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Sodium in PDB 3wvg: Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking

Enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking

All present enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking:
3.1.21.4;

Protein crystallography data

The structure of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking, PDB code: 3wvg was solved by T.Kawamura, T.Kobayashi, N.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.70 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.656, 140.583, 96.294, 90.00, 112.10, 90.00
R / Rfree (%) 17.7 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking (pdb code 3wvg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking, PDB code: 3wvg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3wvg

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Sodium binding site 1 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:35.1
occ:1.00
 O A:ALA109 2.2 26.1 1.0
OP1 E:DA5 2.2 23.8 1.0
OD2 A:ASP93 2.3 34.5 1.0
O A:HOH479 2.3 46.2 1.0
O E:HOH218 2.6 51.1 1.0
OD1 A:ASP108 2.7 50.4 1.0
C A:ALA109 3.3 26.1 1.0
CG A:ASP93 3.3 34.3 1.0
CG A:ASP108 3.4 47.6 1.0
P E:DA5 3.5 27.1 1.0
N A:ALA109 3.6 28.5 1.0
O E:HOH217 3.7 51.0 1.0
OD1 A:ASP93 3.7 32.8 1.0
OD2 A:ASP108 3.8 65.9 1.0
O E:HOH216 3.8 36.6 1.0
NA E:NA101 3.9 37.1 1.0
CA A:ALA109 4.0 28.4 1.0
O5' E:DA5 4.1 24.9 1.0
C5' E:DA5 4.1 26.4 1.0
N A:LYS110 4.3 27.8 1.0
OP2 E:DA5 4.3 23.4 1.0
O A:HOH475 4.3 39.0 1.0
C A:ASP108 4.4 29.1 1.0
CA A:LYS110 4.4 29.5 1.0
OD1 A:ASP68 4.4 67.6 1.0
CB A:ALA109 4.5 29.1 1.0
CA A:ASP108 4.5 30.4 1.0
CB A:ASP108 4.5 37.4 1.0
O3' E:DA4 4.6 24.4 1.0
CB A:ASP93 4.6 28.0 1.0
OG A:SER64 4.7 35.2 1.0
CB A:LYS110 4.8 32.1 1.0

Sodium binding site 2 out of 8 in 3wvg

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Sodium binding site 2 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:40.3
occ:1.00
 O B:ALA109 2.2 31.7 1.0
OP1 F:DA5 2.2 24.5 1.0
OD2 B:ASP93 2.3 30.6 1.0
O B:HOH496 2.3 41.1 1.0
O F:HOH221 2.6 37.5 1.0
OD1 B:ASP108 2.7 57.8 1.0
C B:ALA109 3.1 26.6 1.0
CG B:ASP93 3.3 29.9 1.0
N B:ALA109 3.4 24.8 1.0
O B:HOH490 3.5 31.1 1.0
CG B:ASP108 3.5 49.6 1.0
P F:DA5 3.6 23.9 1.0
OD1 B:ASP93 3.7 32.2 1.0
CA B:ALA109 3.8 25.7 1.0
NA F:NA101 3.8 29.2 1.0
O B:HOH500 3.9 50.1 1.0
OD2 B:ASP108 4.1 57.2 1.0
O5' F:DA5 4.1 22.3 1.0
C5' F:DA5 4.2 20.5 1.0
C B:ASP108 4.2 27.0 1.0
N B:LYS110 4.2 29.5 1.0
O B:HOH499 4.2 36.4 1.0
CB B:ALA109 4.2 24.0 1.0
OD1 B:ASP68 4.3 39.5 1.0
OP2 F:DA5 4.4 22.9 1.0
CA B:ASP108 4.4 29.8 1.0
CA B:LYS110 4.5 29.2 1.0
CB B:ASP108 4.5 36.9 1.0
CB B:ASP93 4.6 25.8 1.0
O3' F:DA4 4.7 20.2 1.0
OG B:SER64 4.8 31.1 1.0
O B:HOH428 5.0 28.9 1.0

