Magnesium in PDB 8rdu: Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map

Other elements in 8rdu:

The structure of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map (pdb code 8rdu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map, PDB code: 8rdu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 8rdu

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Magnesium binding site 1 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg300

b:16.9
occ:1.00
 O 1:HOH447 2.0 13.3 1.0
O C:HOH317 2.1 19.6 1.0
O 1:HOH492 2.1 19.8 1.0
O 1:HOH527 2.1 40.1 1.0
OP1 1:A173 2.2 12.3 1.0
OP2 1:C174 2.2 18.3 1.0
P 1:A173 3.6 12.7 1.0
P 1:C174 3.7 11.3 1.0
C5' 1:A173 3.8 12.9 1.0
O5' 1:A173 3.9 17.1 1.0
OE1 C:GLN93 4.1 28.2 1.0
O 1:HOH451 4.3 17.1 1.0
O 1:HOH551 4.4 27.3 1.0
O5' 1:C174 4.4 12.1 1.0
OP1 1:C174 4.4 13.4 1.0
CG C:PRO96 4.5 12.4 1.0
O3' 1:U172 4.5 13.7 1.0
OP2 1:A173 4.6 13.5 1.0
NE2 C:GLN93 4.6 21.0 1.0
O3' 1:A173 4.6 12.7 1.0
CD C:GLN93 4.7 23.6 1.0
CD C:PRO96 4.8 15.3 1.0
O 1:HOH405 4.8 18.8 1.0
C4' 1:A173 4.8 10.8 1.0
CD B:ARG66 5.0 13.3 1.0

Magnesium binding site 2 out of 17 in 8rdu

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Magnesium binding site 2 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:10.8
occ:1.00
 O2B D:ATP300 2.0 10.7 1.0
OG1 D:THR67 2.0 9.4 1.0
O D:HOH401 2.1 12.7 1.0
O D:HOH405 2.1 8.5 1.0
O D:HOH402 2.1 11.7 1.0
O1G D:ATP300 2.5 8.2 1.0
CB D:THR67 3.0 9.3 1.0
PB D:ATP300 3.2 5.5 1.0
PG D:ATP300 3.4 3.6 1.0
O3B D:ATP300 3.4 9.1 1.0
O2G D:ATP300 3.9 9.0 1.0
O3A D:ATP300 3.9 8.4 1.0
N D:THR67 4.0 9.3 1.0
CA D:THR67 4.0 10.8 1.0
CG2 D:THR67 4.0 10.3 1.0
OD2 D:ASP144 4.1 16.9 1.0
OD1 D:ASP144 4.1 15.3 1.0
OE2 D:GLU145 4.2 27.3 1.0
O1A D:ATP300 4.3 11.9 1.0
O1B D:ATP300 4.4 9.1 1.0
CG D:ASP144 4.5 13.3 1.0
PA D:ATP300 4.6 9.6 1.0
CG D:GLU145 4.7 16.6 1.0
O3G D:ATP300 4.7 8.1 1.0
OE2 E:GLU162 4.7 49.7 1.0
O2A D:ATP300 4.8 12.3 1.0
CD D:GLU145 4.8 23.2 1.0
NH2 E:ARG189 4.9 26.6 1.0

Magnesium binding site 3 out of 17 in 8rdu

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Magnesium binding site 3 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:17.8
occ:1.00
 OG1 E:THR67 2.0 14.6 1.0
O E:HOH413 2.1 10.4 1.0
O E:HOH417 2.1 17.4 1.0
O E:HOH401 2.1 28.8 1.0
O1G E:ATP300 2.3 16.4 1.0
O2B E:ATP300 2.4 19.2 1.0
CB E:THR67 3.2 14.7 1.0
PG E:ATP300 3.3 11.7 1.0
O3B E:ATP300 3.4 21.7 1.0
PB E:ATP300 3.5 13.4 1.0
OE2 E:GLU145 3.6 26.8 1.0
O2G E:ATP300 4.0 18.2 1.0
CG2 E:THR67 4.1 10.4 1.0
OD1 E:ASP144 4.1 30.3 1.0
NH2 F:ARG189 4.1 26.3 1.0
O E:HOH424 4.2 25.7 1.0
N E:THR67 4.2 12.8 1.0
CA E:THR67 4.2 14.9 1.0
OD2 E:ASP144 4.2 32.1 1.0
O1A E:ATP300 4.2 17.5 1.0
O3A E:ATP300 4.3 16.2 1.0
OE2 F:GLU162 4.3 50.7 1.0
CG E:GLU145 4.4 23.3 1.0
CD E:GLU145 4.5 22.9 1.0
CG E:ASP144 4.6 22.0 1.0
O3G E:ATP300 4.6 21.9 1.0
O1B E:ATP300 4.6 16.4 1.0
PA E:ATP300 4.7 14.7 1.0

