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Manganese in PDB 3wvi: Time-Resolved Crystal Structure of Hindiii with 40 Sec Soaking

Enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 40 Sec Soaking

All present enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 40 Sec Soaking:
3.1.21.4;

Protein crystallography data

The structure of Time-Resolved Crystal Structure of Hindiii with 40 Sec Soaking, PDB code: 3wvi 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) 32.23 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.610, 143.236, 94.363, 90.00, 113.44, 90.00
R / Rfree (%) 17.3 / 23.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Time-Resolved Crystal Structure of Hindiii with 40 Sec Soaking (pdb code 3wvi). 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 40 Sec Soaking, PDB code: 3wvi:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3wvi

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Manganese binding site 1 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:24.6
occ:1.00
 OP1 E:DA5 2.0 18.0 1.0
O A:ALA109 2.0 20.9 1.0
OD2 A:ASP93 2.2 21.2 1.0
O A:HOH478 2.2 17.7 1.0
OD1 A:ASP108 2.4 35.3 1.0
O A:HOH486 2.4 31.7 1.0
CG A:ASP108 3.0 35.1 1.0
C A:ALA109 3.1 22.5 1.0
CG A:ASP93 3.2 21.9 1.0
N A:ALA109 3.3 25.6 1.0
OD2 A:ASP108 3.4 41.1 1.0
P E:DA5 3.4 18.0 1.0
OD1 A:ASP93 3.6 21.1 1.0
O E:HOH204 3.7 21.5 1.0
CA A:ALA109 3.8 24.4 1.0
MN E:MN101 4.0 35.3 0.6
C A:ASP108 4.0 26.4 1.0
O A:HOH479 4.0 27.3 1.0
C5' E:DA5 4.0 15.9 1.0
O5' E:DA5 4.1 16.1 1.0
OP2 E:DA5 4.1 18.1 1.0
N A:LYS110 4.1 21.3 1.0
O E:HOH218 4.2 20.8 1.0
CB A:ASP108 4.2 30.2 1.0
CA A:ASP108 4.2 27.5 1.0
OD1 A:ASP68 4.4 26.9 1.0
CA A:LYS110 4.4 22.3 1.0
CB A:ALA109 4.5 23.3 1.0
O3' E:DA4 4.5 18.2 1.0
CB A:ASP93 4.5 23.1 1.0
CB A:LYS110 4.8 24.3 1.0
O A:ASP108 4.9 27.4 1.0

Manganese binding site 2 out of 8 in 3wvi

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Manganese binding site 2 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:23.7
occ:1.00
 OP1 F:DA5 2.0 21.1 1.0
OD2 B:ASP93 2.1 20.7 1.0
O B:ALA109 2.1 24.4 1.0
O B:HOH471 2.2 14.5 1.0
OD1 B:ASP108 2.3 30.8 1.0
O B:HOH483 2.4 27.0 1.0
CG B:ASP93 3.1 22.7 1.0
CG B:ASP108 3.1 30.8 1.0
C B:ALA109 3.1 21.6 1.0
P F:DA5 3.3 19.1 1.0
N B:ALA109 3.4 20.9 1.0
OD1 B:ASP93 3.5 21.9 1.0
OD2 B:ASP108 3.6 40.2 1.0
CA B:ALA109 3.8 21.3 1.0
O B:HOH475 3.9 40.5 1.0
OP2 F:DA5 4.0 20.2 1.0
MN F:MN101 4.0 29.1 0.6
O5' F:DA5 4.1 16.9 1.0
C B:ASP108 4.1 21.7 1.0
O F:HOH201 4.2 26.5 1.0
N B:LYS110 4.2 22.6 1.0
C5' F:DA5 4.2 16.5 1.0
O B:HOH474 4.2 29.1 1.0
OD1 B:ASP68 4.3 27.5 1.0
CB B:ASP108 4.3 27.4 1.0
CA B:ASP108 4.3 23.8 1.0
CA B:LYS110 4.4 23.8 1.0
CB B:ALA109 4.4 22.3 1.0
O3' F:DA4 4.4 21.3 1.0
CB B:ASP93 4.4 21.7 1.0
CB B:LYS110 4.7 25.3 1.0
O B:HOH418 5.0 20.9 1.0

