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Sodium in PDB 6ucz: Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate

Enzymatic activity of Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate

All present enzymatic activity of Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate:
2.5.1.15;

Protein crystallography data

The structure of Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate, PDB code: 6ucz 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) 38.75 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 48.830, 81.480, 71.170, 90.00, 102.67, 90.00
R / Rfree (%) 16.2 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate (pdb code 6ucz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate, PDB code: 6ucz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6ucz

Go back to Sodium Binding Sites List in 6ucz
Sodium binding site 1 out of 5 in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate


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 Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:64.3
occ:1.00
 CA A:HIS108 4.1 39.1 1.0
O A:VAL109 4.1 33.5 1.0
C A:HIS108 4.1 39.7 1.0
CD2 A:HIS105 4.2 36.4 1.0
CG A:GLU110 4.3 40.1 1.0
N A:VAL109 4.4 33.8 1.0
C A:VAL109 4.4 33.3 1.0
O A:HOH493 4.5 52.7 1.0
O A:HIS108 4.5 39.6 1.0
CG A:HIS105 4.7 41.2 1.0
N A:GLU110 4.7 34.5 1.0
CA A:HIS105 4.8 39.0 1.0
NE2 A:HIS105 4.8 41.4 1.0
CA A:GLU110 4.9 34.9 1.0
O A:HIS105 4.9 42.9 1.0
CB A:HIS108 4.9 52.2 1.0
OD1 A:ASP130 4.9 36.8 1.0
CA A:VAL109 5.0 31.0 1.0

Sodium binding site 2 out of 5 in 6ucz

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Sodium binding site 2 out of 5 in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate


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 Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:67.0
occ:1.00
 O B:PRO79 3.7 56.3 1.0
C B:PRO79 4.1 61.8 1.0
CA B:GLY80 4.3 64.2 1.0
N B:GLY80 4.3 62.3 1.0
OD1 A:ASP142 4.4 49.3 1.0
CB B:PRO79 4.5 63.0 1.0
O A:PRO141 4.5 50.7 1.0
CB A:PRO141 4.5 57.4 1.0
CG B:PRO79 4.6 67.9 1.0
CA B:PRO79 4.9 61.0 1.0
C A:PRO141 5.0 50.6 1.0

Sodium binding site 3 out of 5 in 6ucz

Go back to Sodium Binding Sites List in 6ucz
Sodium binding site 3 out of 5 in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate


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 Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:46.8
occ:1.00
 O B:HOH542 2.4 57.9 1.0
N B:ASN37 3.1 27.2 1.0
NA B:NA305 3.4 62.8 1.0
O B:ASN37 3.7 32.8 1.0
O B:ILE35 3.9 28.1 1.0
CA B:LEU36 4.0 26.5 1.0
CA B:ASN37 4.0 27.7 1.0
C B:LEU36 4.0 25.7 1.0
CB B:ASN37 4.1 32.4 1.0
C B:ASN37 4.3 33.0 1.0
CD1 B:LEU36 4.3 40.9 1.0
O B:HOH487 4.3 49.0 1.0
C B:ILE35 4.6 26.2 1.0
ND1 B:HIS58 4.6 57.8 1.0
N B:LEU36 4.6 27.3 1.0
O B:HOH459 4.7 29.3 1.0

Sodium binding site 4 out of 5 in 6ucz

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Sodium binding site 4 out of 5 in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate


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 Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:62.8
occ:1.00
 CB B:HIS58 3.2 37.6 1.0
NA B:NA304 3.4 46.8 1.0
O B:ILE35 3.5 28.1 1.0
O B:HOH459 3.6 29.3 1.0
CG B:HIS58 3.6 55.5 1.0
CD1 B:LEU36 3.7 40.9 1.0
ND1 B:HIS58 3.9 57.8 1.0
CD1 B:LEU62 4.1 24.4 1.0
CA B:HIS58 4.2 38.0 1.0
CG B:LEU62 4.3 30.0 1.0
CA B:LEU36 4.4 26.5 1.0
O B:HIS58 4.4 27.9 1.0
CD2 B:HIS58 4.5 61.4 1.0
C B:HIS58 4.5 34.7 1.0
CD2 B:LEU62 4.5 31.8 1.0
C B:ILE35 4.6 26.2 1.0
O B:HOH542 4.7 57.9 1.0
CB B:LEU36 4.7 24.0 1.0
CE1 B:HIS58 4.8 58.3 1.0
CG B:LEU36 4.8 36.4 1.0
O B:HOH408 4.9 53.3 1.0
N B:LEU36 5.0 27.3 1.0

Sodium binding site 5 out of 5 in 6ucz

Go back to Sodium Binding Sites List in 6ucz
Sodium binding site 5 out of 5 in the Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate


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 Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:51.1
occ:1.00
 O B:HOH403 2.6 57.0 1.0
O B:SER169 3.2 53.7 1.0
C B:SER169 3.9 40.4 1.0
CA B:SER169 4.0 42.9 1.0
O B:ARG168 4.5 48.4 1.0
O B:VAL171 4.6 47.8 1.0
CB B:SER169 4.8 61.5 1.0

Reference:

M.J.Bolejack, S.L.Delker, J.Abendroth, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Dihydropteroate Synthase From Anaplasma Phagocytophilum with Bound 6-Hydroxymethylpterin-Monophosphate To Be Published.
Page generated: Tue Oct 8 14:09:37 2024

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