorococcus Marinus

Enzymatic activity of The Structure of An Aldolase From Prochlorococcus Marinus

All present enzymatic activity of The Structure of An Aldolase From Prochlorococcus Marinus:
2.2.1.2;

Protein crystallography data

The structure of The Structure of An Aldolase From Prochlorococcus Marinus, PDB code: 3hjz was solved by A.U.Singer, X.Xu, H.Cui, A.Joachimiak, A.M.Edwards, A.Savchenko, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.19 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.755, 80.376, 97.866, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 20.3

Other elements in 3hjz:

The structure of The Structure of An Aldolase From Prochlorococcus Marinus also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of An Aldolase From Prochlorococcus Marinus (pdb code 3hjz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Structure of An Aldolase From Prochlorococcus Marinus, PDB code: 3hjz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3hjz

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Sodium binding site 1 out of 6 in the The Structure of An Aldolase From Prochlorococcus Marinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of An Aldolase From Prochlorococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:28.0
occ:1.00
 OE2 A:GLU99 2.5 18.6 1.0
O A:HOH685 2.6 15.7 1.0
O A:PHE306 3.0 12.1 1.0
CB A:ALA309 3.4 12.7 1.0
CA A:PHE306 3.5 13.1 1.0
CD A:GLU99 3.5 18.3 1.0
CG A:PRO36 3.5 12.7 1.0
CD A:PRO36 3.5 12.4 1.0
O A:HOH523 3.6 14.4 1.0
C A:PHE306 3.6 13.4 1.0
CB A:PRO36 3.7 12.2 1.0
O A:HOH621 3.8 19.8 1.0
OE1 A:GLU99 3.8 15.2 1.0
CB A:PHE306 3.9 12.5 1.0
N A:ILE310 4.1 12.7 1.0
CG A:PHE306 4.3 14.3 1.0
N A:PRO36 4.4 12.4 1.0
CA A:ALA309 4.4 13.2 1.0
CD1 A:PHE306 4.4 14.1 1.0
C A:ALA309 4.4 13.0 1.0
CA A:PRO36 4.7 12.7 1.0
OG A:SER37 4.7 18.4 1.0
O A:GLY305 4.7 11.8 1.0
N A:ALA309 4.8 14.0 1.0
N A:PHE306 4.8 11.9 1.0
CG A:GLU99 4.8 14.9 1.0
CB A:ILE310 4.8 12.1 1.0
N A:SER37 4.9 12.4 1.0
CA A:ILE310 4.9 12.6 1.0
N A:SER307 4.9 13.3 1.0
CB A:ASN35 4.9 12.4 1.0

Sodium binding site 2 out of 6 in 3hjz

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Sodium binding site 2 out of 6 in the The Structure of An Aldolase From Prochlorococcus Marinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of An Aldolase From Prochlorococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:25.3
occ:1.00
 O A:HOH676 2.4 12.5 1.0
OD1 A:ASP78 2.7 16.5 1.0
O A:HOH570 2.7 15.8 1.0
O A:HOH689 2.7 32.9 1.0
CG1 A:VAL77 3.6 13.6 1.0
CD A:LYS114 3.9 14.2 1.0
CG A:ASP78 3.9 16.6 1.0
CE A:LYS114 3.9 13.8 1.0
CA A:ASP78 4.0 13.2 1.0
NZ A:LYS114 4.0 17.6 1.0
N A:ASP78 4.0 12.8 1.0
C A:VAL77 4.2 13.3 1.0
O A:VAL77 4.2 13.5 1.0
CB A:ASP101 4.3 11.7 1.0
CD1 A:ILE310 4.4 14.8 1.0
O A:HOH617 4.4 35.1 1.0
O A:HOH543 4.4 23.2 1.0
CB A:VAL77 4.5 12.6 1.0
CB A:ASP78 4.6 12.0 1.0
CG A:LYS114 4.6 12.6 1.0
N A:ASP101 4.6 13.7 1.0
CD2 A:LEU118 4.6 15.1 1.0
OG A:SER81 4.7 13.4 0.5
OD2 A:ASP78 4.9 16.8 1.0
CA A:ASP101 4.9 13.2 1.0
OD2 A:ASP101 5.0 12.5 1.0

