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Sodium in PDB 3tos: Crystal Structure of CALS11, Calicheamicin Methyltransferase

Protein crystallography data

The structure of Crystal Structure of CALS11, Calicheamicin Methyltransferase, PDB code: 3tos was solved by A.Chang, D.J.Aceti, E.T.Beebe, S.-I.Makino, R.L.Wrobel, C.A.Bingman, J.S.Thorson, G.N.Phillips Jr., Center For Eukaryotic Structuralgenomics (Cesg), Enzyme Discovery For Natural Product Biosynthesis(Natpro), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.10 / 1.55
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 78.321, 106.080, 106.330, 68.69, 69.63, 88.56
R / Rfree (%) 14.6 / 17.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of CALS11, Calicheamicin Methyltransferase (pdb code 3tos). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of CALS11, Calicheamicin Methyltransferase, PDB code: 3tos:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3tos

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Sodium binding site 1 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na260

b:10.3
occ:1.00
O A:ASP216 2.7 10.7 1.0
O2 A:EDO261 2.8 20.4 1.0
OE2 A:GLU217 2.8 10.0 0.6
OD1 A:ASP216 2.9 14.3 1.0
OXT A:GLU259 2.9 27.7 1.0
O A:HOH1959 3.1 19.2 1.0
O A:HOH3075 3.1 30.9 1.0
CD A:GLU217 3.3 9.5 0.6
CG A:ASP216 3.6 12.7 1.0
OE1 A:GLU217 3.7 9.8 0.6
CB A:ALA249 3.7 11.7 1.0
C2 A:EDO261 3.7 21.1 1.0
O A:HOH595 3.7 36.2 1.0
C A:ASP216 3.8 10.3 1.0
N A:GLU259 3.9 23.2 1.0
O A:HOH2717 3.9 22.9 1.0
OD2 A:ASP216 4.0 14.4 1.0
C A:GLU259 4.1 27.6 1.0
CG A:GLU217 4.2 8.2 0.6
OE2 A:GLU217 4.3 15.5 0.4
O A:HOH3297 4.4 30.7 1.0
CB A:ASP216 4.5 10.9 1.0
CA A:ASP216 4.5 10.3 1.0
CA A:GLU259 4.7 25.8 1.0
N A:GLU217 4.8 10.4 0.4
N A:GLU217 4.8 9.3 0.6
O A:HOH265 4.8 40.1 1.0
CA A:GLU217 4.9 10.7 0.4
CA A:GLU217 4.9 8.7 0.6
O A:HOH1402 5.0 14.6 1.0
O A:HOH2166 5.0 19.7 1.0
O A:HOH3115 5.0 36.4 1.0

Sodium binding site 2 out of 10 in 3tos

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Sodium binding site 2 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na260

b:9.9
occ:1.00
O B:ASP216 2.7 11.1 1.0
OE2 B:GLU217 2.9 9.8 0.6
OD1 B:ASP216 2.9 15.7 1.0
O B:GLU259 2.9 25.4 1.0
O2 B:EDO261 2.9 23.9 1.0
O B:HOH3520 3.0 23.8 1.0
O B:HOH1917 3.2 19.6 1.0
CD B:GLU217 3.3 9.4 0.6
CG B:ASP216 3.5 15.3 1.0
CB B:ALA249 3.6 10.5 1.0
OE1 B:GLU217 3.6 9.2 0.6
C B:ASP216 3.8 10.2 1.0
O B:HOH2418 3.8 24.7 1.0
O B:HOH3146 3.8 31.1 1.0
C2 B:EDO261 3.8 24.6 1.0
OD2 B:ASP216 3.9 16.2 1.0
N B:GLU259 4.0 23.7 1.0
C B:GLU259 4.1 25.4 1.0
CG B:GLU217 4.2 8.5 0.6
O B:HOH3201 4.2 32.0 1.0
OE2 B:GLU217 4.3 15.4 0.5
CA B:ASP216 4.5 10.2 1.0
CB B:ASP216 4.5 11.3 1.0
CA B:GLU259 4.7 23.7 1.0
O B:HOH544 4.8 32.3 1.0
N B:GLU217 4.8 10.3 0.5
N B:GLU217 4.8 9.3 0.6
O B:HOH3643 4.8 32.3 1.0
CA B:GLU217 4.9 10.9 0.5
CA B:GLU217 5.0 9.4 0.6
O B:HOH4602 5.0 52.8 1.0

