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Magnesium in PDB 4un5: Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3

Protein crystallography data

The structure of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3, PDB code: 4un5 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) 48.349 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 180.182, 68.072, 190.261, 90.00, 111.37, 90.00
R / Rfree (%) 21.49 / 24.65

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3 (pdb code 4un5). 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 Containing Mismatches at Positions 1-3, PDB code: 4un5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4un5

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


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1082

b:29.8
occ:1.00
 OP1 A:U50 2.1 12.9 1.0
O A:HOH2145 2.1 17.5 1.0
O A:HOH2144 2.1 14.8 1.0
O A:HOH2146 2.2 16.1 1.0
O A:HOH2162 2.2 19.4 1.0
P A:U50 3.4 17.9 1.0
OP2 A:U50 3.9 18.1 1.0
O6 A:G62 4.0 22.5 1.0
O A:HOH2025 4.1 25.4 1.0
O5' A:U50 4.1 24.4 1.0
O A:HOH2143 4.1 32.2 1.0
O A:HOH2149 4.1 20.0 1.0
O A:HOH2182 4.2 26.4 1.0
O A:HOH2018 4.2 37.0 1.0
OP1 A:A51 4.4 17.9 1.0
O A:HOH2137 4.4 34.1 1.0
NZ B:LYS1123 4.4 19.3 1.0
OP1 A:A52 4.5 17.8 1.0
C5' A:U50 4.6 18.7 1.0
O3' A:A49 4.6 17.8 1.0
O6 A:G53 4.7 21.0 1.0
OP2 A:A52 4.7 24.1 1.0
N7 A:G53 4.8 20.3 1.0
C6 A:G62 5.0 19.7 1.0

Magnesium binding site 2 out of 8 in 4un5

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


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1083

b:6.3
occ:1.00
 O A:HOH2202 2.2 44.4 1.0
OG1 B:THR1102 2.4 18.4 1.0
O A:HOH2214 2.4 22.4 1.0
O4 A:U66 2.7 23.8 1.0
OP2 A:A65 2.7 22.3 1.0
O A:HOH2192 3.1 18.5 1.0
O A:HOH2194 3.4 38.4 1.0
CB B:THR1102 3.6 19.8 1.0
C4 A:U66 3.6 16.7 1.0
CG2 B:THR1102 3.8 14.6 1.0
C5 A:U66 3.9 9.3 1.0
P A:A65 4.1 16.4 1.0
OP2 A:U64 4.3 24.5 1.0
O B:HOH3387 4.3 9.2 1.0
N7 A:A65 4.6 20.2 1.0
O A:HOH2206 4.6 30.2 1.0
N4 A:C67 4.6 11.6 1.0
O B:HOH3389 4.7 45.4 1.0
O5' A:A65 4.7 12.6 1.0
OP1 A:U64 4.8 19.6 1.0
CA B:THR1102 4.8 21.8 1.0
N B:THR1102 4.9 22.1 1.0
OP1 A:A65 4.9 15.2 1.0
N3 A:U66 4.9 16.5 1.0
C8 A:A65 4.9 20.3 1.0
P A:U64 4.9 21.0 1.0
O B:VAL1100 4.9 20.6 1.0

Magnesium binding site 3 out of 8 in 4un5

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


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1084

b:50.9
occ:1.00
 O A:HOH2082 2.0 43.4 1.0
O A:HOH2084 2.0 39.9 1.0
O A:HOH2233 2.1 24.4 1.0
OP2 A:G21 3.8 25.3 1.0
N7 A:G21 4.1 17.5 1.0
O4 A:U22 4.2 12.8 1.0
O A:HOH2123 4.2 18.0 1.0
MG A:MG1085 4.3 21.2 1.0
O A:HOH2085 4.4 31.2 1.0
O A:HOH2129 4.5 27.9 1.0
NH1 B:ARG403 4.6 40.3 1.0
C8 A:G21 4.7 17.8 1.0
O A:HOH2074 4.7 19.2 1.0
O A:HOH2131 4.9 25.8 1.0
O A:HOH2083 4.9 15.7 1.0

Magnesium binding site 4 out of 8 in 4un5

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Magnesium binding site 4 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1085

b:21.2
occ:1.00
 O A:HOH2082 2.5 43.4 1.0
O A:HOH2080 2.9 22.8 1.0
OP2 A:G21 2.9 25.3 1.0
O A:HOH2121 2.9 26.5 1.0
O A:HOH2083 3.4 15.7 1.0
O A:HOH2079 3.8 33.7 1.0
OP1 A:G21 3.8 26.9 1.0
P A:G21 3.8 27.0 1.0
O A:HOH2126 4.0 27.5 1.0
MG A:MG1084 4.3 50.9 1.0
OP2 A:U45 4.3 22.2 1.0
CB B:ARG403 4.4 24.6 1.0
O A:HOH2123 4.5 18.0 1.0
O5' A:G21 4.7 26.8 1.0
CG B:ARG403 4.9 23.9 1.0

