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Magnesium in PDB 8d2k: Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) (pdb code 8d2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2), PDB code: 8d2k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 8d2k

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Magnesium binding site 1 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1201

b:22.1
occ:1.00
 OP2 T:DC14 2.0 30.3 1.0
OD1 A:ASP590 2.1 24.0 1.0
OD1 A:ASN614 2.1 16.0 1.0
O T:HOH111 2.1 20.1 1.0
O A:HOH1382 2.1 26.6 1.0
CG A:ASN614 3.2 18.3 1.0
O3' X:DA13 3.2 30.8 1.0
CG A:ASP590 3.2 21.2 1.0
P T:DC14 3.3 27.5 1.0
ND2 A:ASN614 3.8 27.1 1.0
O A:GLY618 3.9 34.0 1.0
OP1 T:DC14 3.9 28.9 1.0
O A:HIS591 4.0 26.6 1.0
O5' T:DC14 4.0 22.5 1.0
CB A:ASP590 4.0 17.3 1.0
C3' X:DA13 4.0 22.1 1.0
O A:ASN614 4.1 19.5 1.0
NZ A:LYS617 4.1 29.2 1.0
N A:HIS591 4.2 17.0 1.0
OD2 A:ASP590 4.2 24.8 1.0
CA A:ASP590 4.2 17.2 1.0
OP3 T:DC14 4.4 21.4 1.0
O A:HOH1315 4.4 30.2 1.0
CB A:ASN614 4.4 21.9 1.0
CA A:ASN614 4.5 21.7 1.0
C A:ASP590 4.6 17.7 1.0
C A:ASN614 4.7 20.2 1.0
C4' X:DA13 4.8 23.4 1.0
C A:HIS591 4.8 24.7 1.0
N A:GLY618 4.9 27.4 1.0
C A:GLY618 4.9 29.1 1.0
CA A:HIS591 5.0 21.5 1.0

Magnesium binding site 2 out of 10 in 8d2k

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Magnesium binding site 2 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1202

b:30.3
occ:1.00
 OP2 D:DT28 2.0 35.5 1.0
O A:HOH1309 2.0 18.2 1.0
OD1 A:ASP18 2.0 32.4 1.0
O A:HOH1336 2.1 20.2 1.0
O A:HOH1304 2.1 28.1 1.0
OE2 A:GLU516 2.5 31.0 1.0
OE1 A:GLU516 2.7 30.1 1.0
CG A:ASP18 2.8 26.7 1.0
CD A:GLU516 2.9 28.5 1.0
OD2 A:ASP18 3.0 22.5 1.0
P D:DT28 3.4 38.6 1.0
O A:HOH1451 3.6 25.2 1.0
OP1 D:DT28 3.9 40.8 1.0
MG A:MG1203 4.0 21.0 1.0
O A:VAL19 4.1 20.1 1.0
O A:HOH1369 4.2 29.1 1.0
CB A:ASP18 4.2 20.0 1.0
CG A:GLU516 4.2 21.8 1.0
O A:HOH1321 4.2 29.6 1.0
OP3 D:DT28 4.3 35.2 1.0
O5' D:DT28 4.3 39.2 1.0
CA A:ASP18 4.6 17.3 1.0
CB A:GLU516 4.6 16.2 1.0
OD2 A:ASP753 4.6 31.4 1.0
C5' D:DT28 4.6 35.6 1.0
NZ A:LYS743 4.8 27.8 1.0
C A:ASP18 4.9 20.3 1.0

Magnesium binding site 3 out of 10 in 8d2k

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Magnesium binding site 3 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1203

b:21.0
occ:1.00
 OD2 A:ASP18 2.0 22.5 1.0
OP3 D:DT28 2.0 35.2 1.0
ND1 A:HIS750 2.1 21.4 1.0
O A:HOH1321 2.3 29.6 1.0
O A:HOH1324 2.6 25.3 1.0
OP2 D:DT28 2.7 35.5 1.0
P D:DT28 2.9 38.6 1.0
CE1 A:HIS750 3.0 21.4 1.0
CG A:HIS750 3.2 19.9 1.0
CG A:ASP18 3.2 26.7 1.0
CB A:HIS750 3.5 22.2 1.0
CA A:HIS750 3.8 20.1 1.0
O5' D:DT28 4.0 39.2 1.0
OD1 A:ASP18 4.0 32.4 1.0
OP1 D:DT28 4.0 40.8 1.0
MG A:MG1202 4.0 30.3 1.0
C5' D:DT28 4.1 35.6 1.0
NE2 A:HIS750 4.2 17.9 1.0
CB A:ASP18 4.2 20.0 1.0
CD2 A:HIS750 4.3 19.5 1.0
OG A:SER23 4.3 22.5 1.0
O A:HOH1336 4.3 20.2 1.0
O A:HOH1309 4.3 18.2 1.0
CD2 A:HIS749 4.4 21.0 1.0
NE2 A:HIS749 4.4 21.4 1.0
O A:VAL19 4.4 20.1 1.0
OD2 A:ASP753 4.5 31.4 1.0
N A:HIS750 4.6 23.9 1.0
O A:ASP18 4.7 19.0 1.0
NZ A:LYS743 4.8 27.8 1.0
C A:HIS750 4.9 17.7 1.0

