Atomistry » Magnesium » PDB 4um5-4uuw » 4un3
Atomistry »
  Magnesium »
    PDB 4um5-4uuw »
      4un3 »

Magnesium in PDB 4un3: Crystal Structure of CAS9 Bound to Pam-Containing Dna Target

Protein crystallography data

The structure of Crystal Structure of CAS9 Bound to Pam-Containing Dna Target, PDB code: 4un3 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) 48.154 / 2.59
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.723, 68.142, 188.230, 90.00, 111.17, 90.00
R / Rfree (%) 21.71 / 25.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target (pdb code 4un3). 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, PDB code: 4un3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 1 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1082

b:28.0
occ:1.00
O A:HOH2101 2.0 43.2 1.0
OP1 A:U50 2.1 12.0 1.0
O A:HOH2083 2.1 12.9 1.0
O A:HOH2084 2.1 20.0 1.0
O A:HOH2086 2.2 26.5 1.0
O A:HOH2085 3.0 30.4 1.0
P A:U50 3.4 15.5 1.0
O A:HOH2118 3.7 47.6 1.0
O A:HOH2088 3.8 12.2 1.0
O6 A:G62 3.9 29.2 1.0
OP2 A:U50 4.0 22.6 1.0
O5' A:U50 4.1 22.3 1.0
OP1 A:A51 4.3 15.9 1.0
O6 A:G53 4.3 17.6 1.0
O A:HOH2011 4.3 15.1 1.0
OP1 A:A52 4.5 21.1 1.0
O A:HOH2008 4.5 31.7 1.0
C5' A:U50 4.5 10.0 1.0
O3' A:A49 4.5 22.1 1.0
OP2 A:A52 4.5 15.6 1.0
N7 A:G53 4.6 27.5 1.0
NZ B:LYS1123 4.7 35.6 1.0
N1 A:G62 4.8 32.1 1.0
C6 A:G62 4.8 27.8 1.0

Magnesium binding site 2 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 2 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1083

b:11.0
occ:1.00
O A:HOH2137 2.1 30.7 1.0
OG1 B:THR1102 2.3 19.0 1.0
O4 A:U66 2.6 29.2 1.0
OP2 A:A65 2.7 30.4 1.0
O A:HOH2126 3.2 19.4 1.0
O A:HOH2136 3.4 28.0 1.0
CB B:THR1102 3.5 22.9 1.0
C4 A:U66 3.6 29.2 1.0
CG2 B:THR1102 3.6 11.7 1.0
C5 A:U66 3.9 22.1 1.0
P A:A65 4.1 14.5 1.0
O B:HOH2186 4.1 41.5 1.0
OP2 A:U64 4.2 24.9 1.0
O A:HOH2132 4.5 32.5 1.0
N7 A:A65 4.5 22.4 1.0
OP1 A:U64 4.6 16.5 1.0
N4 A:C67 4.6 19.5 1.0
CA B:THR1102 4.7 22.3 1.0
O5' A:A65 4.7 24.6 1.0
OP1 A:A65 4.8 12.1 1.0
P A:U64 4.8 21.1 1.0
N B:THR1102 4.8 14.0 1.0
N3 A:U66 4.8 21.5 1.0
O B:VAL1100 4.8 24.0 1.0
C8 A:A65 4.9 23.3 1.0
O B:HOH2188 4.9 36.0 1.0

Magnesium binding site 3 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 3 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1084

b:27.6
occ:1.00
O A:HOH2043 1.9 29.2 1.0
OP2 A:G21 2.5 19.8 1.0
O A:HOH2041 3.0 29.1 1.0
O A:HOH2042 3.3 12.5 1.0
O A:HOH2070 3.3 29.5 1.0
P A:G21 3.6 32.1 1.0
OP1 A:G21 3.8 22.0 1.0
O A:HOH2040 3.9 25.0 1.0
MG A:MG1085 4.0 53.8 1.0
CB B:ARG403 4.3 29.5 1.0
OP2 A:U45 4.4 27.9 1.0
O5' A:G21 4.4 34.8 1.0
O A:HOH2073 4.5 20.4 1.0
O B:ARG403 4.7 27.1 1.0
O3' A:A20 4.8 29.9 1.0
CG B:ARG403 4.9 26.8 1.0

Magnesium binding site 4 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 4 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1085

b:53.8
occ:1.00
O A:HOH2045 2.1 47.4 1.0
O A:HOH2043 2.4 29.2 1.0
O A:HOH2071 3.9 23.4 1.0
MG A:MG1084 4.0 27.6 1.0
OP2 A:G21 4.1 19.8 1.0
O4 A:U22 4.1 24.4 1.0
N7 A:G21 4.2 30.0 1.0
NH1 B:ARG403 4.3 39.8 1.0
O A:HOH2076 4.5 26.8 1.0
O A:HOH2038 4.5 22.8 1.0
O A:HOH2042 4.7 12.5 1.0
C8 A:G21 4.8 25.7 1.0
CZ B:ARG403 4.9 43.0 1.0
C4 A:U22 5.0 23.4 1.0