Magnesium binding site 5 out of 8 in 4un5

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Magnesium binding site 5 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2365

b:22.2
occ:1.00
 O B:HOH3261 2.1 43.9 1.0
O B:TYR656 2.2 25.9 1.0
O B:THR624 2.3 22.4 1.0
O B:PHE626 2.5 32.0 1.0
O B:LEU623 2.6 23.1 1.0
C B:THR624 3.0 22.4 1.0
CA B:THR624 3.3 18.6 1.0
C B:TYR656 3.4 20.9 1.0
C B:LEU623 3.6 22.2 1.0
C B:PHE626 3.6 30.8 1.0
N B:THR624 3.9 21.9 1.0
N B:TYR656 4.0 25.2 1.0
N B:PHE626 4.1 30.4 1.0
N B:LEU625 4.2 23.8 1.0
CA B:TYR656 4.3 23.5 1.0
CG2 B:THR657 4.3 23.5 1.0
O B:HOH3262 4.4 41.5 1.0
N B:THR657 4.4 19.8 1.0
CA B:PHE626 4.4 30.2 1.0
N B:GLU627 4.5 30.4 1.0
C B:LEU625 4.5 29.5 1.0
CA B:THR657 4.6 21.5 1.0
CA B:GLU627 4.6 34.6 1.0
CB B:THR624 4.7 12.6 1.0
CB B:GLU627 4.8 39.4 1.0
CB B:ARG655 4.8 49.2 1.0
OP1 E:DC16 4.8 34.9 1.0
CG2 B:THR624 4.8 8.8 1.0
CA B:LEU625 4.9 21.6 1.0
C B:ARG655 4.9 29.4 1.0
CA B:LEU623 4.9 18.0 1.0

Magnesium binding site 6 out of 8 in 4un5

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Magnesium binding site 6 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2366

b:13.8
occ:1.00
 O B:GLN1350 2.3 17.7 1.0
O A:HOH2215 2.3 21.8 1.0
O B:HOH3489 3.0 31.4 1.0
O B:HOH3385 3.1 26.5 1.0
O A:HOH2217 3.2 30.5 1.0
O4' A:A68 3.2 27.7 1.0
C B:GLN1350 3.4 22.6 1.0
C1' A:A68 3.7 31.3 1.0
O B:SER1351 3.9 20.1 1.0
C B:SER1351 4.0 21.5 1.0
N9 A:A68 4.1 29.9 1.0
N B:SER1351 4.3 21.5 1.0
CA B:SER1351 4.3 23.1 1.0
CA B:GLN1350 4.3 23.2 1.0
CB B:GLN1350 4.4 21.2 1.0
C8 A:A68 4.4 30.7 1.0
O A:HOH2218 4.5 21.9 1.0
OG1 B:THR1098 4.5 20.8 1.0
O5' A:A68 4.5 21.9 1.0
C4' A:A68 4.5 29.7 1.0
N B:GLN1350 4.6 21.9 1.0
N B:ILE1352 4.6 18.7 1.0
OP1 A:A68 4.7 27.4 1.0
CG1 B:VAL1095 4.9 17.0 1.0
CA B:ILE1352 4.9 20.9 1.0
C4 A:A68 4.9 28.6 1.0
P A:A68 5.0 26.7 1.0
OP2 A:A68 5.0 25.2 1.0

Magnesium binding site 7 out of 8 in 4un5

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Magnesium binding site 7 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target Containing Mismatches at Positions 1-3


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2367

b:43.8
occ:1.00
 O B:GLU232 2.2 52.8 1.0
O B:LEU229 2.3 55.8 1.0
O B:ILE226 3.0 34.6 1.0
O B:HOH3490 3.3 40.0 1.0
C B:GLU232 3.3 53.6 1.0
C B:LEU229 3.5 48.4 1.0
CG2 B:ILE226 3.6 40.8 1.0
N B:GLU232 3.7 55.3 1.0
C B:ILE226 4.0 38.9 1.0
CA B:GLU232 4.0 51.9 1.0
N B:GLY231 4.2 49.6 1.0
CA B:PRO230 4.3 41.0 1.0
N B:LYS233 4.4 51.0 1.0
N B:PRO230 4.4 44.6 1.0
CB B:GLU232 4.4 47.8 1.0
C B:PRO230 4.5 45.4 1.0
CA B:LEU229 4.5 39.0 1.0
C B:GLY231 4.6 60.5 1.0
CA B:LYS233 4.6 48.3 1.0
N B:LEU229 4.7 36.7 1.0
CB B:LEU229 4.8 36.9 1.0
CB B:ILE226 4.8 39.5 1.0
N B:ALA227 4.8 42.2 1.0
CA B:ILE226 4.8 38.3 1.0
CA B:ALA227 4.8 44.3 1.0
CA B:GLY231 5.0 55.7 1.0

Magnesium binding site 8 out of 8 in 4un5

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


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 Containing Mismatches at Positions 1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2368

b:31.5
occ:1.00
 O B:GLU584 2.3 23.8 1.0
CG B:GLU584 2.4 61.4 1.0
O B:ARG586 2.5 25.4 1.0
CD B:GLU584 3.3 61.3 1.0
OD1 B:ASN588 3.4 29.1 1.0
C B:GLU584 3.4 29.5 1.0
OE2 B:GLU584 3.4 56.1 1.0
O B:HOH3243 3.6 37.0 1.0
CB B:GLU584 3.6 51.5 1.0
C B:ARG586 3.7 25.8 1.0
N B:ARG586 3.8 22.5 1.0
CA B:GLU584 3.9 35.9 1.0
N B:GLU584 3.9 31.2 1.0
CG B:ASN588 4.0 25.2 1.0
ND2 B:ASN588 4.2 24.6 1.0
OE1 B:GLU584 4.3 65.6 1.0
CA B:ARG586 4.3 27.8 1.0
N B:ASP585 4.5 26.2 1.0
CG B:ARG586 4.5 43.1 1.0
O B:HOH3240 4.6 28.7 1.0
CG2 B:VAL583 4.6 19.2 1.0
CB B:ASP585 4.7 33.8 1.0
N B:ASN588 4.7 14.0 1.0
N B:PHE587 4.7 18.1 1.0
C B:PHE587 4.8 17.7 1.0
C B:ASP585 4.8 24.8 1.0
CA B:ASP585 4.9 27.1 1.0
CA B:PHE587 4.9 15.9 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 04:52:15 2024

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