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Manganese in PDB 3wvh: Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking

Enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking

All present enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking:
3.1.21.4;

Protein crystallography data

The structure of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking, PDB code: 3wvh 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) 32.91 / 2.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.782, 143.285, 94.324, 90.00, 113.49, 90.00
R / Rfree (%) 17.6 / 24.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking (pdb code 3wvh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking, PDB code: 3wvh:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3wvh

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Manganese binding site 1 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:22.1
occ:1.00
 OP1 F:DA5 2.1 16.4 1.0
O B:ALA109 2.1 20.5 1.0
O B:HOH468 2.2 13.7 1.0
OD2 B:ASP93 2.2 19.8 1.0
OD1 B:ASP108 2.3 29.2 1.0
O F:HOH216 2.5 17.1 1.0
CG B:ASP108 3.1 29.0 1.0
C B:ALA109 3.2 19.9 1.0
CG B:ASP93 3.2 22.3 1.0
P F:DA5 3.4 15.1 1.0
N B:ALA109 3.5 19.4 1.0
OD2 B:ASP108 3.6 37.0 1.0
OD1 B:ASP93 3.6 23.3 1.0
MN F:MN101 3.8 27.4 0.4
CA B:ALA109 3.9 19.8 1.0
O F:HOH214 3.9 26.2 1.0
OP2 F:DA5 4.1 15.5 1.0
O5' F:DA5 4.1 14.1 1.0
C B:ASP108 4.1 19.7 1.0
C5' F:DA5 4.2 14.1 1.0
N B:LYS110 4.2 22.3 1.0
CA B:ASP108 4.3 21.0 1.0
CB B:ASP108 4.3 24.3 1.0
CA B:LYS110 4.4 23.2 1.0
O B:HOH476 4.4 20.1 1.0
OD1 B:ASP68 4.4 30.9 1.0
CB B:ALA109 4.5 20.0 1.0
O3' F:DA4 4.5 15.1 1.0
CB B:ASP93 4.5 22.0 1.0
CB B:LYS110 4.8 25.9 1.0
O B:HOH419 5.0 16.1 1.0

Manganese binding site 2 out of 8 in 3wvh

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Manganese binding site 2 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:19.1
occ:1.00
 O A:ALA109 2.0 21.3 1.0
OP1 E:DA5 2.0 14.0 1.0
OD2 A:ASP93 2.1 16.2 1.0
O A:HOH466 2.2 19.4 1.0
OD1 A:ASP108 2.5 27.5 1.0
O A:HOH472 2.5 17.2 1.0
CG A:ASP108 3.0 27.5 1.0
C A:ALA109 3.1 21.8 1.0
CG A:ASP93 3.1 18.1 1.0
OD2 A:ASP108 3.2 36.2 1.0
N A:ALA109 3.4 22.2 1.0
P E:DA5 3.4 14.7 1.0
O A:HOH423 3.5 29.9 1.0
OD1 A:ASP93 3.5 20.0 1.0
MN E:MN101 3.8 20.4 0.5
CA A:ALA109 3.9 21.7 1.0
C5' E:DA5 4.0 12.8 1.0
O5' E:DA5 4.0 13.3 1.0
O E:HOH202 4.1 20.4 1.0
C A:ASP108 4.1 23.8 1.0
OP2 E:DA5 4.1 14.6 1.0
N A:LYS110 4.2 21.3 1.0
CB A:ASP108 4.2 26.3 1.0
CA A:ASP108 4.3 24.1 1.0
O A:HOH470 4.3 21.3 1.0
OD1 A:ASP68 4.3 33.0 1.0
CA A:LYS110 4.4 23.1 1.0
CB A:ASP93 4.5 17.6 1.0
O3' E:DA4 4.5 14.8 1.0
CB A:ALA109 4.5 22.0 1.0
CB A:LYS110 4.8 25.6 1.0