Sodium binding site 3 out of 6 in 3hjz

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Sodium binding site 3 out of 6 in the The Structure of An Aldolase From Prochlorococcus Marinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of An Aldolase From Prochlorococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:27.1
occ:1.00
 O A:HOH456 2.5 11.7 1.0
O A:MSE11 2.6 11.0 1.0
O A:HOH616 2.7 21.8 1.0
O A:HOH677 2.7 30.4 1.0
NH2 A:ARG264 3.3 14.4 1.0
O A:GLY241 3.3 10.5 1.0
O A:CYS242 3.4 9.0 1.0
C A:MSE11 3.6 12.0 1.0
CA A:ASP243 3.8 10.0 1.0
C A:CYS242 3.9 10.8 1.0
CA A:THR12 4.0 11.5 1.0
N A:ASP243 4.1 9.2 1.0
C A:GLY241 4.1 10.7 1.0
O A:ASP243 4.1 11.0 1.0
N A:THR12 4.1 10.5 1.0
CZ A:ARG264 4.3 16.3 1.0
OD1 A:ASP243 4.4 10.1 1.0
C A:ASP243 4.4 10.6 1.0
O A:HOH503 4.5 29.7 1.0
OH A:TYR213 4.5 10.7 1.0
O A:HOH436 4.6 22.1 1.0
NH1 A:ARG264 4.6 15.7 1.0
OG1 A:THR12 4.6 12.7 1.0
CA A:GLY241 4.7 10.1 1.0
CA A:MSE11 4.8 12.6 1.0
O A:HOH496 4.9 36.0 1.0
N A:CYS242 4.9 9.8 1.0
CA A:CYS242 4.9 9.9 1.0
C A:THR12 4.9 11.7 1.0
CB A:THR12 5.0 11.7 1.0
N A:VAL13 5.0 12.0 1.0
CB A:ASP243 5.0 11.2 1.0
O A:HOH370 5.0 32.1 1.0

Sodium binding site 4 out of 6 in 3hjz

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Sodium binding site 4 out of 6 in the The Structure of An Aldolase From Prochlorococcus Marinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of An Aldolase From Prochlorococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na343

b:31.6
occ:1.00
 O A:HOH681 2.4 27.4 1.0
O A:HOH519 2.6 30.9 1.0
OD2 A:ASP101 2.7 12.5 1.0
O A:HOH619 3.2 28.1 1.0
CG A:ASP101 3.6 14.1 1.0
NH2 A:ARG103 3.7 13.1 1.0
NE A:ARG103 3.8 14.7 1.0
CZ A:ARG103 3.9 16.7 1.0
CD2 A:LEU104 3.9 13.6 1.0
OD1 A:ASP101 4.1 12.3 1.0
O A:HOH570 4.3 15.8 1.0
CB A:ARG103 4.4 12.7 1.0
O A:HOH498 4.5 29.4 1.0
CG A:LEU104 4.5 14.5 1.0
CB A:ASP101 4.6 11.7 1.0
CD A:ARG103 4.7 12.5 1.0
NH1 A:ARG103 4.7 13.3 1.0
NZ A:LYS74 4.8 31.3 1.0

Sodium binding site 5 out of 6 in 3hjz

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Sodium binding site 5 out of 6 in the The Structure of An Aldolase From Prochlorococcus Marinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of An Aldolase From Prochlorococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na347

b:39.4
occ:1.00
 NZ A:LYS265 3.0 12.1 1.0
OE1 A:GLU238 3.1 13.0 1.0
O A:HOH667 3.2 30.2 1.0
O A:HOH377 3.4 32.4 1.0
CE A:LYS265 3.9 13.1 1.0
O A:HOH546 3.9 27.5 1.0
CD A:GLU238 4.1 10.4 1.0
OE2 A:GLU238 4.2 13.1 1.0
O A:HOH684 4.3 34.5 1.0
O A:HOH683 4.5 29.8 1.0

Sodium binding site 6 out of 6 in 3hjz

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Sodium binding site 6 out of 6 in the The Structure of An Aldolase From Prochlorococcus Marinus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of An Aldolase From Prochlorococcus Marinus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na348

b:26.7
occ:1.00
 CD2 A:LEU63 3.3 14.3 1.0
O A:HOH645 3.4 32.4 1.0
CD A:PRO64 3.6 19.6 1.0
CA A:LEU63 3.8 16.4 1.0
O A:THR62 3.9 15.8 1.0
CG2 A:THR62 4.0 16.1 1.0
CG A:LEU63 4.2 16.1 1.0
C A:THR62 4.3 16.1 1.0
N A:LEU63 4.4 16.3 1.0
O A:HOH678 4.5 25.9 1.0
CB A:LEU63 4.5 14.8 1.0
N A:PRO64 4.6 19.5 1.0
CG A:PRO64 4.6 21.2 1.0
C A:LEU63 4.7 17.4 1.0
OE2 A:GLU75 4.9 15.5 1.0
CD A:GLU75 5.0 13.1 1.0

Reference:

L.R.Thompson, Q.Zeng, L.Kelly, K.H.Huang, A.U.Singer, J.Stubbe, S.W.Chisholm. Phage Auxiliary Metabolic Genes and the Redirection of Cyanobacterial Host Carbon Metabolism. Proc.Natl.Acad.Sci.Usa V. 108 E757 2011.
ISSN: ISSN 0027-8424
PubMed: 21844365
DOI: 10.1073/PNAS.1102164108
Page generated: Mon Oct 7 10:24:02 2024

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