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Manganese in PDB 3wvk: Time-Resolved Crystal Structure of Hindiii with 230SEC Soaking

Enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 230SEC Soaking

All present enzymatic activity of Time-Resolved Crystal Structure of Hindiii with 230SEC Soaking:
3.1.21.4;

Protein crystallography data

The structure of Time-Resolved Crystal Structure of Hindiii with 230SEC Soaking, PDB code: 3wvk 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) 39.77 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.250, 141.158, 96.583, 90.00, 111.96, 90.00
R / Rfree (%) 17.9 / 22.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Time-Resolved Crystal Structure of Hindiii with 230SEC Soaking (pdb code 3wvk). 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 230SEC Soaking, PDB code: 3wvk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3wvk

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Manganese binding site 1 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:26.3
occ:1.00
 OD2 A:ASP93 2.1 26.1 1.0
O A:ALA109 2.1 20.6 1.0
OP3 F:DA1 2.2 30.3 1.0
OD1 A:ASP108 2.2 32.0 1.0
O A:HOH482 2.4 25.1 1.0
OP2 F:DA1 2.4 27.0 1.0
P F:DA1 2.9 26.2 1.0
CG A:ASP108 3.1 39.8 1.0
CG A:ASP93 3.1 23.2 1.0
C A:ALA109 3.2 22.2 1.0
N A:ALA109 3.4 24.4 1.0
OD1 A:ASP93 3.5 24.3 1.0
OD2 A:ASP108 3.6 47.6 1.0
CA A:ALA109 3.9 23.9 1.0
O5' F:DA1 3.9 21.4 1.0
MN A:MN304 4.0 28.2 1.0
OP1 F:DA1 4.0 25.0 1.0
C A:ASP108 4.1 27.2 1.0
C5' F:DA1 4.1 23.6 1.0
O A:HOH466 4.1 27.0 1.0
CB A:ASP108 4.2 31.0 1.0
OD1 A:ASP68 4.3 33.1 1.0
CA A:ASP108 4.3 26.3 1.0
N A:LYS110 4.4 22.6 1.0
CB A:ALA109 4.4 25.2 1.0
CB A:ASP93 4.5 23.4 1.0
CA A:LYS110 4.7 26.6 1.0
O A:HOH483 4.8 31.6 1.0
O E:HOH108 4.9 27.9 1.0
O A:ASP108 5.0 28.1 1.0

Manganese binding site 2 out of 8 in 3wvk

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Manganese binding site 2 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:28.2
occ:1.00
 O A:HOH483 2.2 31.6 1.0
OD1 A:ASP93 2.2 24.3 1.0
O3' E:DA4 2.2 29.7 1.0
OP2 F:DA1 2.3 27.0 1.0
O E:HOH108 2.3 27.9 1.0
OE1 A:GLN87 2.4 33.8 1.0
CD A:GLN87 3.2 40.3 1.0
C3' E:DA4 3.3 26.2 1.0
CG A:ASP93 3.3 23.2 1.0
NE2 A:GLN87 3.3 43.0 1.0
P F:DA1 3.5 26.2 1.0
OD2 A:ASP93 3.8 26.1 1.0
C5' F:DA1 4.0 23.6 1.0
MN A:MN303 4.0 26.3 1.0
O5' F:DA1 4.0 21.4 1.0
O E:HOH106 4.1 35.9 1.0
OD2 A:ASP108 4.2 47.6 1.0
C2' E:DA4 4.3 26.4 1.0
O A:HOH441 4.3 30.6 1.0
OP1 F:DA1 4.3 25.0 1.0
O A:HOH482 4.4 25.1 1.0
C4' E:DA4 4.4 24.2 1.0
O A:ALA91 4.4 32.4 1.0
OP3 F:DA1 4.5 30.3 1.0
CB A:ASP93 4.6 23.4 1.0
O A:HOH419 4.6 29.1 1.0
CG A:GLN87 4.7 42.2 1.0
O A:GLY92 4.7 25.9 1.0
CA A:ASP93 4.7 24.4 1.0
C A:GLY92 4.8 27.3 1.0
N A:ASP93 4.9 23.9 1.0
CG A:ASP108 5.0 39.8 1.0

