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Sodium in PDB 3vs9: Crystal Structure of Type III Pks Arsc Mutant

Enzymatic activity of Crystal Structure of Type III Pks Arsc Mutant

All present enzymatic activity of Crystal Structure of Type III Pks Arsc Mutant:
2.3.1.74;

Protein crystallography data

The structure of Crystal Structure of Type III Pks Arsc Mutant, PDB code: 3vs9 was solved by R.Satou, A.Miyanaga, H.Ozawa, N.Funa, K.Miyazono, M.Tanokura, Y.Ohnishi, S.Horinouchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.78 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.915, 142.720, 129.873, 90.00, 110.43, 90.00
R / Rfree (%) 20.5 / 27.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Type III Pks Arsc Mutant (pdb code 3vs9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Type III Pks Arsc Mutant, PDB code: 3vs9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3vs9

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Sodium binding site 1 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:19.1
occ:1.00
 O C:VAL178 2.3 20.1 1.0
OE2 A:GLU272 2.3 23.4 1.0
O C:HOH872 2.3 20.0 1.0
O C:HOH871 2.3 12.2 1.0
OH A:TYR187 2.5 21.8 1.0
O A:HOH650 3.4 13.4 1.0
C C:VAL178 3.4 21.5 1.0
CD A:GLU272 3.5 22.7 1.0
CZ A:TYR187 3.5 24.2 1.0
O A:HOH688 3.6 21.9 1.0
CE1 A:TYR187 3.7 22.2 1.0
OE2 C:GLU165 3.7 22.3 1.0
SD A:MET184 4.0 20.8 1.0
OE1 A:GLU272 4.0 24.8 1.0
CB C:VAL178 4.3 23.9 1.0
CA C:VAL178 4.3 21.7 1.0
N C:THR179 4.3 21.4 1.0
CG2 A:THR400 4.3 20.8 1.0
O A:HOH617 4.3 18.2 1.0
CA C:THR179 4.4 22.4 1.0
CG A:MET184 4.4 20.1 1.0
N C:VAL178 4.5 23.1 1.0
OG1 A:THR400 4.5 22.4 1.0
CG A:GLU272 4.7 23.5 1.0
CG1 C:VAL178 4.7 24.3 1.0
CE2 A:TYR187 4.8 23.2 1.0
CB A:MET184 4.9 22.0 1.0
CD C:GLU165 4.9 21.7 1.0

Sodium binding site 2 out of 8 in 3vs9

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Sodium binding site 2 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:29.1
occ:1.00
 O B:HOH745 2.4 22.9 1.0
OH B:TYR187 2.4 28.7 1.0
OE1 B:GLU272 2.4 37.9 1.0
O H:HOH659 2.4 27.4 1.0
O H:VAL178 2.4 30.4 1.0
CZ B:TYR187 3.3 29.8 1.0
CE1 B:TYR187 3.5 26.2 1.0
CD B:GLU272 3.5 28.5 1.0
O B:HOH631 3.5 24.3 1.0
C H:VAL178 3.6 30.3 1.0
O B:HOH642 3.7 22.9 1.0
OE2 H:GLU165 3.9 29.4 1.0
SD B:MET184 4.0 27.0 1.0
OE2 B:GLU272 4.0 35.0 1.0
CG B:MET184 4.1 27.1 1.0
O H:HOH629 4.3 14.4 1.0
CB H:VAL178 4.4 30.6 1.0
CA H:VAL178 4.4 30.7 1.0
N H:THR179 4.4 30.0 1.0
OG1 B:THR400 4.5 36.5 1.0
CA H:THR179 4.5 28.9 1.0
CG2 B:THR400 4.5 33.8 1.0
CE2 B:TYR187 4.6 28.5 1.0
N H:VAL178 4.6 31.5 1.0
CG B:GLU272 4.6 31.4 1.0
CD1 B:TYR187 4.8 32.0 1.0
CB B:MET184 4.9 28.9 1.0

Sodium binding site 3 out of 8 in 3vs9

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Sodium binding site 3 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:23.2
occ:1.00
 OE2 C:GLU272 2.3 23.1 1.0
O A:HOH926 2.3 16.5 1.0
OH C:TYR187 2.4 18.1 1.0
O A:VAL178 2.4 23.6 1.0
O A:HOH927 2.5 15.2 1.0
CZ C:TYR187 3.4 19.9 1.0
CD C:GLU272 3.5 23.5 1.0
C A:VAL178 3.5 22.5 1.0
O C:HOH706 3.5 14.2 1.0
OE2 A:GLU165 3.6 23.3 1.0
O C:HOH625 3.7 17.1 1.0
CE1 C:TYR187 3.7 22.4 1.0
SD C:MET184 4.0 22.2 1.0
OE1 C:GLU272 4.1 25.7 1.0
CG C:MET184 4.1 21.4 1.0
O C:HOH629 4.1 14.8 1.0
CA A:VAL178 4.3 23.6 1.0
CG2 C:THR400 4.3 22.2 1.0
CB A:VAL178 4.4 24.1 1.0
N A:THR179 4.4 22.4 1.0
OG1 C:THR400 4.5 24.2 1.0
CA A:THR179 4.5 21.4 1.0
N A:VAL178 4.6 22.7 1.0
CG C:GLU272 4.7 21.1 1.0
CE2 C:TYR187 4.7 22.8 1.0
CD A:GLU165 4.8 25.0 1.0
CB C:MET184 4.8 23.9 1.0
CB C:THR400 5.0 23.6 1.0

