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Magnesium in PDB 4un4: Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2

Protein crystallography data

The structure of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2, PDB code: 4un4 was solved by C.Anders, O.Niewoehner, A.Duerst, M.Jinek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.493 / 2.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.780, 66.816, 186.834, 90.00, 111.39, 90.00
R / Rfree (%) 21.69 / 24.81

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 (pdb code 4un4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2, PDB code: 4un4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4un4

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Magnesium binding site 1 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1082

b:36.1
occ:1.00
 O A:HOH3069 1.9 40.9 1.0
O A:HOH3067 2.0 33.4 1.0
O A:HOH3070 2.1 28.9 1.0
O A:HOH3204 2.1 17.2 1.0
O4 A:U22 3.8 19.4 1.0
OP2 A:G21 3.8 20.9 1.0
N7 A:G21 4.0 17.6 1.0
O A:HOH3104 4.0 16.2 1.0
MG A:MG1085 4.3 13.8 1.0
O A:HOH3111 4.3 27.7 1.0
O A:HOH3071 4.4 21.8 1.0
C4 A:U22 4.7 22.9 1.0
C8 A:G21 4.7 18.0 1.0
NH1 B:ARG403 4.7 33.0 1.0
O A:HOH3113 4.9 26.2 1.0
C5 A:U22 4.9 19.8 1.0
O A:HOH3068 4.9 27.9 1.0

Magnesium binding site 2 out of 8 in 4un4

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Magnesium binding site 2 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1083

b:34.1
occ:1.00
 OP1 A:U50 2.0 14.2 1.0
O A:HOH3138 2.1 17.3 1.0
O A:HOH3122 2.2 19.8 1.0
O A:HOH3124 2.3 9.8 1.0
O A:HOH3121 2.5 14.5 1.0
P A:U50 3.1 19.3 1.0
O A:HOH3126 3.5 19.0 1.0
OP2 A:U50 3.5 20.6 1.0
O5' A:U50 3.8 24.6 1.0
O A:HOH3158 3.8 18.9 1.0
OP1 A:A51 4.0 16.6 1.0
O6 A:G62 4.1 21.4 1.0
O A:HOH3123 4.2 35.2 1.0
O3' A:A49 4.4 18.3 1.0
C5' A:U50 4.5 22.2 1.0
NZ B:LYS1123 4.7 18.1 1.0
OP1 A:A52 4.9 18.1 1.0
O6 A:G53 5.0 26.8 1.0

Magnesium binding site 3 out of 8 in 4un4

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Magnesium binding site 3 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1084

b:6.6
occ:1.00
 OG1 B:THR1102 2.4 16.9 1.0
O4 A:U66 2.6 22.5 1.0
OP2 A:A65 2.7 21.0 1.0
O A:HOH3189 2.9 25.4 1.0
O A:HOH3171 3.0 15.6 1.0
O A:HOH3188 3.2 21.9 1.0
O A:HOH3173 3.3 41.1 1.0
C4 A:U66 3.5 21.1 1.0
CB B:THR1102 3.6 22.1 1.0
C5 A:U66 3.8 17.5 1.0
CG2 B:THR1102 3.8 18.9 1.0
O B:HOH3353 4.1 20.2 1.0
P A:A65 4.1 21.5 1.0
OP2 A:U64 4.3 25.3 1.0
N4 A:C67 4.4 13.6 1.0
N7 A:A65 4.5 20.8 1.0
O A:HOH3181 4.6 36.0 1.0
O5' A:A65 4.7 17.7 1.0
CA B:THR1102 4.8 21.2 1.0
O B:HOH3357 4.8 41.3 1.0
O B:VAL1100 4.8 22.5 1.0
OP1 A:U64 4.8 17.6 1.0
N B:THR1102 4.8 17.2 1.0
N3 A:U66 4.8 18.6 1.0
OP1 A:A65 4.8 20.8 1.0
C8 A:A65 4.9 20.6 1.0
P A:U64 4.9 20.5 1.0