Magnesium binding site 4 out of 17 in 8rdu

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Magnesium binding site 4 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:24.0
occ:1.00
 OG1 F:THR67 2.0 23.1 1.0
O F:HOH413 2.1 34.8 1.0
O F:HOH407 2.1 19.1 1.0
O F:HOH401 2.1 26.8 1.0
O1G F:ATP300 2.3 28.5 1.0
O2B F:ATP300 2.3 18.7 1.0
CB F:THR67 3.0 18.6 1.0
PG F:ATP300 3.3 19.4 1.0
PB F:ATP300 3.3 15.8 1.0
O3B F:ATP300 3.3 21.8 1.0
OE2 F:GLU145 3.8 30.9 1.0
CG2 F:THR67 3.9 14.9 1.0
O2G F:ATP300 3.9 18.2 1.0
CA F:THR67 4.1 18.4 1.0
O3A F:ATP300 4.1 19.6 1.0
O1A F:ATP300 4.1 24.9 1.0
N F:THR67 4.2 19.8 1.0
OD2 F:ASP144 4.2 23.3 1.0
OE2 G:GLU162 4.2 40.6 1.0
OD1 F:ASP144 4.2 25.5 1.0
NH2 G:ARG189 4.3 28.8 1.0
O3G F:ATP300 4.5 21.7 1.0
O1B F:ATP300 4.5 19.2 1.0
PA F:ATP300 4.6 19.5 1.0
CG F:ASP144 4.6 20.7 1.0
OE1 G:GLU162 4.7 49.5 1.0
CD F:GLU145 4.8 29.2 1.0
O2A F:ATP300 4.8 22.5 1.0
CG F:GLU145 4.9 25.4 1.0
CD G:GLU162 4.9 47.1 1.0

Magnesium binding site 5 out of 17 in 8rdu

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Magnesium binding site 5 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:25.5
occ:1.00
 OG1 G:THR67 2.0 21.8 1.0
O G:HOH413 2.1 21.0 1.0
O G:HOH411 2.1 20.7 1.0
O G:HOH406 2.1 28.9 1.0
O2B G:ATP300 2.2 22.9 1.0
O1G G:ATP300 2.4 25.0 1.0
CB G:THR67 3.3 19.6 1.0
PG G:ATP300 3.4 20.6 1.0
PB G:ATP300 3.4 16.0 1.0
O3B G:ATP300 3.5 24.2 1.0
OE2 G:GLU145 3.9 31.9 1.0
O2G G:ATP300 4.0 23.1 1.0
OD1 G:ASP144 4.0 25.2 1.0
CG2 G:THR67 4.1 17.6 1.0
O1A G:ATP300 4.2 23.4 1.0
O3A G:ATP300 4.2 23.3 1.0
OD2 G:ASP144 4.3 25.4 1.0
N G:THR67 4.3 18.4 1.0
CA G:THR67 4.3 17.9 1.0
NH2 H:ARG189 4.4 35.1 1.0
O G:HOH432 4.5 23.4 1.0
OE2 H:GLU162 4.5 50.2 1.0
O1B G:ATP300 4.5 19.3 1.0
CG G:ASP144 4.5 23.1 1.0
O3G G:ATP300 4.7 28.2 1.0
CG G:GLU145 4.7 27.3 1.0
PA G:ATP300 4.7 22.6 1.0
CD G:GLU145 4.7 30.0 1.0
NE2 H:GLN185 5.0 35.7 1.0
OE1 H:GLU162 5.0 60.0 1.0

