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Manganese in PDB 7mi4: Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex

Enzymatic activity of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex

All present enzymatic activity of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex:
3.1.12.1;

Other elements in 7mi4:

The structure of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex (pdb code 7mi4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex, PDB code: 7mi4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7mi4

Go back to Manganese Binding Sites List in 7mi4
Manganese binding site 1 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:55.4
occ:1.00
 OE2 A:GLU380 2.1 73.7 1.0
OE2 A:GLU466 2.3 57.5 1.0
CD A:GLU466 3.1 57.5 1.0
CD A:GLU380 3.2 73.7 1.0
NE2 A:HIS451 3.3 59.7 1.0
OE1 A:GLU466 3.3 57.5 1.0
OE1 A:GLU380 3.6 73.7 1.0
CE1 A:HIS451 3.8 59.7 1.0
CG A:GLU380 4.5 73.7 1.0
CG A:GLU466 4.5 57.5 1.0
CD2 A:HIS451 4.5 59.7 1.0
NH1 A:ARG469 4.8 57.2 1.0
CZ A:ARG469 4.9 57.2 1.0

Manganese binding site 2 out of 8 in 7mi4

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Manganese binding site 2 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:78.9
occ:1.00
 OE2 B:GLU380 2.4 95.7 1.0
OE1 B:GLU466 2.5 77.1 1.0
CD B:GLU466 3.3 77.1 1.0
OE2 B:GLU466 3.4 77.1 1.0
CD B:GLU380 3.4 95.7 1.0
NE2 B:HIS451 3.9 64.5 1.0
OE1 B:GLU380 4.0 95.7 1.0
CE1 B:HIS451 4.2 64.5 1.0
CG B:GLU380 4.6 95.7 1.0
CG B:GLU466 4.6 77.1 1.0
NH1 B:ARG469 4.8 83.9 1.0
NE B:ARG469 4.9 83.9 1.0

Manganese binding site 3 out of 8 in 7mi4

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Manganese binding site 3 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:60.7
occ:1.00
 OE2 C:GLU380 2.1 74.4 1.0
OE2 C:GLU466 2.3 57.3 1.0
CD C:GLU466 3.1 57.3 1.0
CD C:GLU380 3.2 74.4 1.0
NE2 C:HIS451 3.3 59.2 1.0
OE1 C:GLU466 3.3 57.3 1.0
OE1 C:GLU380 3.6 74.4 1.0
CE1 C:HIS451 3.8 59.2 1.0
CG C:GLU380 4.5 74.4 1.0
CG C:GLU466 4.5 57.3 1.0
CD2 C:HIS451 4.5 59.2 1.0
NH1 C:ARG469 4.8 59.0 1.0
CZ C:ARG469 4.9 59.0 1.0

Manganese binding site 4 out of 8 in 7mi4

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Manganese binding site 4 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn603

b:86.0
occ:1.00
 NE2 C:HIS48 1.8 75.9 1.0
OD2 C:ASP87 1.8 80.0 1.0
OD1 C:ASP100 2.3 76.8 1.0
OP1 G:DG32 2.4 64.9 1.0
O C:TYR101 2.4 75.3 1.0
CE1 C:HIS48 2.8 75.9 1.0
CD2 C:HIS48 2.9 75.9 1.0
CG C:ASP87 3.1 80.0 1.0
N C:TYR101 3.2 75.3 1.0
C C:TYR101 3.3 75.3 1.0
CG C:ASP100 3.5 76.8 1.0
CA C:TYR101 3.5 75.3 1.0
CB C:TYR101 3.7 75.3 1.0
OD1 C:ASP87 3.7 80.0 1.0
P G:DG32 3.8 64.9 1.0
ND1 C:HIS48 3.9 75.9 1.0
CG C:HIS48 4.0 75.9 1.0
C C:ASP100 4.1 76.8 1.0
CB C:ASP87 4.2 80.0 1.0
OD2 C:ASP100 4.2 76.8 1.0
O5' G:DG32 4.5 64.9 1.0
CA C:ASP100 4.5 76.8 1.0
N C:LYS102 4.5 73.5 1.0
OP1 G:DA33 4.6 61.8 1.0
CB C:ASP100 4.6 76.8 1.0
OP2 G:DG32 4.7 64.9 1.0
C5' G:DG32 4.7 64.9 1.0
O3' G:DT31 4.8 70.1 1.0
CG C:TYR101 4.9 75.3 1.0
OP2 G:DA33 4.9 61.8 1.0

Manganese binding site 5 out of 8 in 7mi4

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Manganese binding site 5 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn701

b:81.4
occ:1.00
 OE2 D:GLU380 2.4 102.2 1.0
OE1 D:GLU466 2.5 85.5 1.0
CD D:GLU466 3.3 85.5 1.0
OE2 D:GLU466 3.4 85.5 1.0
CD D:GLU380 3.4 102.2 1.0
NE2 D:HIS451 3.9 72.0 1.0
OE1 D:GLU380 4.0 102.2 1.0
CE1 D:HIS451 4.2 72.0 1.0
CG D:GLU380 4.6 102.2 1.0
CG D:GLU466 4.6 85.5 1.0
NH1 D:ARG469 4.8 89.0 1.0
NE D:ARG469 4.9 89.0 1.0