Magnesium binding site 4 out of 8 in 4un4

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Magnesium binding site 4 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1085

b:13.8
occ:1.00
 O A:HOH3066 2.8 24.3 1.0
O A:HOH3067 2.8 33.4 1.0
OP2 A:G21 2.9 20.9 1.0
O A:HOH3102 3.0 31.4 1.0
O A:HOH3068 3.5 27.9 1.0
OP1 A:G21 3.6 23.0 1.0
P A:G21 3.7 24.6 1.0
O A:HOH3108 4.1 32.4 1.0
OP2 A:U45 4.2 24.9 1.0
CB B:ARG403 4.2 33.2 1.0
MG A:MG1082 4.3 36.1 1.0
O A:HOH3069 4.4 40.9 1.0
O A:HOH3104 4.5 16.2 1.0
O5' A:G21 4.7 23.5 1.0
CG B:ARG403 4.7 31.6 1.0
O B:ARG403 4.9 28.7 1.0
O3' A:A20 5.0 25.2 1.0

Magnesium binding site 5 out of 8 in 4un4

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Magnesium binding site 5 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2365

b:23.1
occ:1.00
 O B:TYR656 2.2 29.8 1.0
O B:HOH3245 2.2 48.4 1.0
O B:THR624 2.3 19.1 1.0
O B:PHE626 2.5 37.6 1.0
O B:LEU623 2.6 29.3 1.0
C B:THR624 3.1 20.3 1.0
CA B:THR624 3.4 21.1 1.0
C B:TYR656 3.4 20.1 1.0
O B:HOH3244 3.5 33.5 1.0
C B:PHE626 3.6 35.7 1.0
C B:LEU623 3.6 24.0 1.0
N B:THR624 4.0 21.5 1.0
N B:TYR656 4.0 23.7 1.0
N B:PHE626 4.0 36.0 1.0
N B:LEU625 4.2 25.8 1.0
CA B:TYR656 4.3 21.2 1.0
N B:THR657 4.3 18.5 1.0
CG2 B:THR657 4.4 26.6 1.0
CA B:PHE626 4.4 34.0 1.0
CA B:THR657 4.4 22.3 1.0
N B:GLU627 4.5 36.7 1.0
C B:LEU625 4.5 33.8 1.0
CA B:GLU627 4.6 38.3 1.0
OP1 E:DC16 4.6 40.3 1.0
CB B:THR624 4.7 13.2 1.0
CB B:GLU627 4.8 40.8 1.0
CB B:ARG655 4.8 49.5 1.0
CA B:LEU625 4.9 28.2 1.0
CG2 B:THR624 4.9 9.0 1.0
C B:ARG655 4.9 29.0 1.0
CB B:THR657 5.0 24.8 1.0

Magnesium binding site 6 out of 8 in 4un4

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Magnesium binding site 6 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2366

b:16.4
occ:1.00
 O A:HOH3190 2.4 28.0 1.0
O B:GLN1350 2.8 32.6 1.0
O A:HOH3192 2.9 28.2 1.0
O B:HOH3351 3.0 24.8 1.0
O4' A:A68 3.3 32.8 1.0
C B:GLN1350 3.8 30.5 1.0
C1' A:A68 3.8 33.8 1.0
O B:SER1351 3.9 24.2 1.0
C B:SER1351 4.1 24.8 1.0
N9 A:A68 4.3 33.5 1.0
OG1 B:THR1098 4.4 17.4 1.0
O5' A:A68 4.5 21.9 1.0
O A:HOH3193 4.5 21.8 1.0
C4' A:A68 4.5 31.3 1.0
CA B:SER1351 4.6 31.4 1.0
N B:SER1351 4.6 30.8 1.0
CB B:GLN1350 4.6 27.6 1.0
CA B:GLN1350 4.6 28.2 1.0
CG1 B:VAL1095 4.6 13.0 1.0
C8 A:A68 4.6 34.1 1.0
OP1 A:A68 4.7 28.7 1.0
N B:ILE1352 4.7 18.5 1.0
N B:GLN1350 4.8 27.5 1.0
N B:THR1098 4.9 15.7 1.0
OP2 A:A68 4.9 28.1 1.0
O B:HOH3450 4.9 33.4 1.0
P A:A68 4.9 26.5 1.0
CA B:ILE1352 5.0 21.9 1.0
CG2 B:THR1098 5.0 13.2 1.0