Manganese binding site 3 out of 8 in 3wvi

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Manganese binding site 3 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:25.1
occ:1.00
 OP1 G:DA5 1.9 22.5 1.0
O C:ALA109 2.2 23.0 1.0
OD2 C:ASP93 2.2 21.0 1.0
O C:HOH459 2.3 16.0 1.0
O C:HOH465 2.3 25.1 1.0
OD1 C:ASP108 2.4 41.3 1.0
CG C:ASP108 3.1 39.4 1.0
P G:DA5 3.2 21.2 1.0
C C:ALA109 3.2 23.2 1.0
CG C:ASP93 3.3 24.1 1.0
OD2 C:ASP108 3.4 55.8 1.0
N C:ALA109 3.4 25.1 1.0
MN G:MN101 3.7 34.9 0.6
OP2 G:DA5 3.8 23.3 1.0
OD1 C:ASP93 3.8 24.6 1.0
O G:HOH214 3.9 31.5 1.0
CA C:ALA109 3.9 24.1 1.0
O5' G:DA5 4.0 19.3 1.0
C C:ASP108 4.1 26.9 1.0
O G:HOH211 4.2 31.2 1.0
C5' G:DA5 4.2 17.1 1.0
CB C:ASP108 4.2 31.3 1.0
N C:LYS110 4.2 25.0 1.0
O C:HOH461 4.2 39.6 1.0
OD1 C:ASP68 4.3 23.8 1.0
CA C:ASP108 4.3 28.0 1.0
O3' G:DA4 4.4 22.8 1.0
CA C:LYS110 4.5 26.5 1.0
CB C:ALA109 4.6 23.7 1.0
CB C:ASP93 4.6 23.7 1.0
CB C:LYS110 5.0 29.6 1.0
OG C:SER64 5.0 24.1 1.0

Manganese binding site 4 out of 8 in 3wvi

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Manganese binding site 4 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:23.1
occ:1.00
 OP1 H:DA5 1.9 19.6 1.0
O D:ALA109 2.1 20.8 1.0
OD2 D:ASP93 2.1 23.0 1.0
OD1 D:ASP108 2.3 31.3 1.0
O H:HOH115 2.4 21.3 1.0
O D:HOH471 2.5 21.9 1.0
CG D:ASP108 3.0 31.0 1.0
C D:ALA109 3.2 21.3 1.0
P H:DA5 3.2 25.6 1.0
CG D:ASP93 3.2 23.8 1.0
N D:ALA109 3.3 21.8 1.0
OD2 D:ASP108 3.4 38.2 1.0
OD1 D:ASP93 3.7 24.7 1.0
CA D:ALA109 3.8 21.1 1.0
MN D:MN302 3.8 31.2 0.6
O5' H:DA5 3.9 20.7 1.0
O D:HOH468 3.9 27.4 1.0
OP2 H:DA5 4.0 23.5 1.0
C D:ASP108 4.1 24.6 1.0
C5' H:DA5 4.1 18.0 1.0
O D:HOH469 4.2 23.0 1.0
CB D:ASP108 4.2 27.2 1.0
CA D:ASP108 4.2 24.8 1.0
O H:HOH101 4.3 16.8 1.0
N D:LYS110 4.3 22.0 1.0
O3' H:DA4 4.3 26.9 1.0
CB D:ALA109 4.4 21.4 1.0
OD1 D:ASP68 4.5 30.7 1.0
CB D:ASP93 4.5 24.2 1.0
CA D:LYS110 4.6 24.4 1.0
CB D:LYS110 5.0 29.3 1.0

Manganese binding site 5 out of 8 in 3wvi

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Manganese binding site 5 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:31.2
occ:0.61
 OD1 D:ASP93 2.2 24.7 1.0
O D:HOH469 2.3 23.0 1.0
O D:HOH470 2.4 22.8 1.0
O3' H:DA4 2.4 26.9 1.0
OP1 H:DA5 2.6 19.6 1.0
O D:HOH472 2.6 28.8 1.0
CG D:ASP93 3.1 23.8 1.0
P H:DA5 3.1 25.6 1.0
OD2 D:ASP93 3.4 23.0 1.0
C3' H:DA4 3.6 24.2 1.0
O D:HOH477 3.7 32.9 1.0
MN D:MN301 3.8 23.1 1.0
C4' H:DA4 3.9 23.7 1.0
C5' H:DA5 4.1 18.0 1.0
O5' H:DA5 4.1 20.7 1.0
O D:ALA91 4.1 27.2 1.0
O D:GLY92 4.2 26.4 1.0
OP2 H:DA5 4.2 23.5 1.0
C2' H:DA4 4.3 24.6 1.0
O D:HOH466 4.3 24.5 1.0
CB D:ASP93 4.4 24.2 1.0
C D:GLY92 4.4 25.6 1.0
O D:HOH473 4.4 27.1 1.0
OD2 D:ASP108 4.4 38.2 1.0
O D:ARG88 4.5 28.4 1.0
O D:HOH471 4.5 21.9 1.0
CA D:ASP93 4.6 23.5 1.0
N D:ASP93 4.6 24.1 1.0
C5' H:DA4 4.7 22.8 1.0
CG D:ASP108 5.0 31.0 1.0