Magnesium binding site 6 out of 17 in 8rdu

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Magnesium binding site 6 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:32.5
occ:1.00
 O H:HOH402 2.1 19.8 1.0
O H:HOH409 2.1 34.9 1.0
O H:HOH408 2.1 21.4 1.0
OG1 H:THR67 2.2 27.7 1.0
O1G H:ATP300 2.4 31.3 1.0
O2B H:ATP300 2.9 27.7 1.0
OE2 H:GLU145 3.3 39.4 1.0
OD2 H:ASP144 3.3 29.5 1.0
CB H:THR67 3.4 22.2 1.0
PG H:ATP300 3.5 29.2 1.0
O3B H:ATP300 3.9 27.3 1.0
OD1 H:ASP144 3.9 31.1 1.0
CG H:ASP144 4.0 26.5 1.0
PB H:ATP300 4.0 22.3 1.0
CG H:GLU145 4.0 31.4 1.0
O2G H:ATP300 4.0 21.1 1.0
CD H:GLU145 4.1 33.1 1.0
CG2 H:THR67 4.2 17.6 1.0
NH2 I:ARG189 4.3 29.7 1.0
OE2 I:GLU162 4.5 49.8 1.0
CA H:THR67 4.5 20.2 1.0
N H:THR67 4.6 20.6 1.0
O3G H:ATP300 4.8 30.2 1.0
O1A H:ATP300 4.8 28.3 1.0
O3A H:ATP300 4.9 22.1 1.0
OE1 I:GLN185 4.9 24.8 1.0

Magnesium binding site 7 out of 17 in 8rdu

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Magnesium binding site 7 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:32.9
occ:1.00
 O I:HOH415 2.1 26.0 1.0
O I:HOH409 2.1 37.0 1.0
O I:HOH405 2.1 15.4 1.0
OG1 I:THR67 2.2 22.6 1.0
O1G I:ATP300 2.4 33.8 1.0
O2B I:ATP300 2.8 19.8 1.0
OE2 I:GLU145 3.1 39.9 1.0
CB I:THR67 3.5 19.2 1.0
PG I:ATP300 3.5 29.9 1.0
OD2 I:ASP144 3.7 31.0 1.0
O3B I:ATP300 3.8 27.3 1.0
PB I:ATP300 3.9 16.9 1.0
CD I:GLU145 4.0 34.0 1.0
CG I:GLU145 4.0 29.7 1.0
OD1 I:ASP144 4.0 32.5 1.0
O2G I:ATP300 4.0 28.2 1.0
CG2 I:THR67 4.1 17.1 1.0
CG I:ASP144 4.2 27.3 1.0
NH2 J:ARG189 4.3 33.7 1.0
OE2 J:GLU162 4.4 48.4 1.0
CA I:THR67 4.6 17.7 1.0
N I:THR67 4.7 17.9 1.0
O3A I:ATP300 4.7 22.1 1.0
O3G I:ATP300 4.8 32.6 1.0
O1A I:ATP300 4.8 21.6 1.0
OE1 J:GLU162 4.9 47.8 1.0
OE1 J:GLN185 4.9 24.3 1.0

Magnesium binding site 8 out of 17 in 8rdu

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Magnesium binding site 8 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:27.8
occ:1.00
 O J:HOH412 2.1 23.4 1.0
O J:HOH404 2.1 32.9 1.0
O J:HOH411 2.1 17.6 1.0
OG1 J:THR67 2.2 21.9 1.0
O1G J:ATP300 2.5 26.5 1.0
O2B J:ATP300 2.8 22.1 1.0
OE1 J:GLU145 3.3 27.9 1.0
CB J:THR67 3.5 18.8 1.0
PG J:ATP300 3.7 21.1 1.0
O3B J:ATP300 3.9 22.1 1.0
PB J:ATP300 4.0 17.6 1.0
OD2 J:ASP144 4.0 23.8 1.0
CG2 J:THR67 4.0 16.5 1.0
O J:HOH423 4.0 21.4 1.0
CG J:GLU145 4.2 25.2 1.0
CD J:GLU145 4.2 28.2 1.0
OD1 J:ASP144 4.2 25.5 1.0
O2G J:ATP300 4.2 21.6 1.0
NH2 K:ARG189 4.2 42.6 1.0
OE2 K:GLU162 4.3 52.8 1.0
CG J:ASP144 4.4 22.1 1.0
CA J:THR67 4.6 19.1 1.0
O1A J:ATP300 4.7 21.3 1.0
OE1 K:GLN185 4.8 35.8 1.0
O3A J:ATP300 4.8 20.4 1.0
OE1 K:GLU162 4.8 55.0 1.0
N J:THR67 4.8 18.1 1.0
O3G J:ATP300 4.9 23.7 1.0