Sodium binding site 3 out of 10 in 3tos

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Sodium binding site 3 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na260

b:9.2
occ:1.00
O C:ASP216 2.7 11.8 1.0
OE2 C:GLU217 2.8 10.5 0.6
OD1 C:ASP216 2.9 15.6 1.0
O C:GLU259 2.9 21.1 1.0
O1 C:EDO261 2.9 23.9 1.0
O C:HOH472 3.0 21.3 1.0
O C:HOH1805 3.0 16.3 1.0
CD C:GLU217 3.3 9.3 0.6
CG C:ASP216 3.6 13.6 1.0
C1 C:EDO261 3.6 19.4 1.0
OE1 C:GLU217 3.6 8.9 0.6
CB C:ALA249 3.7 10.8 1.0
O C:HOH596 3.8 32.4 1.0
C C:ASP216 3.8 9.7 1.0
N C:GLU259 4.0 21.9 1.0
O C:HOH2712 4.0 22.7 1.0
OD2 C:ASP216 4.0 13.8 1.0
C C:GLU259 4.0 23.3 1.0
CG C:GLU217 4.1 9.1 0.6
O C:HOH3194 4.1 31.5 1.0
CA C:ASP216 4.5 9.5 1.0
CB C:ASP216 4.5 11.0 1.0
OE1 C:GLU217 4.5 18.4 0.4
CA C:GLU259 4.7 22.8 1.0
O C:HOH688 4.7 47.1 1.0
N C:GLU217 4.8 10.3 0.4
N C:GLU217 4.8 9.3 0.6
O C:HOH4195 4.9 32.5 1.0
CA C:GLU217 4.9 9.3 0.6
CA C:GLU217 5.0 11.0 0.4
O C:HOH573 5.0 27.1 1.0
O C:HOH1461 5.0 12.4 1.0

Sodium binding site 4 out of 10 in 3tos

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Sodium binding site 4 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na260

b:11.7
occ:1.00
O D:ASP216 2.7 10.1 1.0
OE2 D:GLU217 2.8 11.8 0.6
OXT D:GLU259 2.8 26.8 1.0
O2 D:EDO261 2.9 23.8 1.0
OD1 D:ASP216 2.9 15.8 1.0
O D:HOH2055 3.1 21.4 1.0
O D:HOH3306 3.2 33.8 1.0
CD D:GLU217 3.3 9.9 0.6
CG D:ASP216 3.6 14.9 1.0
OE1 D:GLU217 3.6 9.4 0.6
CB D:ALA249 3.6 8.9 1.0
O D:HOH3668 3.6 33.7 1.0
C2 D:EDO261 3.8 23.0 1.0
C D:ASP216 3.8 10.8 1.0
O D:HOH2389 3.9 23.6 1.0
N D:GLU259 4.0 27.7 1.0
OD2 D:ASP216 4.0 17.5 1.0
C D:GLU259 4.0 27.7 1.0
CG D:GLU217 4.2 9.5 0.6
O D:HOH3661 4.2 31.1 1.0
OE1 D:GLU217 4.4 17.9 0.4
CB D:ASP216 4.5 12.5 1.0
CA D:ASP216 4.5 11.2 1.0
CA D:GLU259 4.7 28.4 1.0
N D:GLU217 4.8 11.1 0.6
N D:GLU217 4.8 12.0 0.4
O D:HOH736 4.9 27.0 1.0
CA D:GLU217 4.9 10.8 0.6
CA D:GLU217 4.9 12.5 0.4
O D:HOH1793 5.0 14.7 1.0
O D:GLU259 5.0 28.4 1.0
O D:HOH652 5.0 43.6 1.0
O D:HOH1399 5.0 18.3 1.0