Manganese binding site 6 out of 8 in 3wvi

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Manganese binding site 6 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn101

b:29.1
occ:0.55
 OD1 B:ASP93 2.3 21.9 1.0
O B:HOH472 2.3 22.2 1.0
O3' F:DA4 2.3 21.3 1.0
O B:HOH473 2.6 27.1 1.0
O B:HOH474 2.6 29.1 1.0
OP1 F:DA5 2.6 21.1 1.0
P F:DA5 3.1 19.1 1.0
CG B:ASP93 3.3 22.7 1.0
C3' F:DA4 3.5 19.4 1.0
O B:HOH476 3.7 22.8 1.0
C4' F:DA4 3.7 18.9 1.0
OD2 B:ASP93 3.8 20.7 1.0
MN B:MN303 4.0 23.7 1.0
C5' F:DA5 4.0 16.5 1.0
O5' F:DA5 4.0 16.9 1.0
C2' F:DA4 4.1 18.7 1.0
O B:ALA91 4.2 26.6 1.0
O B:HOH470 4.2 19.9 1.0
OP2 F:DA5 4.2 20.2 1.0
O B:HOH471 4.3 14.5 1.0
O B:ARG88 4.3 31.7 1.0
C5' F:DA4 4.4 19.4 1.0
CB B:ASP93 4.6 21.7 1.0
O B:HOH418 4.6 20.9 1.0
OD2 B:ASP108 4.7 40.2 1.0
CA B:ASP93 4.7 22.1 1.0
N B:ASP93 4.7 22.1 1.0
O B:GLY92 4.7 24.8 1.0
C B:GLY92 4.7 23.2 1.0
O4' F:DA4 4.9 17.7 1.0

Manganese binding site 7 out of 8 in 3wvi

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Manganese binding site 7 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn101

b:35.3
occ:0.60
 OD1 A:ASP93 2.3 21.1 1.0
O A:HOH479 2.4 27.3 1.0
O A:HOH481 2.4 19.6 1.0
O A:HOH480 2.5 22.2 1.0
O3' E:DA4 2.5 18.2 1.0
OP1 E:DA5 2.8 18.0 1.0
P E:DA5 3.2 18.0 1.0
CG A:ASP93 3.3 21.9 1.0
O A:HOH471 3.4 26.8 1.0
C3' E:DA4 3.7 18.3 1.0
OD2 A:ASP93 3.7 21.2 1.0
O A:HOH485 3.9 31.9 1.0
C5' E:DA5 4.0 15.9 1.0
MN A:MN301 4.0 24.6 1.0
C4' E:DA4 4.0 18.7 1.0
O5' E:DA5 4.1 16.1 1.0
O A:HOH483 4.1 21.2 1.0
C2' E:DA4 4.2 18.6 1.0
O A:ALA91 4.2 23.8 1.0
O A:HOH478 4.3 17.7 1.0
O A:GLY92 4.3 27.1 1.0
O A:ARG88 4.4 25.3 1.0
OD2 A:ASP108 4.5 41.1 1.0
OP2 E:DA5 4.5 18.1 1.0
C A:GLY92 4.5 24.7 1.0
CB A:ASP93 4.5 23.1 1.0
N A:ASP93 4.7 24.3 1.0
CA A:ASP93 4.7 24.1 1.0
C5' E:DA4 4.8 18.7 1.0

Manganese binding site 8 out of 8 in 3wvi

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Manganese binding site 8 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 40 Sec 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 40 Sec Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn101

b:34.9
occ:0.63
 O3' G:DA4 2.3 22.8 1.0
O C:HOH461 2.3 39.6 1.0
OD1 C:ASP93 2.4 24.6 1.0
OP1 G:DA5 2.5 22.5 1.0
O C:HOH460 2.5 20.1 1.0
O C:HOH462 2.6 16.0 1.0
P G:DA5 2.9 21.2 1.0
CG C:ASP93 3.2 24.1 1.0
OD2 C:ASP93 3.5 21.0 1.0
C3' G:DA4 3.5 21.6 1.0
MN C:MN303 3.7 25.1 1.0
O5' G:DA5 3.9 19.3 1.0
C4' G:DA4 3.9 20.9 1.0
C5' G:DA5 3.9 17.1 1.0
O C:HOH464 4.0 22.6 1.0
O C:HOH459 4.1 16.0 1.0
OP2 G:DA5 4.1 23.3 1.0
C2' G:DA4 4.2 20.4 1.0
O C:ALA91 4.2 29.3 1.0
O C:GLY92 4.4 23.1 1.0
O C:HOH442 4.5 18.0 1.0
CB C:ASP93 4.5 23.7 1.0
C C:GLY92 4.5 23.5 1.0
N C:ASP93 4.6 22.3 1.0
C5' G:DA4 4.6 20.1 1.0
O C:ARG88 4.7 30.7 1.0
CA C:ASP93 4.7 21.8 1.0
OD2 C:ASP108 4.8 55.8 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: Sat Oct 5 18:28:22 2024

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