Magnesium binding site 9 out of 17 in 8rdu

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Magnesium binding site 9 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg301

b:29.1
occ:1.00
 OG1 K:THR67 2.0 30.8 1.0
O K:HOH408 2.1 21.2 1.0
O K:HOH412 2.1 22.6 1.0
O K:HOH401 2.1 29.6 1.0
O1G K:ATP300 2.3 32.7 1.0
O2B K:ATP300 2.4 26.9 1.0
CB K:THR67 3.3 26.6 1.0
PG K:ATP300 3.3 29.4 1.0
O3B K:ATP300 3.4 28.4 1.0
PB K:ATP300 3.5 23.2 1.0
OE2 K:GLU145 3.9 31.7 1.0
O2G K:ATP300 3.9 25.3 1.0
OD1 K:ASP144 4.0 35.1 1.0
O K:HOH441 4.1 27.6 1.0
CG2 K:THR67 4.1 22.9 1.0
O1A K:ATP300 4.1 29.7 1.0
NH2 L:ARG189 4.2 31.7 1.0
O3A K:ATP300 4.3 25.3 1.0
OD2 K:ASP144 4.3 27.5 1.0
N K:THR67 4.3 29.1 1.0
CA K:THR67 4.3 27.5 1.0
O3G K:ATP300 4.6 38.2 1.0
CG K:ASP144 4.6 24.7 1.0
OE2 L:GLU162 4.6 37.9 1.0
O1B K:ATP300 4.6 26.7 1.0
PA K:ATP300 4.6 27.2 1.0
CD K:GLU145 4.8 32.7 1.0
O2A K:ATP300 4.9 26.6 1.0
OE1 L:GLU162 4.9 43.6 1.0
CG K:GLU145 4.9 29.4 1.0

Magnesium binding site 10 out of 17 in 8rdu

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Magnesium binding site 10 out of 17 in the Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Conformational Landscape of the Type V-K Crispr-Associated Transposonintegration Assembly Cast V-K Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:27.7
occ:1.00
 O L:HOH401 2.1 16.1 1.0
O L:HOH417 2.1 26.6 1.0
O L:HOH416 2.1 21.6 1.0
OG1 L:THR67 2.2 25.3 1.0
O1G L:ATP300 2.5 29.8 1.0
O2B L:ATP300 2.8 20.8 1.0
OE2 L:GLU145 3.1 28.3 1.0
CB L:THR67 3.5 20.8 1.0
PG L:ATP300 3.6 26.1 1.0
OD1 L:ASP144 3.7 25.4 1.0
OD2 L:ASP144 3.7 19.6 1.0
O3B L:ATP300 3.9 23.5 1.0
CD L:GLU145 3.9 22.5 1.0
PB L:ATP300 4.0 23.4 1.0
CG L:GLU145 4.0 21.7 1.0
O2G L:ATP300 4.0 24.6 1.0
CG L:ASP144 4.0 20.6 1.0
CG2 L:THR67 4.2 15.6 1.0
NH2 M:ARG189 4.4 29.3 1.0
CA L:THR67 4.6 20.4 1.0
OE2 M:GLU162 4.7 43.4 1.0
N L:THR67 4.7 20.2 1.0
O3G L:ATP300 4.9 34.2 1.0
OE1 M:GLN185 4.9 19.9 1.0
O1A L:ATP300 4.9 28.3 1.0
O3A L:ATP300 4.9 21.1 1.0

Reference:

F.Tenjo-Castano, N.Sofos, L.S.Stutzke, P.Temperini, A.Fuglsang, T.Pape, P.Mesa, G.Montoya. Conformational Landscape of the Type V-K Crispr-Associated Transposon Integration Assembly. Mol.Cell 2024.
ISSN: ISSN 1097-2765
PubMed: 38834066
DOI: 10.1016/J.MOLCEL.2024.05.005
Page generated: Fri Oct 4 17:31:49 2024

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