Sodium binding site 5 out of 10 in 3tos

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Sodium binding site 5 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na260

b:12.3
occ:1.00
O E:ASP216 2.7 10.4 1.0
O E:GLU259 2.9 33.4 1.0
OD1 E:ASP216 2.9 16.6 1.0
OE2 E:GLU217 2.9 13.3 0.6
O2 E:EDO261 2.9 24.7 1.0
O E:HOH2297 3.1 20.8 1.0
O E:HOH3412 3.2 32.7 1.0
CD E:GLU217 3.3 11.2 0.6
OE1 E:GLU217 3.5 10.8 0.6
CG E:ASP216 3.6 14.8 1.0
O E:HOH3081 3.6 31.1 1.0
CB E:ALA249 3.6 10.2 1.0
C2 E:EDO261 3.8 19.0 1.0
C E:ASP216 3.8 9.7 1.0
O E:HOH2568 3.9 27.4 1.0
N E:GLU259 4.0 32.7 1.0
OD2 E:ASP216 4.0 16.7 1.0
C E:GLU259 4.1 34.0 1.0
CG E:GLU217 4.2 10.0 0.6
O E:HOH3595 4.2 33.8 1.0
OE1 E:GLU217 4.3 15.9 0.5
CB E:ASP216 4.5 11.4 1.0
CA E:ASP216 4.5 10.1 1.0
CA E:GLU259 4.7 33.8 1.0
N E:GLU217 4.8 10.8 0.5
N E:GLU217 4.8 10.1 0.6
CA E:GLU217 4.9 9.7 0.6
CA E:GLU217 4.9 11.3 0.5
O E:HOH1773 5.0 19.1 1.0
O E:HOH262 5.0 20.6 1.0
O E:HOH3409 5.0 36.4 1.0
O E:HOH1765 5.0 17.0 1.0

Sodium binding site 6 out of 10 in 3tos

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Sodium binding site 6 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na260

b:9.0
occ:1.00
O F:ASP216 2.7 10.3 1.0
OD1 F:ASP216 2.9 15.9 1.0
OE2 F:GLU217 2.9 9.3 0.6
O F:GLU259 2.9 25.3 1.0
O1 F:EDO261 2.9 24.5 1.0
O F:HOH3682 3.0 28.2 1.0
O F:HOH1850 3.1 20.9 1.0
CD F:GLU217 3.3 8.3 0.6
CG F:ASP216 3.5 14.4 1.0
OE1 F:GLU217 3.6 8.4 0.6
CB F:ALA249 3.6 10.4 1.0
O F:HOH3812 3.8 35.2 1.0
C F:ASP216 3.8 9.9 1.0
C1 F:EDO261 3.8 26.1 1.0
O F:HOH2207 4.0 23.7 1.0
N F:GLU259 4.0 24.9 1.0
OD2 F:ASP216 4.0 17.6 1.0
C F:GLU259 4.1 26.4 1.0
CG F:GLU217 4.1 8.1 0.6
OE1 F:GLU217 4.3 17.1 0.5
O F:HOH2723 4.4 30.1 1.0
O F:HOH4672 4.4 47.0 1.0
CA F:ASP216 4.5 10.0 1.0
CB F:ASP216 4.5 9.8 1.0
CA F:GLU259 4.7 25.2 1.0
N F:GLU217 4.8 10.6 0.5
N F:GLU217 4.8 9.3 0.6
O F:HOH5221 4.8 43.0 1.0
O F:HOH568 4.9 37.2 1.0
CA F:GLU217 4.9 9.1 0.6
CA F:GLU217 4.9 11.5 0.5
O F:HOH668 5.0 36.2 1.0
OXT F:GLU259 5.0 28.2 1.0