Manganese binding site 3 out of 8 in 3wvk

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Manganese binding site 3 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:24.5
occ:1.00
 OD2 B:ASP93 2.1 21.8 1.0
O B:ALA109 2.1 25.2 1.0
O B:HOH497 2.2 20.5 1.0
OD1 B:ASP108 2.2 30.9 1.0
OP3 H:DA1 2.3 29.5 1.0
OP2 H:DA1 2.5 21.3 1.0
P H:DA1 2.9 24.0 1.0
CG B:ASP93 3.1 22.1 1.0
CG B:ASP108 3.1 36.1 1.0
C B:ALA109 3.2 23.9 1.0
OD1 B:ASP93 3.4 20.1 1.0
N B:ALA109 3.4 20.6 1.0
OD2 B:ASP108 3.6 40.8 1.0
CA B:ALA109 3.8 21.5 1.0
O5' H:DA1 3.9 20.9 1.0
MN B:MN302 4.0 24.6 1.0
C5' H:DA1 4.0 21.6 1.0
OP1 H:DA1 4.0 23.2 1.0
C B:ASP108 4.1 22.7 1.0
O B:HOH407 4.1 21.9 1.0
OD1 B:ASP68 4.2 26.3 1.0
CB B:ASP108 4.2 30.4 1.0
CB B:ALA109 4.3 20.6 1.0
CA B:ASP108 4.3 21.4 1.0
N B:LYS110 4.4 23.9 1.0
CB B:ASP93 4.4 20.8 1.0
CA B:LYS110 4.7 22.1 1.0
O G:HOH115 4.7 20.1 1.0
O B:HOH498 4.8 22.2 1.0

Manganese binding site 4 out of 8 in 3wvk

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Manganese binding site 4 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:24.6
occ:1.00
 O G:HOH115 2.1 20.1 1.0
OP2 H:DA1 2.1 21.3 1.0
O B:HOH498 2.2 22.2 1.0
OD1 B:ASP93 2.2 20.1 1.0
O3' G:DA4 2.3 23.7 1.0
OE1 B:GLN87 2.3 25.9 1.0
CD B:GLN87 3.1 31.1 1.0
CG B:ASP93 3.3 22.1 1.0
NE2 B:GLN87 3.3 28.9 1.0
C3' G:DA4 3.4 21.7 1.0
P H:DA1 3.5 24.0 1.0
OD2 B:ASP93 3.8 21.8 1.0
MN B:MN301 4.0 24.5 1.0
C5' H:DA1 4.0 21.6 1.0
O5' H:DA1 4.0 20.9 1.0
OD2 B:ASP108 4.1 40.8 1.0
O B:HOH413 4.2 25.4 1.0
OP1 H:DA1 4.3 23.2 1.0
C2' G:DA4 4.3 19.6 1.0
C4' G:DA4 4.4 19.9 1.0
O B:HOH497 4.4 20.5 1.0
O B:HOH414 4.5 24.7 1.0
CG B:GLN87 4.5 28.9 1.0
CB B:ASP93 4.6 20.8 1.0
O B:ALA91 4.6 29.2 1.0
O G:HOH109 4.6 38.0 1.0
OP3 H:DA1 4.6 29.5 1.0
CA B:ASP93 4.7 21.4 1.0
C B:GLY92 4.8 24.9 1.0
O B:GLY92 4.8 28.4 1.0
N B:ASP93 4.8 20.8 1.0
CG B:ASP108 4.9 36.1 1.0
OD1 B:ASP108 5.0 30.9 1.0

Manganese binding site 5 out of 8 in 3wvk

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Manganese binding site 5 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:26.1
occ:1.00
 OP3 J:DA1 2.1 27.3 1.0
OD2 C:ASP93 2.1 23.9 1.0
O C:ALA109 2.1 22.7 1.0
OD1 C:ASP108 2.2 30.0 1.0
O C:HOH471 2.2 21.5 1.0
OP2 J:DA1 2.5 27.7 1.0
P J:DA1 2.8 25.1 1.0
CG C:ASP93 3.1 25.4 1.0
CG C:ASP108 3.2 43.1 1.0
C C:ALA109 3.2 26.5 1.0
N C:ALA109 3.4 25.6 1.0
OD1 C:ASP93 3.4 22.6 1.0
OD2 C:ASP108 3.6 49.1 1.0
CA C:ALA109 3.9 23.4 1.0
O5' J:DA1 3.9 23.5 1.0
MN C:MN303 4.0 28.6 1.0
OP1 J:DA1 4.0 26.5 1.0
C C:ASP108 4.1 24.1 1.0
C5' J:DA1 4.1 23.8 1.0
O C:HOH438 4.1 26.6 1.0
OD1 C:ASP68 4.2 32.2 1.0
CB C:ASP108 4.3 29.5 1.0
CA C:ASP108 4.3 26.8 1.0
CB C:ALA109 4.3 28.1 1.0
N C:LYS110 4.4 24.7 1.0
CB C:ASP93 4.4 26.9 1.0
O C:HOH472 4.7 29.7 1.0
CA C:LYS110 4.7 23.7 1.0
O C:HOH473 4.8 27.9 1.0
OG C:SER64 4.9 27.3 1.0
O C:ASP108 5.0 24.6 1.0