Sodium binding site 4 out of 8 in 3vs9

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Sodium binding site 4 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:25.3
occ:1.00
 OE2 D:GLU272 2.0 24.4 1.0
O E:VAL178 2.3 23.2 1.0
O E:HOH652 2.5 17.5 1.0
OH D:TYR187 2.5 21.0 1.0
O E:HOH602 2.6 16.6 1.0
CD D:GLU272 3.2 21.8 1.0
O D:HOH637 3.4 22.9 1.0
C E:VAL178 3.4 22.9 1.0
O E:HOH689 3.5 17.3 1.0
CZ D:TYR187 3.5 23.9 1.0
CE1 D:TYR187 3.6 16.9 1.0
OE1 D:GLU272 3.8 27.6 1.0
SD D:MET184 4.0 21.7 1.0
OE2 E:GLU165 4.0 21.6 1.0
CG D:MET184 4.2 22.3 1.0
CA E:VAL178 4.3 23.8 1.0
CG2 D:THR400 4.4 19.4 1.0
CG D:GLU272 4.4 23.9 1.0
CB E:VAL178 4.4 25.9 1.0
N E:THR179 4.4 22.4 1.0
O D:HOH613 4.4 13.7 1.0
N E:VAL178 4.5 23.0 1.0
OG1 D:THR400 4.5 24.3 1.0
CA E:THR179 4.5 22.8 1.0
CE2 D:TYR187 4.8 14.4 1.0
CB D:MET184 4.9 23.9 1.0
CD1 D:TYR187 5.0 19.2 1.0

Sodium binding site 5 out of 8 in 3vs9

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Sodium binding site 5 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:21.1
occ:1.00
 O D:HOH883 2.2 18.9 1.0
OE2 E:GLU272 2.2 25.9 1.0
O D:VAL178 2.3 21.6 1.0
OH E:TYR187 2.4 25.4 1.0
O D:HOH884 2.4 11.3 1.0
CD E:GLU272 3.4 26.5 1.0
C D:VAL178 3.4 21.7 1.0
CZ E:TYR187 3.5 28.9 1.0
O E:HOH622 3.5 13.9 1.0
O E:HOH659 3.6 20.2 1.0
CE1 E:TYR187 3.7 24.6 1.0
OE2 D:GLU165 3.7 22.1 1.0
SD E:MET184 4.0 21.1 1.0
OE1 E:GLU272 4.0 26.4 1.0
O E:HOH623 4.1 14.1 1.0
CG2 E:THR400 4.3 21.1 1.0
CA D:VAL178 4.3 20.2 1.0
CB D:VAL178 4.3 21.5 1.0
CG E:MET184 4.4 22.1 1.0
N D:THR179 4.4 21.7 1.0
CA D:THR179 4.5 21.9 1.0
OG1 E:THR400 4.5 23.0 1.0
N D:VAL178 4.5 22.1 1.0
CG E:GLU272 4.6 24.6 1.0
CE2 E:TYR187 4.7 23.9 1.0
CG1 D:VAL178 4.9 23.1 1.0
CD D:GLU165 4.9 22.5 1.0
CB E:MET184 4.9 21.1 1.0
CB E:THR400 5.0 20.7 1.0

Sodium binding site 6 out of 8 in 3vs9

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Sodium binding site 6 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:35.4
occ:1.00
 O F:HOH833 2.2 24.2 1.0
OE2 F:GLU272 2.4 40.6 1.0
OH F:TYR187 2.4 30.5 1.0
O G:VAL178 2.4 32.7 1.0
O G:HOH785 2.5 21.9 1.0
CZ F:TYR187 3.3 33.0 1.0
CE1 F:TYR187 3.4 32.5 1.0
CD F:GLU272 3.4 36.0 1.0
C G:VAL178 3.5 34.0 1.0
O G:HOH640 3.7 19.6 1.0
OE2 G:GLU165 3.9 28.8 1.0
SD F:MET184 4.0 32.5 1.0
O F:HOH678 4.0 23.2 1.0
OE1 F:GLU272 4.1 38.7 1.0
CG F:MET184 4.1 31.3 1.0
CG2 F:THR400 4.2 34.0 1.0
O F:HOH650 4.3 25.2 1.0
OG1 F:THR400 4.4 32.6 1.0
CA G:VAL178 4.4 34.2 1.0
N G:THR179 4.4 35.1 1.0
CB G:VAL178 4.5 34.8 1.0
CG F:GLU272 4.5 32.4 1.0
CA G:THR179 4.5 36.0 1.0
CE2 F:TYR187 4.6 33.0 1.0
N G:VAL178 4.6 34.4 1.0
CD1 F:TYR187 4.8 31.3 1.0
CB F:MET184 4.8 33.9 1.0
CB F:THR400 4.9 35.5 1.0