Manganese binding site 3 out of 8 in 3wvh

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Manganese binding site 3 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:24.1
occ:1.00
 OP1 H:DA5 2.1 15.2 1.0
O D:ALA109 2.1 21.2 1.0
OD1 D:ASP108 2.2 33.8 1.0
OD2 D:ASP93 2.2 22.1 1.0
O D:HOH442 2.3 28.7 1.0
O H:HOH215 2.4 20.1 1.0
CG D:ASP108 2.9 30.7 1.0
C D:ALA109 3.2 22.4 1.0
OD2 D:ASP108 3.3 34.9 1.0
N D:ALA109 3.3 21.9 1.0
CG D:ASP93 3.3 24.6 1.0
P H:DA5 3.4 18.7 1.0
O H:HOH216 3.8 25.9 1.0
CA D:ALA109 3.8 22.2 1.0
OD1 D:ASP93 3.9 29.2 1.0
MN H:MN101 4.0 27.0 0.5
O5' H:DA5 4.0 15.8 1.0
OP2 H:DA5 4.1 17.9 1.0
C D:ASP108 4.1 22.4 1.0
C5' H:DA5 4.1 14.1 1.0
CB D:ASP108 4.1 25.8 1.0
O D:HOH444 4.2 30.5 1.0
O H:HOH207 4.2 27.6 1.0
N D:LYS110 4.2 23.3 1.0
CA D:ASP108 4.2 22.9 1.0
CB D:ALA109 4.3 23.7 1.0
CA D:LYS110 4.4 25.3 1.0
OD1 D:ASP68 4.5 34.7 1.0
O3' H:DA4 4.5 17.6 1.0
CB D:ASP93 4.6 24.3 1.0
CB D:LYS110 4.8 28.4 1.0

Manganese binding site 4 out of 8 in 3wvh

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Manganese binding site 4 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:21.8
occ:1.00
 OP1 G:DA5 2.0 17.4 1.0
O C:ALA109 2.1 21.9 1.0
O C:HOH479 2.2 15.0 1.0
OD2 C:ASP93 2.2 20.4 1.0
O C:HOH477 2.3 13.7 1.0
OD1 C:ASP108 2.4 37.3 1.0
CG C:ASP108 3.1 34.0 1.0
C C:ALA109 3.2 23.1 1.0
OD2 C:ASP108 3.3 39.6 1.0
P G:DA5 3.3 16.5 1.0
CG C:ASP93 3.3 22.0 1.0
N C:ALA109 3.5 24.6 1.0
O C:HOH451 3.8 40.8 1.0
OD1 C:ASP93 3.8 23.9 1.0
MN G:MN101 3.9 21.9 0.5
CA C:ALA109 3.9 24.8 1.0
O5' G:DA5 4.0 16.2 1.0
OP2 G:DA5 4.0 18.0 1.0
N C:LYS110 4.1 24.3 1.0
C5' G:DA5 4.1 16.1 1.0
O C:HOH483 4.1 26.8 1.0
C C:ASP108 4.2 26.1 1.0
OD1 C:ASP68 4.2 28.7 1.0
CB C:ASP108 4.3 29.5 1.0
CA C:ASP108 4.3 27.0 1.0
CA C:LYS110 4.3 23.6 1.0
O G:HOH211 4.5 35.8 1.0
O3' G:DA4 4.5 17.1 1.0
CB C:ASP93 4.6 21.4 1.0
CB C:ALA109 4.6 24.9 1.0
CB C:LYS110 4.7 25.2 1.0
OG C:SER64 4.9 27.3 1.0

Manganese binding site 5 out of 8 in 3wvh

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Manganese binding site 5 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn101

b:27.4
occ:0.43
 O F:HOH214 2.1 26.2 1.0
OD1 B:ASP93 2.1 23.3 1.0
O B:HOH469 2.3 17.9 1.0
O3' F:DA4 2.4 15.1 1.0
O B:HOH473 2.5 22.6 1.0
OP1 F:DA5 2.5 16.4 1.0
P F:DA5 3.1 15.1 1.0
CG B:ASP93 3.2 22.3 1.0
O B:HOH462 3.6 20.2 1.0
C3' F:DA4 3.6 14.6 1.0
OD2 B:ASP93 3.6 19.8 1.0
MN B:MN302 3.8 22.1 1.0
C4' F:DA4 3.9 14.7 1.0
C5' F:DA5 4.1 14.1 1.0
O B:ALA91 4.1 24.3 1.0
O5' F:DA5 4.1 14.1 1.0
OP2 F:DA5 4.2 15.5 1.0
O B:HOH471 4.2 7.5 1.0
O B:HOH468 4.3 13.7 1.0
C2' F:DA4 4.3 14.4 1.0
O B:ARG88 4.4 25.1 1.0
C5' F:DA4 4.4 14.6 1.0
CB B:ASP93 4.5 22.0 1.0
C B:GLY92 4.5 21.5 1.0
O B:GLY92 4.6 23.0 1.0
N B:ASP93 4.6 20.8 1.0
CA B:ASP93 4.6 21.6 1.0
O B:HOH419 4.7 16.1 1.0
OD2 B:ASP108 4.8 37.0 1.0