Sodium binding site 7 out of 10 in 3tos

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Sodium binding site 7 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na260

b:9.4
occ:1.00
O G:ASP216 2.7 10.2 1.0
OD1 G:ASP216 2.8 16.1 1.0
O G:GLU259 2.9 23.1 1.0
OE2 G:GLU217 2.9 8.8 0.6
O G:HOH876 3.0 21.8 1.0
O2 G:EDO261 3.0 24.2 1.0
O G:HOH1761 3.1 16.6 1.0
CD G:GLU217 3.3 8.4 0.6
CG G:ASP216 3.6 14.3 1.0
C2 G:EDO261 3.6 22.9 1.0
OE1 G:GLU217 3.6 8.3 0.6
CB G:ALA249 3.7 9.7 1.0
O G:HOH3904 3.7 30.8 1.0
C G:ASP216 3.8 9.5 1.0
O G:HOH2107 4.0 22.0 1.0
N G:GLU259 4.0 24.4 1.0
OD2 G:ASP216 4.0 14.7 1.0
C G:GLU259 4.1 25.1 1.0
CG G:GLU217 4.1 7.4 0.6
O G:HOH3059 4.2 30.6 1.0
OE1 G:GLU217 4.4 15.3 0.5
CA G:ASP216 4.5 9.5 1.0
CB G:ASP216 4.5 10.7 1.0
CA G:GLU259 4.7 24.1 1.0
O G:HOH264 4.7 45.2 1.0
N G:GLU217 4.8 10.3 0.5
N G:GLU217 4.8 8.9 0.6
O G:HOH1345 4.9 12.1 1.0
O G:HOH3236 4.9 34.0 1.0
CA G:GLU217 4.9 9.7 0.6
O G:HOH598 4.9 28.2 1.0
CA G:GLU217 4.9 12.1 0.5
O G:HOH2059 5.0 17.4 1.0
OXT G:GLU259 5.0 26.5 1.0

Sodium binding site 8 out of 10 in 3tos

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Sodium binding site 8 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


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 CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na260

b:10.9
occ:1.00
O H:ASP216 2.7 11.3 1.0
O2 H:EDO261 2.8 21.8 1.0
OXT H:GLU259 2.9 23.4 1.0
OD1 H:ASP216 2.9 16.2 1.0
OE2 H:GLU217 2.9 11.3 0.6
O H:HOH522 3.1 27.0 1.0
O H:HOH1525 3.1 16.3 1.0
CD H:GLU217 3.3 11.0 0.6
CG H:ASP216 3.5 15.7 1.0
O H:HOH1025 3.6 36.8 1.0
OE1 H:GLU217 3.7 11.4 0.6
C2 H:EDO261 3.7 20.5 1.0
CB H:ALA249 3.7 12.8 1.0
C H:ASP216 3.8 10.7 1.0
OD2 H:ASP216 3.9 15.9 1.0
O H:HOH3740 4.0 22.4 1.0
N H:GLU259 4.0 23.7 1.0
CG H:GLU217 4.0 10.2 0.6
C H:GLU259 4.0 25.4 1.0
OE1 H:GLU217 4.3 16.2 0.4
O H:HOH3770 4.4 30.6 1.0
CB H:ASP216 4.4 12.4 1.0
CA H:ASP216 4.5 11.8 1.0
CA H:GLU259 4.7 24.9 1.0
N H:GLU217 4.8 11.9 0.4
N H:GLU217 4.8 11.1 0.6
O H:HOH4313 4.9 48.3 1.0
CA H:GLU217 4.9 11.2 0.6
CA H:GLU217 5.0 12.7 0.4
O H:HOH2658 5.0 19.2 1.0
O H:HOH1597 5.0 16.1 1.0
O H:GLU259 5.0 26.1 1.0