Manganese binding site 6 out of 8 in 3wvk

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Manganese binding site 6 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:28.6
occ:1.00
 O C:HOH472 2.0 29.7 1.0
OD1 C:ASP93 2.1 22.6 1.0
OP2 J:DA1 2.1 27.7 1.0
O C:HOH473 2.2 27.9 1.0
O3' I:DA4 2.2 25.4 1.0
OE1 C:GLN87 2.3 29.4 1.0
CD C:GLN87 3.1 34.2 1.0
CG C:ASP93 3.2 25.4 1.0
NE2 C:GLN87 3.3 32.6 1.0
C3' I:DA4 3.4 24.6 1.0
P J:DA1 3.5 25.1 1.0
OD2 C:ASP93 3.8 23.9 1.0
MN C:MN302 4.0 26.1 1.0
C5' J:DA1 4.1 23.8 1.0
O5' J:DA1 4.1 23.5 1.0
OD2 C:ASP108 4.3 49.1 1.0
OP1 J:DA1 4.3 26.5 1.0
O C:HOH471 4.3 21.5 1.0
O C:HOH412 4.4 30.0 1.0
C2' I:DA4 4.4 22.7 1.0
C4' I:DA4 4.5 23.0 1.0
OP3 J:DA1 4.5 27.3 1.0
CB C:ASP93 4.5 26.9 1.0
O C:ALA91 4.5 31.3 1.0
O C:HOH439 4.6 32.1 1.0
CG C:GLN87 4.6 34.2 1.0
CA C:ASP93 4.7 24.7 1.0
C C:GLY92 4.7 27.8 1.0
N C:ASP93 4.8 23.1 1.0
O C:GLY92 4.9 27.9 1.0
OD1 C:ASP108 5.0 30.0 1.0
CG C:ASP108 5.0 43.1 1.0

Manganese binding site 7 out of 8 in 3wvk

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Manganese binding site 7 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:25.4
occ:1.00
 OP3 L:DA1 2.0 27.1 1.0
O D:HOH483 2.1 25.3 1.0
O D:ALA109 2.1 24.4 1.0
OD2 D:ASP93 2.2 23.9 1.0
OD1 D:ASP108 2.3 30.4 1.0
OP2 L:DA1 2.5 26.7 1.0
P L:DA1 2.9 28.6 1.0
CG D:ASP108 3.1 36.1 1.0
CG D:ASP93 3.2 23.8 1.0
C D:ALA109 3.3 26.5 1.0
OD1 D:ASP93 3.5 24.9 1.0
N D:ALA109 3.5 24.8 1.0
OD2 D:ASP108 3.6 42.5 1.0
CA D:ALA109 3.9 25.7 1.0
O5' L:DA1 3.9 22.6 1.0
OP1 L:DA1 4.0 26.0 1.0
MN D:MN303 4.0 29.3 1.0
C5' L:DA1 4.1 22.9 1.0
O L:HOH102 4.1 24.3 1.0
C D:ASP108 4.1 28.8 1.0
CB D:ASP108 4.2 28.1 1.0
OD1 D:ASP68 4.3 30.5 1.0
CA D:ASP108 4.3 24.2 1.0
CB D:ALA109 4.4 28.1 1.0
N D:LYS110 4.4 25.2 1.0
CB D:ASP93 4.5 23.8 1.0
O D:HOH485 4.6 27.1 1.0
CA D:LYS110 4.6 24.5 1.0
O D:HOH484 5.0 25.4 1.0
O D:ASP108 5.0 32.8 1.0

Manganese binding site 8 out of 8 in 3wvk

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Manganese binding site 8 out of 8 in the Time-Resolved Crystal Structure of Hindiii with 230SEC 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 230SEC Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn303

b:29.3
occ:1.00
 OP2 L:DA1 2.1 26.7 1.0
O3' K:DA4 2.2 26.4 1.0
O D:HOH485 2.2 27.1 1.0
OD1 D:ASP93 2.2 24.9 1.0
O D:HOH484 2.2 25.4 1.0
OE1 D:GLN87 2.2 30.0 1.0
CD D:GLN87 3.1 39.8 1.0
C3' K:DA4 3.2 23.5 1.0
NE2 D:GLN87 3.3 36.2 1.0
CG D:ASP93 3.3 23.8 1.0
P L:DA1 3.4 28.6 1.0
OD2 D:ASP93 3.8 23.9 1.0
C5' L:DA1 4.0 22.9 1.0
O5' L:DA1 4.0 22.6 1.0
MN D:MN302 4.0 25.4 1.0
OD2 D:ASP108 4.1 42.5 1.0
O D:HOH431 4.2 27.9 1.0
O D:HOH483 4.2 25.3 1.0
C2' K:DA4 4.3 23.9 1.0
OP1 L:DA1 4.3 26.0 1.0
C4' K:DA4 4.3 23.8 1.0
O K:HOH108 4.3 40.0 1.0
OP3 L:DA1 4.4 27.1 1.0
O D:ALA91 4.5 34.3 1.0
CG D:GLN87 4.5 41.8 1.0
CB D:ASP93 4.6 23.8 1.0
O D:HOH404 4.6 26.2 1.0
CA D:ASP93 4.7 22.9 1.0
C D:GLY92 4.8 26.6 1.0
N D:ASP93 4.8 25.3 1.0
O D:GLY92 4.8 28.9 1.0
CG D:ASP108 4.9 36.1 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 18:28:39 2024

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