Magnesium binding site 7 out of 8 in 4un4

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Magnesium binding site 7 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2367

b:33.0
occ:1.00
 O B:HOH3112 2.1 45.2 1.0
O B:GLU232 2.2 52.1 1.0
O B:LEU229 2.3 45.4 1.0
O B:ILE226 2.6 28.0 1.0
C B:GLU232 3.4 47.6 1.0
CG2 B:ILE226 3.4 42.8 1.0
C B:LEU229 3.4 40.2 1.0
C B:ILE226 3.6 35.0 1.0
N B:GLU232 3.8 55.9 1.0
CA B:GLU232 4.1 48.1 1.0
N B:GLY231 4.2 46.6 1.0
CA B:PRO230 4.3 38.5 1.0
N B:PRO230 4.3 39.2 1.0
CA B:LEU229 4.4 34.1 1.0
N B:ALA227 4.4 40.2 1.0
CB B:GLU232 4.4 44.6 1.0
N B:LYS233 4.4 42.8 1.0
CA B:ALA227 4.4 41.3 1.0
C B:PRO230 4.5 40.9 1.0
CA B:ILE226 4.5 36.5 1.0
N B:LEU229 4.5 33.7 1.0
CB B:ILE226 4.6 41.4 1.0
CB B:LEU229 4.6 30.3 1.0
C B:GLY231 4.6 59.9 1.0
CA B:LYS233 4.7 40.9 1.0
C B:ALA227 4.7 40.8 1.0
O B:ALA227 4.7 45.0 1.0
CA B:GLY231 5.0 53.7 1.0

Magnesium binding site 8 out of 8 in 4un4

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Magnesium binding site 8 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target with Mismatches at Positions 1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2368

b:19.4
occ:1.00
 CG B:GLU584 2.2 59.9 1.0
OD1 B:ASN588 2.4 27.8 1.0
O B:GLU584 2.7 31.2 1.0
OE2 B:GLU584 2.7 53.7 1.0
CD B:GLU584 2.7 57.8 1.0
O B:ARG586 2.8 28.4 1.0
CG B:ASN588 3.4 24.6 1.0
CB B:GLU584 3.4 51.9 1.0
C B:GLU584 3.6 34.5 1.0
OE1 B:GLU584 3.7 59.6 1.0
ND2 B:ASN588 3.8 25.0 1.0
CA B:GLU584 3.9 38.3 1.0
N B:GLU584 3.9 34.9 1.0
C B:ARG586 4.0 30.0 1.0
O B:HOH3225 4.3 41.2 1.0
N B:ARG586 4.3 26.4 1.0
N B:ASN588 4.5 17.1 1.0
CB B:ASN588 4.7 26.3 1.0
CA B:ARG586 4.8 30.4 1.0
CG2 B:VAL583 4.8 28.2 1.0
N B:ASP585 4.8 32.8 1.0
O B:HOH3191 4.8 21.6 1.0
C B:PHE587 4.9 21.0 1.0
CA B:ASN588 4.9 23.1 1.0
CG B:ARG586 4.9 46.0 1.0
N B:PHE587 5.0 22.5 1.0

Reference:

C.Anders, O.Niewoehner, A.Duerst, M.Jinek. Structural Basis of Pam-Dependent Target Dna Recognition By the CAS9 Endonuclease Nature V. 513 569 2014.
ISSN: ISSN 0028-0836
PubMed: 25079318
DOI: 10.1038/NATURE13579
Page generated: Tue Aug 20 04:52:12 2024

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