Sodium binding site 9 out of 10 in 3tos

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Sodium binding site 9 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na259

b:9.6
occ:1.00
O I:ASP216 2.7 9.9 1.0
OD1 I:ASP216 2.9 15.8 1.0
OE2 I:GLU217 2.9 9.8 0.6
O1 I:EDO260 2.9 21.8 1.0
O I:GLU258 2.9 25.6 1.0
O I:HOH2780 2.9 26.1 1.0
O I:HOH1770 3.1 17.9 1.0
CD I:GLU217 3.3 9.1 0.6
CG I:ASP216 3.6 14.7 1.0
OE1 I:GLU217 3.6 9.9 0.6
CB I:ALA249 3.6 11.4 1.0
C1 I:EDO260 3.6 26.5 1.0
O I:HOH559 3.7 36.2 1.0
C I:ASP216 3.8 9.0 1.0
O I:HOH2368 3.9 21.9 1.0
OD2 I:ASP216 4.0 17.8 1.0
N I:GLU258 4.0 26.1 1.0
C I:GLU258 4.0 26.8 1.0
CG I:GLU217 4.2 6.8 0.6
OE1 I:GLU217 4.3 16.0 0.4
O I:HOH3038 4.3 29.3 1.0
O I:HOH5958 4.3 45.1 1.0
CB I:ASP216 4.5 11.3 1.0
CA I:ASP216 4.5 9.1 1.0
CA I:GLU258 4.7 26.1 1.0
N I:GLU217 4.8 9.9 0.4
N I:GLU217 4.8 8.8 0.6
O I:HOH4255 4.9 43.8 1.0
O I:HOH2242 4.9 16.9 1.0
O I:HOH868 4.9 29.4 1.0
CA I:GLU217 4.9 10.4 0.4
CA I:GLU217 5.0 8.1 0.6
OXT I:GLU258 5.0 27.9 1.0

Sodium binding site 10 out of 10 in 3tos

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Sodium binding site 10 out of 10 in the Crystal Structure of CALS11, Calicheamicin Methyltransferase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of CALS11, Calicheamicin Methyltransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na260

b:11.0
occ:1.00
O J:ASP216 2.8 10.7 1.0
O1 J:EDO262 2.8 25.9 1.0
OD1 J:ASP216 2.8 14.9 1.0
OE2 J:GLU217 2.9 11.2 0.6
OXT J:GLU259 2.9 22.4 1.0
O J:HOH2617 3.1 27.9 1.0
O J:HOH1686 3.1 16.3 1.0
CD J:GLU217 3.3 9.9 0.6
CG J:ASP216 3.5 15.0 1.0
C1 J:EDO262 3.6 23.5 1.0
OE1 J:GLU217 3.6 10.1 0.6
O J:HOH3578 3.6 30.4 1.0
CB J:ALA249 3.7 10.9 1.0
O J:HOH3055 3.8 22.4 1.0
C J:ASP216 3.8 10.4 1.0
OD2 J:ASP216 4.0 16.5 1.0
N J:GLU259 4.1 23.9 1.0
CG J:GLU217 4.1 8.5 0.6
C J:GLU259 4.1 24.9 1.0
O J:HOH3419 4.4 29.8 1.0
OE1 J:GLU217 4.4 16.1 0.4
CB J:ASP216 4.5 11.7 1.0
CA J:ASP216 4.5 10.9 1.0
CA J:GLU259 4.7 24.9 1.0
N J:GLU217 4.8 11.0 0.4
N J:GLU217 4.8 9.8 0.6
CA J:GLU217 4.9 9.7 0.6
CA J:GLU217 4.9 11.9 0.4
O J:HOH546 4.9 38.4 1.0
O J:HOH4877 4.9 42.0 1.0
O J:HOH927 4.9 34.3 1.0

Reference:

A.Chang, D.J.Aceti, E.T.Beebe, S.-I.Makino, R.L.Wrobel, C.A.Bingman, J.S.Thorson, G.N.Phillips Jr.. Crystal Structure of CALS11, Calicheamicin Methyltransferase To Be Published.
Page generated: Tue Dec 15 06:26:32 2020

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