Sodium binding site 3 out of 8 in 3wvg

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Sodium binding site 3 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:29.0
occ:1.00
 OP1 G:DA5 2.1 19.5 1.0
O C:ALA109 2.2 26.1 1.0
O C:HOH471 2.3 40.3 1.0
OD2 C:ASP93 2.4 40.4 1.0
O G:HOH220 2.5 34.5 1.0
OD1 C:ASP108 2.5 54.7 1.0
C C:ALA109 3.2 29.9 1.0
CG C:ASP108 3.3 49.9 1.0
CG C:ASP93 3.4 40.4 1.0
N C:ALA109 3.4 29.2 1.0
P G:DA5 3.5 21.5 1.0
O C:HOH476 3.7 58.0 1.0
OD2 C:ASP108 3.7 59.6 1.0
NA G:NA101 3.8 38.9 1.0
CA C:ALA109 3.8 28.6 1.0
OD1 C:ASP93 3.8 45.6 1.0
O C:HOH467 3.9 38.1 1.0
C5' G:DA5 4.1 19.5 1.0
O5' G:DA5 4.1 18.1 1.0
C C:ASP108 4.2 30.1 1.0
N C:LYS110 4.3 30.8 1.0
OP2 G:DA5 4.3 20.9 1.0
O C:HOH468 4.3 33.9 1.0
OD1 C:ASP68 4.3 43.0 1.0
CA C:ASP108 4.4 33.2 1.0
CB C:ALA109 4.4 29.7 1.0
CB C:ASP108 4.4 38.6 1.0
O3' G:DA4 4.6 20.5 1.0
CA C:LYS110 4.6 28.8 1.0
CB C:ASP93 4.7 33.4 1.0
OG C:SER64 4.7 28.2 1.0

Sodium binding site 4 out of 8 in 3wvg

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Sodium binding site 4 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:40.0
occ:1.00
 OP1 H:DA5 2.1 23.6 1.0
O D:ALA109 2.2 29.1 1.0
OD2 D:ASP93 2.3 32.5 1.0
O D:HOH473 2.4 41.0 1.0
OD1 D:ASP108 2.6 52.3 1.0
C D:ALA109 3.3 28.3 1.0
CG D:ASP108 3.4 48.4 1.0
CG D:ASP93 3.4 32.8 1.0
P H:DA5 3.5 24.0 1.0
N D:ALA109 3.5 30.1 1.0
NA D:NA302 3.5 37.3 1.0
O H:HOH118 3.8 33.3 1.0
OD1 D:ASP93 3.8 39.9 1.0
OD2 D:ASP108 3.8 65.2 1.0
CA D:ALA109 4.0 27.8 1.0
O5' H:DA5 4.1 24.7 1.0
C5' H:DA5 4.1 24.3 1.0
OP2 H:DA5 4.3 21.9 1.0
C D:ASP108 4.3 30.6 1.0
O D:HOH474 4.3 29.4 1.0
N D:LYS110 4.3 25.4 1.0
OD1 D:ASP68 4.4 47.3 1.0
CA D:ASP108 4.4 30.1 1.0
CA D:LYS110 4.5 28.6 1.0
CB D:ASP108 4.5 34.7 1.0
O3' H:DA4 4.5 21.1 1.0
CB D:ALA109 4.5 30.8 1.0
CB D:ASP93 4.7 29.9 1.0
CB D:LYS110 4.9 35.5 1.0
OG D:SER64 4.9 28.6 1.0

Sodium binding site 5 out of 8 in 3wvg

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Sodium binding site 5 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:37.3
occ:1.00
 OP1 H:DA5 2.2 23.6 1.0
OD1 D:ASP93 2.3 39.9 1.0
O D:HOH474 2.4 29.4 1.0
O3' H:DA4 2.5 21.1 1.0
O D:HOH475 2.7 23.5 1.0
O D:HOH476 2.8 38.3 1.0
P H:DA5 2.9 24.0 1.0
CG D:ASP93 3.1 32.8 1.0
OD2 D:ASP93 3.4 32.5 1.0
NA D:NA301 3.5 40.0 1.0
O D:HOH477 3.7 42.0 1.0
C3' H:DA4 3.7 19.7 1.0
O5' H:DA5 4.0 24.7 1.0
C4' H:DA4 4.1 19.6 1.0
C5' H:DA5 4.1 24.3 1.0
OP2 H:DA5 4.1 21.9 1.0
O D:ALA91 4.1 29.4 1.0
O D:HOH473 4.2 41.0 1.0
OD2 D:ASP108 4.3 65.2 1.0
O D:GLY92 4.3 28.6 1.0
C2' H:DA4 4.4 21.0 1.0
C D:GLY92 4.5 27.8 1.0
O D:ARG88 4.5 28.7 1.0
CB D:ASP93 4.5 29.9 1.0
C5' H:DA4 4.6 21.6 1.0
N D:ASP93 4.7 28.3 1.0
CG D:ASP108 4.8 48.4 1.0
O D:HOH430 4.8 33.7 1.0
CA D:ASP93 4.8 28.4 1.0
OD1 D:ASP108 4.9 52.3 1.0