Manganese binding site 6 out of 8 in 3wvh

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Manganese binding site 6 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn101

b:20.4
occ:0.48
 OD1 A:ASP93 2.2 20.0 1.0
O A:HOH470 2.3 21.3 1.0
O3' E:DA4 2.5 14.8 1.0
OP1 E:DA5 2.5 14.0 1.0
O A:HOH469 2.5 11.4 1.0
O A:HOH468 2.6 25.5 1.0
P E:DA5 3.0 14.7 1.0
CG A:ASP93 3.1 18.1 1.0
OD2 A:ASP93 3.5 16.2 1.0
C3' E:DA4 3.7 14.4 1.0
O A:HOH415 3.8 27.0 1.0
MN A:MN302 3.8 19.1 1.0
OD2 A:ASP108 4.0 36.2 1.0
O A:ALA91 4.0 16.7 1.0
O5' E:DA5 4.0 13.3 1.0
C4' E:DA4 4.1 14.6 1.0
C5' E:DA5 4.1 12.8 1.0
OP2 E:DA5 4.2 14.6 1.0
O A:HOH466 4.3 19.4 1.0
O A:GLY92 4.3 18.6 1.0
C2' E:DA4 4.3 14.8 1.0
C A:GLY92 4.3 17.1 1.0
CB A:ASP93 4.4 17.6 1.0
N A:ASP93 4.4 17.6 1.0
O A:ARG88 4.5 22.9 1.0
CA A:ASP93 4.5 18.1 1.0
C5' E:DA4 4.7 15.6 1.0
O A:HOH467 4.7 22.0 1.0
CG A:ASP108 4.8 27.5 1.0

Manganese binding site 7 out of 8 in 3wvh

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Manganese binding site 7 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn101

b:27.0
occ:0.48
 OD1 D:ASP93 2.3 29.2 1.0
O D:HOH444 2.3 30.5 1.0
O3' H:DA4 2.3 17.6 1.0
O D:HOH443 2.4 15.2 1.0
OP1 H:DA5 2.5 15.2 1.0
O D:HOH447 2.6 29.1 1.0
P H:DA5 3.0 18.7 1.0
CG D:ASP93 3.2 24.6 1.0
OD2 D:ASP93 3.5 22.1 1.0
C3' H:DA4 3.6 17.6 1.0
C4' H:DA4 3.9 18.1 1.0
C5' H:DA5 4.0 14.1 1.0
O D:ALA91 4.0 21.7 1.0
MN D:MN301 4.0 24.1 1.0
O5' H:DA5 4.0 15.8 1.0
OP2 H:DA5 4.2 17.9 1.0
C2' H:DA4 4.2 18.1 1.0
O D:GLY92 4.3 21.0 1.0
O D:HOH442 4.3 28.7 1.0
O D:HOH413 4.3 18.2 1.0
O D:ARG88 4.4 22.5 1.0
O D:HOH405 4.4 24.9 1.0
OD2 D:ASP108 4.4 34.9 1.0
C D:GLY92 4.5 21.8 1.0
CB D:ASP93 4.5 24.3 1.0
C5' H:DA4 4.5 17.8 1.0
N D:ASP93 4.7 22.4 1.0
CA D:ASP93 4.7 23.2 1.0

Manganese binding site 8 out of 8 in 3wvh

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Manganese binding site 8 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Time-Resolved Crystal Structure of Hindiii with 25SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn101

b:21.9
occ:0.48
 O C:HOH483 2.1 26.8 1.0
O3' G:DA4 2.3 17.1 1.0
OP1 G:DA5 2.4 17.4 1.0
OD1 C:ASP93 2.5 23.9 1.0
O C:HOH478 2.6 9.8 1.0
O C:HOH480 2.8 16.2 1.0
P G:DA5 2.9 16.5 1.0
CG C:ASP93 3.3 22.0 1.0
C3' G:DA4 3.5 16.6 1.0
OD2 C:ASP93 3.6 20.4 1.0
MN C:MN303 3.9 21.8 1.0
C4' G:DA4 3.9 16.4 1.0
O5' G:DA5 3.9 16.2 1.0
C5' G:DA5 3.9 16.1 1.0
O C:ALA91 4.0 19.0 1.0
O C:HOH413 4.0 17.9 1.0
OP2 G:DA5 4.1 18.0 1.0
C2' G:DA4 4.2 16.4 1.0
OD2 C:ASP108 4.3 39.6 1.0
O C:GLY92 4.3 20.1 1.0
O C:HOH477 4.4 13.7 1.0
C C:GLY92 4.5 19.1 1.0
C5' G:DA4 4.5 15.6 1.0
O C:ARG88 4.5 20.9 1.0
CB C:ASP93 4.5 21.4 1.0
O C:HOH471 4.6 18.3 1.0
N C:ASP93 4.6 19.6 1.0
CA C:ASP93 4.7 20.0 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: Sat Oct 5 18:28:01 2024

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