Magnesium binding site 4 out of 10 in 8d2k

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Magnesium binding site 4 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1204

b:13.8
occ:1.00
 O A:HOH1388 2.4 8.7 1.0
OP1 B:U22 2.8 6.3 1.0
OP2 B:A23 2.9 20.9 1.0
N A:ARG139 3.1 11.6 1.0
CG A:ARG139 3.2 6.6 1.0
O A:ARG137 3.3 14.5 1.0
O5' B:U22 3.6 16.1 1.0
P B:A23 3.6 9.3 1.0
C5' B:U22 3.7 9.8 1.0
OP1 B:A23 3.7 14.4 1.0
O B:HOH326 3.7 18.5 1.0
P B:U22 3.8 7.4 1.0
CA A:HIS138 3.9 12.4 1.0
C A:ARG137 3.9 5.5 1.0
CD A:ARG139 3.9 2.5 1.0
NE A:ARG139 4.0 6.0 1.0
C A:HIS138 4.0 11.3 1.0
O3' B:U22 4.0 13.3 1.0
CB A:ARG139 4.0 5.7 1.0
CA A:ARG139 4.0 8.4 1.0
N A:HIS138 4.1 15.4 1.0
O A:ALA136 4.1 10.1 1.0
N A:GLY140 4.2 10.0 1.0
C3' B:U22 4.4 7.5 1.0
C A:ARG139 4.5 10.4 1.0
O B:HOH348 4.5 16.6 1.0
OP2 B:U22 4.6 17.3 1.0
C4' B:U22 4.6 9.3 1.0
O A:GLY140 4.8 15.4 1.0
NH2 A:ARG80 4.8 1.3 1.0
CA A:ARG137 4.9 5.3 1.0

Magnesium binding site 5 out of 10 in 8d2k

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Magnesium binding site 5 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1205

b:21.5
occ:1.00
 OP1 B:C47 2.3 12.9 1.0
OP1 B:U24 2.5 27.4 1.0
N A:ASN198 2.9 14.3 1.0
O A:HOH1323 2.9 23.2 1.0
N A:LEU197 3.4 9.8 1.0
CB A:LEU197 3.6 10.6 1.0
CB A:ASN198 3.6 13.7 1.0
P B:C47 3.6 15.2 1.0
O B:HOH408 3.7 21.5 1.0
CA A:LEU197 3.7 9.3 1.0
CA A:ASN198 3.7 8.7 1.0
C A:LEU197 3.7 13.1 1.0
CG A:ARG196 3.8 14.2 1.0
O A:ASN198 3.9 24.2 1.0
ND2 A:ASN198 4.0 15.6 1.0
P B:U24 4.0 18.2 1.0
CG A:ASN198 4.1 15.5 1.0
OP2 B:C47 4.2 21.2 1.0
C5' B:U24 4.3 22.0 1.0
C A:ASN198 4.3 13.9 1.0
C A:ARG196 4.4 13.8 1.0
NH1 A:ARG196 4.4 18.6 1.0
O5' B:C47 4.5 18.5 1.0
CG A:LEU197 4.6 13.9 1.0
O5' B:U24 4.6 23.8 1.0
O3' B:A46 4.7 15.6 1.0
O3' B:A23 4.7 12.9 1.0
CD A:ARG196 4.7 11.9 1.0
O B:HOH328 4.8 19.9 1.0
CA A:ARG196 4.8 13.1 1.0
CB A:ARG196 4.9 14.3 1.0
O A:LEU197 4.9 17.4 1.0
C5' B:C47 4.9 11.6 1.0
OP2 B:U24 5.0 26.9 1.0
C4' B:U24 5.0 22.2 1.0

Magnesium binding site 6 out of 10 in 8d2k

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Magnesium binding site 6 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:32.3
occ:1.00
 O B:HOH383 2.4 22.3 1.0
O B:HOH328 2.8 19.9 1.0
OP2 B:C48 2.8 13.0 1.0
C5 B:C48 3.3 8.6 1.0
O B:HOH396 3.5 11.7 1.0
C6 B:C47 3.8 8.6 1.0
C6 B:C48 3.8 7.7 1.0
C5 B:C47 3.9 9.4 1.0
O B:HOH338 3.9 19.1 1.0
MG B:MG202 4.0 35.8 1.0
C3' B:C47 4.0 12.2 1.0
P B:C48 4.1 8.9 1.0
O5' B:C47 4.2 18.5 1.0
N1 B:C47 4.3 9.5 1.0
O5' B:C48 4.3 15.7 1.0
C4 B:C48 4.4 9.8 1.0
C4 B:C47 4.5 11.3 1.0
C2' B:C47 4.5 11.7 1.0
O3' B:C47 4.5 20.2 1.0
OP2 B:C47 4.5 21.2 1.0
O4 B:U49 4.6 21.3 1.0
N4 B:C48 4.7 15.0 1.0
C2 B:C47 4.8 13.8 1.0
N3 B:C47 4.9 13.4 1.0
C1' B:C47 4.9 10.7 1.0
C5 B:U49 5.0 8.7 1.0
C4' B:C47 5.0 11.6 1.0