Sodium binding site 6 out of 8 in 3wvg

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Sodium binding site 6 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na101

b:38.9
occ:1.00
 OD1 C:ASP93 2.4 45.6 1.0
O C:HOH470 2.4 33.8 1.0
O3' G:DA4 2.4 20.5 1.0
O C:HOH468 2.5 33.9 1.0
OP1 G:DA5 2.5 19.5 1.0
O C:HOH469 2.6 23.9 1.0
P G:DA5 3.1 21.5 1.0
CG C:ASP93 3.2 40.4 1.0
OD2 C:ASP93 3.5 40.4 1.0
C3' G:DA4 3.7 19.9 1.0
O C:HOH473 3.7 35.1 1.0
NA C:NA301 3.8 29.0 1.0
O C:HOH471 4.0 40.3 1.0
O C:ALA91 4.0 23.9 1.0
C4' G:DA4 4.0 20.8 1.0
O5' G:DA5 4.0 18.1 1.0
C5' G:DA5 4.1 19.5 1.0
OP2 G:DA5 4.2 20.9 1.0
O C:GLY92 4.2 31.7 1.0
C2' G:DA4 4.3 19.7 1.0
C C:GLY92 4.4 27.2 1.0
O C:ARG88 4.5 25.6 1.0
CB C:ASP93 4.6 33.4 1.0
OD2 C:ASP108 4.6 59.6 1.0
C5' G:DA4 4.6 20.4 1.0
N C:ASP93 4.7 26.4 1.0
CA C:ASP93 4.8 30.8 1.0
CA C:GLY92 5.0 25.9 1.0

Sodium binding site 7 out of 8 in 3wvg

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Sodium binding site 7 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:37.1
occ:1.00
 OD1 A:ASP93 2.3 32.8 1.0
O3' E:DA4 2.4 24.4 1.0
OP1 E:DA5 2.4 23.8 1.0
O A:HOH474 2.5 23.2 1.0
O A:HOH475 2.6 39.0 1.0
O A:HOH476 2.6 35.1 1.0
P E:DA5 3.0 27.1 1.0
CG A:ASP93 3.3 34.3 1.0
C3' E:DA4 3.6 22.6 1.0
O A:HOH480 3.6 44.2 1.0
OD2 A:ASP93 3.7 34.5 1.0
NA A:NA301 3.9 35.1 1.0
O A:ALA91 3.9 28.9 1.0
C4' E:DA4 3.9 22.2 1.0
O5' E:DA5 4.0 24.9 1.0
C5' E:DA5 4.0 26.4 1.0
O A:HOH479 4.2 46.2 1.0
OP2 E:DA5 4.2 23.4 1.0
C2' E:DA4 4.3 22.2 1.0
O A:ARG88 4.4 33.5 1.0
O A:GLY92 4.4 27.3 1.0
C A:GLY92 4.4 27.8 1.0
OD2 A:ASP108 4.5 65.9 1.0
C5' E:DA4 4.6 22.8 1.0
O A:HOH472 4.6 42.0 1.0
CB A:ASP93 4.6 28.0 1.0
N A:ASP93 4.7 27.1 1.0
CA A:ASP93 4.8 27.6 1.0
CA A:GLY92 4.9 29.0 0.9
C A:ALA91 5.0 28.8 1.0

Sodium binding site 8 out of 8 in 3wvg

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Sodium binding site 8 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Time-Resolved Crystal Structure of Hindiii with 0SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na101

b:29.2
occ:1.00
 OP1 F:DA5 2.4 24.5 1.0
OD1 B:ASP93 2.4 32.2 1.0
O B:HOH499 2.4 36.4 1.0
O B:HOH498 2.4 24.3 1.0
O B:HOH497 2.4 24.7 1.0
O3' F:DA4 2.5 20.2 1.0
P F:DA5 3.0 23.9 1.0
CG B:ASP93 3.3 29.9 1.0
OD2 B:ASP93 3.5 30.6 1.0
C3' F:DA4 3.7 21.6 1.0
NA B:NA301 3.8 40.3 1.0
O B:HOH501 4.0 36.4 1.0
O5' F:DA5 4.0 22.3 1.0
C5' F:DA5 4.0 20.5 1.0
O B:ALA91 4.0 24.7 1.0
C4' F:DA4 4.1 22.3 1.0
O B:HOH496 4.1 41.1 1.0
OP2 F:DA5 4.3 22.9 1.0
C2' F:DA4 4.3 22.1 1.0
O B:GLY92 4.3 30.4 1.0
OD2 B:ASP108 4.4 57.2 1.0
O B:ARG88 4.5 26.7 1.0
C B:GLY92 4.5 24.4 1.0
CB B:ASP93 4.6 25.8 1.0
O B:HOH428 4.6 28.9 1.0
C5' F:DA4 4.6 21.0 1.0
N B:ASP93 4.8 20.8 1.0
CA B:ASP93 4.8 26.5 1.0
CG B:ASP108 5.0 49.6 1.0
OD1 B:ASP108 5.0 57.8 1.0

Reference:

T.Kawamura, T.Kobayashi, N.Watanabe. Analysis of the Hindiii-Catalyzed Reaction By Time-Resolved Crystallography Acta Crystallogr.,Sect.D V. 71 256 2015.
ISSN: ISSN 0907-4449
PubMed: 25664735
DOI: 10.1107/S1399004714025188
Page generated: Sun Aug 17 18:14:07 2025

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