Manganese binding site 6 out of 8 in 7mi4

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Manganese binding site 6 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn101

b:37.3
occ:1.00
 OP1 H:DC15 2.0 59.8 1.0
OG E:SER34 2.3 47.3 1.0
O E:TYR9 2.4 50.6 1.0
OD1 E:ASP10 2.4 53.9 1.0
CB E:SER34 3.1 47.3 1.0
P H:DC15 3.5 59.8 1.0
C E:TYR9 3.5 50.6 1.0
CG E:ASP10 3.7 53.9 1.0
N E:ASP10 4.2 53.9 1.0
CA E:ASP10 4.2 53.9 1.0
CB F:LEU33 4.3 49.5 1.0
O3' H:DC14 4.3 65.5 1.0
OP2 H:DC15 4.4 59.8 1.0
O5' H:DC15 4.4 59.8 1.0
OD2 E:ASP10 4.5 53.9 1.0
N E:TYR9 4.5 50.6 1.0
CB E:ASP10 4.5 53.9 1.0
C5' H:DC15 4.5 59.8 1.0
CA E:SER34 4.6 47.3 1.0
CA E:TYR9 4.6 50.6 1.0
O E:SER34 4.6 47.3 1.0

Manganese binding site 7 out of 8 in 7mi4

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Manganese binding site 7 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn101

b:43.8
occ:1.00
 OP1 G:DC15 2.0 60.0 1.0
OG F:SER34 2.3 49.9 1.0
O F:TYR9 2.4 51.5 1.0
OD1 F:ASP10 2.4 56.2 1.0
CB F:SER34 3.1 49.9 1.0
P G:DC15 3.5 60.0 1.0
C F:TYR9 3.5 51.5 1.0
CG F:ASP10 3.7 56.2 1.0
C5' G:DC15 4.0 60.0 1.0
O5' G:DC15 4.0 60.0 1.0
N F:ASP10 4.2 56.2 1.0
CB E:LEU33 4.2 49.8 1.0
CA F:ASP10 4.2 56.2 1.0
O3' G:DC14 4.4 65.0 1.0
OP2 G:DC15 4.4 60.0 1.0
OD2 F:ASP10 4.5 56.2 1.0
N F:TYR9 4.5 51.5 1.0
CB F:ASP10 4.5 56.2 1.0
CA F:SER34 4.6 49.9 1.0
CA F:TYR9 4.6 51.5 1.0
O F:SER34 4.6 49.9 1.0
N E:LEU33 5.0 49.8 1.0

Manganese binding site 8 out of 8 in 7mi4

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Manganese binding site 8 out of 8 in the Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Symmetrical Pam-Pam Prespacer Bound CAS4/CAS1/CAS2 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn801

b:80.0
occ:1.00
 OP1 H:DG32 1.6 64.3 1.0
NE2 A:HIS48 1.8 70.0 1.0
OD2 A:ASP87 1.8 72.8 1.0
OD1 A:ASP100 2.3 70.7 1.0
O A:TYR101 2.4 70.6 1.0
CE1 A:HIS48 2.8 70.0 1.0
CD2 A:HIS48 2.9 70.0 1.0
P H:DG32 3.0 64.3 1.0
CG A:ASP87 3.1 72.8 1.0
N A:TYR101 3.2 70.6 1.0
C A:TYR101 3.3 70.6 1.0
CG A:ASP100 3.5 70.7 1.0
CA A:TYR101 3.5 70.6 1.0
CB A:TYR101 3.7 70.6 1.0
OD1 A:ASP87 3.7 72.8 1.0
OP2 H:DG32 3.9 64.3 1.0
O3' H:DT31 3.9 66.0 1.0
ND1 A:HIS48 3.9 70.0 1.0
CG A:HIS48 4.0 70.0 1.0
O5' H:DG32 4.0 64.3 1.0
C A:ASP100 4.1 70.7 1.0
CB A:ASP87 4.2 72.8 1.0
OD2 A:ASP100 4.2 70.7 1.0
C5' H:DG32 4.4 64.3 1.0
CA A:ASP100 4.5 70.7 1.0
N A:LYS102 4.5 68.7 1.0
CB A:ASP100 4.6 70.7 1.0
CG A:TYR101 4.9 70.6 1.0

Reference:

C.Hu, C.Almendros, K.H.Nam, A.R.Costa, J.N.A.Vink, A.C.Haagsma, S.R.Bagde, S.J.J.Brouns, A.Ke. Mechanism For CAS4-Assisted Directional Spacer Acquisition in Crispr-Cas. Nature V. 598 515 2021.
ISSN: ESSN 1476-4687
PubMed: 34588691
DOI: 10.1038/S41586-021-03951-Z
Page generated: Sun Oct 6 10:07:44 2024

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