Magnesium binding site 7 out of 10 in 8d2k

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Magnesium binding site 7 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:35.8
occ:1.00
 O B:HOH400 2.1 28.8 1.0
O B:HOH383 2.5 22.3 1.0
O B:HOH412 2.7 21.0 1.0
O B:HOH338 3.3 19.1 1.0
O B:HOH374 3.7 34.0 1.0
MG B:MG201 4.0 32.3 1.0
O B:HOH386 4.0 20.4 1.0
O B:HOH396 4.0 11.7 1.0
O B:HOH328 4.4 19.9 1.0
O4 B:U49 4.7 21.3 1.0
C5' B:U24 4.9 22.0 1.0
O B:HOH357 4.9 18.7 1.0
OP2 B:G25 4.9 15.9 1.0
OP2 B:C48 4.9 13.0 1.0
O5' B:U24 4.9 23.8 1.0
OP2 B:U24 4.9 26.9 1.0

Magnesium binding site 8 out of 10 in 8d2k

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Magnesium binding site 8 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:20.9
occ:1.00
 O B:HOH376 2.2 22.8 1.0
OP1 B:C52 2.2 22.4 1.0
O B:HOH329 2.3 15.9 1.0
O B:HOH305 2.3 17.2 1.0
P B:C52 3.6 13.1 1.0
O B:HOH390 4.1 15.2 1.0
O3' B:G51 4.1 22.8 1.0
C5' B:C52 4.1 9.0 1.0
O6 B:G72 4.1 12.4 1.0
O5' B:C52 4.2 19.9 1.0
OP1 B:A54 4.3 17.8 1.0
OP1 B:A53 4.3 12.4 1.0
O B:HOH341 4.5 21.5 1.0
O6 B:G55 4.5 25.4 1.0
OP2 B:A54 4.6 18.9 1.0
OP2 B:C52 4.7 17.5 1.0
P B:A54 4.9 7.1 1.0

Magnesium binding site 9 out of 10 in 8d2k

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Magnesium binding site 9 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:26.8
occ:1.00
 OP1 B:U78 2.0 20.2 1.0
O B:HOH324 2.1 21.9 1.0
O B:HOH308 2.2 12.1 1.0
O B:HOH364 2.2 20.7 1.0
P B:U78 3.5 18.8 1.0
O B:HOH409 4.1 16.9 1.0
O5' B:U78 4.1 16.1 1.0
O3' B:C77 4.3 8.4 1.0
OP2 B:U78 4.4 21.4 1.0
OP2 B:C77 4.5 21.4 1.0
C5' B:U78 4.5 10.5 1.0
C3' B:C77 4.6 7.9 1.0
O5' B:C77 4.7 8.4 1.0
OP2 B:U79 4.7 20.1 1.0
NH2 A:ARG832 4.8 5.3 1.0

Magnesium binding site 10 out of 10 in 8d2k

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Magnesium binding site 10 out of 10 in the Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Acidothermus Cellulolyticus CAS9 Ternary Complex (Cleavage Intermediate 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg205

b:20.7
occ:1.00
 OP2 B:U22 2.6 17.3 1.0
NH2 A:ARG80 3.0 1.3 1.0
O A:HOH1356 3.1 9.1 1.0
P B:U22 3.2 7.4 1.0
OP1 B:U22 3.3 6.3 1.0
O A:HOH1421 3.4 17.3 1.0
O3' B:G21 3.7 14.2 1.0
NH2 A:ARG139 3.7 1.4 1.0
CB A:ARG77 3.8 6.9 1.0
C5' B:G21 3.9 5.8 1.0
CG A:ARG77 3.9 4.1 1.0
CD A:ARG77 3.9 8.7 1.0
CZ A:ARG80 4.0 8.6 1.0
CG A:LEU73 4.1 7.0 1.0
NE A:ARG80 4.1 9.6 1.0
C3' B:G21 4.3 6.5 1.0
CD2 A:LEU73 4.3 14.6 1.0
O A:LEU73 4.3 14.6 1.0
CA A:ARG77 4.4 4.9 1.0
O A:HOH1388 4.5 8.7 1.0
CD1 A:LEU73 4.5 9.2 1.0
CZ A:ARG139 4.6 3.9 1.0
C4' B:G21 4.6 4.5 1.0
NE A:ARG139 4.7 6.0 1.0
O5' B:U22 4.7 16.1 1.0
O5' B:G21 4.7 11.1 1.0
N A:ARG77 4.8 4.9 1.0
NE A:ARG77 4.9 8.2 1.0

Reference:

A.Das, J.Rai, M.O.Roth, Y.Shu, M.L.Medina, M.R.Barakat, H.Li. Coupled Catalytic States and the Role of Metal Coordination in CAS9 Nat Catal V. 6 969 2023.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-023-01031-1
Page generated: Thu Dec 28 08:58:49 2023

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