Sodium binding site 7 out of 8 in 3vs9

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Sodium binding site 7 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na501

b:27.9
occ:1.00
 O F:VAL178 2.1 31.3 1.0
OE2 G:GLU272 2.3 28.8 1.0
OH G:TYR187 2.3 37.2 1.0
O F:HOH640 2.4 15.9 1.0
O F:HOH603 2.5 16.3 1.0
C F:VAL178 3.3 32.5 1.0
CD G:GLU272 3.3 32.3 1.0
CZ G:TYR187 3.4 30.9 1.0
O G:HOH642 3.5 20.1 1.0
CE1 G:TYR187 3.6 28.0 1.0
O G:HOH745 3.8 20.7 1.0
OE2 F:GLU165 3.8 36.9 1.0
OE1 G:GLU272 3.8 30.8 1.0
SD G:MET184 4.0 31.0 1.0
CA F:VAL178 4.2 31.9 1.0
N F:THR179 4.3 32.2 1.0
CB F:VAL178 4.4 31.7 1.0
CG G:MET184 4.4 30.5 1.0
OG1 G:THR400 4.4 42.0 1.0
CA F:THR179 4.5 32.9 1.0
N F:VAL178 4.5 34.5 1.0
O F:HOH705 4.5 16.0 1.0
CE2 G:TYR187 4.6 33.8 1.0
CG G:GLU272 4.6 33.9 1.0
CG2 G:THR400 4.7 35.0 1.0
CD F:GLU165 4.9 35.6 1.0
CB G:THR400 5.0 38.5 1.0
CD1 G:TYR187 5.0 29.4 1.0

Sodium binding site 8 out of 8 in 3vs9

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Sodium binding site 8 out of 8 in the Crystal Structure of Type III Pks Arsc Mutant


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 Type III Pks Arsc Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na501

b:32.1
occ:1.00
 OE2 H:GLU272 2.2 33.4 1.0
O B:VAL178 2.3 27.6 1.0
OH H:TYR187 2.5 32.9 1.0
O B:HOH798 2.5 16.7 1.0
O B:HOH630 2.6 24.4 1.0
CD H:GLU272 3.3 33.5 1.0
C B:VAL178 3.4 29.5 1.0
O H:HOH754 3.5 29.4 1.0
CZ H:TYR187 3.5 34.6 1.0
CE1 H:TYR187 3.7 33.6 1.0
OE2 B:GLU165 3.8 34.4 1.0
SD H:MET184 3.9 32.9 1.0
OE1 H:GLU272 3.9 33.1 1.0
O H:HOH693 4.1 17.1 1.0
CA B:VAL178 4.3 29.2 1.0
CG2 H:THR400 4.3 35.3 1.0
CB B:VAL178 4.3 29.5 1.0
OG1 H:THR400 4.3 35.7 1.0
N B:THR179 4.3 27.9 1.0
CG H:MET184 4.4 31.8 1.0
O B:HOH644 4.4 17.9 1.0
CA B:THR179 4.4 29.8 1.0
CG H:GLU272 4.5 30.5 1.0
N B:VAL178 4.5 31.4 1.0
CE2 H:TYR187 4.8 28.6 1.0
CB H:MET184 4.9 30.7 1.0
CB H:THR400 4.9 33.7 1.0
CD B:GLU165 4.9 37.1 1.0
CG1 B:VAL178 5.0 26.7 1.0
CD1 H:TYR187 5.0 30.0 1.0

Reference:

R.Satou, A.Miyanaga, H.Ozawa, N.Funa, Y.Katsuyama, K.Miyazono, M.Tanokura, Y.Ohnishi, S.Horinouchi. Structural Basis For Cyclization Specificity of Two Azotobacter Type III Polyketide Synthases: A Single Amino Acid Substitution Reverses Their Cyclization Specificity J.Biol.Chem. V. 288 34146 2013.
ISSN: ISSN 0021-9258
PubMed: 24100027
DOI: 10.1074/JBC.M113.487272
Page generated: Mon Oct 7 13:52:30 2024

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