Magnesium binding site 5 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 5 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2365

b:53.0
occ:1.00
OD2 B:ASP10 2.1 58.6 1.0
CG B:ASP10 2.8 48.9 1.0
OD1 B:ASP10 2.8 54.1 1.0
OE2 B:GLU762 3.1 37.0 1.0
O B:HOH2244 3.2 28.1 1.0
OD2 B:ASP986 3.3 39.1 1.0
OE1 B:GLU762 3.4 37.7 1.0
CD B:GLU762 3.5 41.2 1.0
CG B:ASP986 4.0 29.0 1.0
O B:HOH2010 4.1 32.9 1.0
CB B:ASP986 4.1 24.1 1.0
CB B:ASP10 4.2 34.1 1.0
CG B:GLU762 4.9 37.7 1.0
NZ B:LYS974 4.9 43.9 1.0

Magnesium binding site 6 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 6 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2366

b:25.6
occ:1.00
O B:HOH2139 2.1 39.9 1.0
O B:TYR656 2.1 40.3 1.0
O B:LEU623 2.6 26.1 1.0
O B:THR624 2.7 30.8 1.0
O B:PHE626 3.0 35.6 1.0
C B:THR624 3.3 26.4 1.0
C B:TYR656 3.3 38.7 1.0
CA B:THR624 3.4 22.5 1.0
C B:LEU623 3.6 22.3 1.0
N B:TYR656 3.8 45.8 1.0
C B:PHE626 3.9 29.1 1.0
N B:THR624 4.0 19.4 1.0
CA B:TYR656 4.2 41.8 1.0
N B:THR657 4.2 43.1 1.0
CG2 B:THR657 4.2 33.4 1.0
CB B:GLU627 4.3 47.3 1.0
CA B:THR657 4.4 36.5 1.0
N B:LEU625 4.4 26.2 1.0
N B:PHE626 4.5 31.2 1.0
N B:GLU627 4.5 30.8 1.0
CA B:GLU627 4.6 49.3 1.0
OP1 C:DC16 4.6 43.9 1.0
CB B:THR624 4.7 33.0 1.0
CB B:ARG655 4.7 61.0 1.0
C B:ARG655 4.7 52.3 1.0
CA B:PHE626 4.8 23.6 1.0
CG2 B:THR624 4.8 33.1 1.0
C B:LEU625 4.9 26.5 1.0
CB B:THR657 4.9 28.3 1.0
CA B:ARG655 5.0 58.4 1.0
CG B:ARG655 5.0 67.3 1.0

Magnesium binding site 7 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 7 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2367

b:15.8
occ:1.00
O B:GLN1350 2.2 35.4 1.0
O B:HOH2184 2.4 13.9 1.0
O B:HOH2242 2.9 40.4 1.0
O A:HOH2138 3.0 23.2 1.0
O A:HOH2140 3.1 32.1 1.0
O4' A:A68 3.1 34.4 1.0
C B:GLN1350 3.3 30.0 1.0
O B:SER1351 3.6 22.6 1.0
C1' A:A68 3.6 45.4 1.0
C B:SER1351 3.8 26.4 1.0
N9 A:A68 4.0 48.7 1.0
N B:SER1351 4.2 32.7 1.0
CA B:GLN1350 4.2 32.5 1.0
CB B:GLN1350 4.2 31.0 1.0
CA B:SER1351 4.3 28.1 1.0
O5' A:A68 4.4 14.3 1.0
C8 A:A68 4.4 49.4 1.0
C4' A:A68 4.4 33.0 1.0
N B:ILE1352 4.4 22.9 1.0
O A:HOH2139 4.5 36.5 1.0
N B:GLN1350 4.5 33.1 1.0
OP1 A:A68 4.7 26.1 1.0
OG1 B:THR1098 4.8 28.2 1.0
C4 A:A68 4.8 50.2 1.0
CG1 B:VAL1095 4.8 25.1 1.0
CA B:ILE1352 4.8 29.6 1.0
O B:HOH2243 4.8 40.0 1.0
C5' A:A68 4.9 20.7 1.0
CG2 B:THR1098 5.0 17.9 1.0
P A:A68 5.0 25.9 1.0

Magnesium binding site 8 out of 8 in 4un3

Go back to Magnesium Binding Sites List in 4un3
Magnesium binding site 8 out of 8 in the Crystal Structure of CAS9 Bound to Pam-Containing Dna Target


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2368

b:36.8
occ:1.00
O B:GLU584 2.2 65.6 1.0
O B:HOH2128 2.3 39.1 1.0
O B:ARG586 2.7 47.8 1.0
C B:GLU584 3.2 58.5 1.0
ND2 B:ASN588 3.5 41.2 1.0
CB B:GLU584 3.6 80.5 1.0
N B:ARG586 3.7 46.8 1.0
CA B:GLU584 3.7 58.0 1.0
C B:ARG586 3.8 42.1 1.0
O B:HOH2131 3.8 40.0 1.0
N B:GLU584 3.9 48.6 1.0
CG B:ASN588 4.2 40.2 1.0
CG B:GLU584 4.3 0.3 1.0
OD1 B:ASN588 4.3 36.2 1.0
CA B:ARG586 4.3 38.5 1.0
N B:ASP585 4.4 55.8 1.0
CB B:ASP585 4.5 52.2 1.0
C B:ASP585 4.7 51.4 1.0
CA B:ASP585 4.7 52.6 1.0
CG B:ARG586 4.7 48.5 1.0
N B:ASN588 4.8 29.1 1.0
OE1 B:GLU584 4.8 0.7 1.0
CG2 B:VAL583 4.9 36.9 1.0
N B:PHE587 4.9 39.2 1.0
CD B:GLU584 4.9 0.5 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: Mon Dec 14 19:37:36 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy