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Magnesium in PDB 6i1l: Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target

Enzymatic activity of Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target

All present enzymatic activity of Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target:
3.1.21.1; 3.1.27.2;

Protein crystallography data

The structure of Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target, PDB code: 6i1l was solved by M.Jinek, D.C.Swarts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 2.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.800, 188.580, 284.120, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.1

Other elements in 6i1l:

The structure of Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target also contains other interesting chemical elements:

Potassium (K) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target (pdb code 6i1l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target, PDB code: 6i1l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6i1l

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Magnesium binding site 1 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:74.4
occ:1.00
 O A:HOH1510 2.2 74.4 1.0
O A:HOH1536 2.2 74.4 1.0
O A:HOH1530 2.2 74.4 1.0
OD1 A:ASN602 2.9 58.1 1.0
OG1 A:THR604 2.9 56.7 1.0
O A:ASP616 3.2 62.5 1.0
NZ A:LYS635 3.7 71.2 1.0
CG A:ASN602 3.9 57.1 1.0
OG A:SER603 3.9 62.9 1.0
CG2 A:THR604 3.9 49.9 1.0
CB A:THR604 3.9 55.9 1.0
N A:THR604 4.1 63.6 1.0
ND2 A:ASN602 4.3 51.3 1.0
C A:ASP616 4.4 61.2 1.0
CE A:LYS635 4.4 73.6 1.0
N A:SER603 4.4 59.8 1.0
O A:HOH1543 4.4 55.7 1.0
CA A:THR604 4.6 56.8 1.0
CA A:ASP616 4.9 58.6 1.0
O A:HOH1534 4.9 60.5 1.0
C A:SER603 5.0 59.6 1.0
CA A:ASN602 5.0 58.5 1.0

Magnesium binding site 2 out of 9 in 6i1l

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Magnesium binding site 2 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:70.9
occ:1.00
 O A:HOH1535 2.2 70.9 1.0
O A:HOH1503 2.2 70.9 1.0
O A:HOH1526 2.2 70.9 1.0
O A:HOH1501 2.2 70.9 1.0
O A:HOH1540 2.2 70.9 1.0
O A:HOH1521 2.2 70.9 1.0
OD1 A:ASN607 3.9 63.4 1.0
NZ A:LYS597 4.1 43.4 1.0
CE A:LYS597 4.4 53.3 1.0
ND2 A:ASN607 4.5 69.3 1.0
CG A:ASN607 4.5 65.1 1.0
CB A:GLU827 4.9 54.7 1.0
CG A:GLU829 4.9 45.1 1.0
O A:ALA828 4.9 59.5 1.0
OE2 A:GLU829 5.0 55.8 1.0

Magnesium binding site 3 out of 9 in 6i1l

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Magnesium binding site 3 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1403

b:95.9
occ:1.00
 O A:HOH1538 2.2 95.9 1.0
O A:HOH1542 2.2 95.9 1.0
O A:HOH1544 2.2 95.9 1.0
SG A:CYS70 3.1 82.7 1.0
CB A:CYS70 4.2 81.6 1.0
CA A:SER72 4.9 71.2 1.0
O A:CYS70 5.0 84.1 1.0

Magnesium binding site 4 out of 9 in 6i1l

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Magnesium binding site 4 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1404

b:78.3
occ:1.00
 O B:HOH205 2.2 78.3 1.0
O A:HOH1502 2.2 78.3 1.0
O A:HOH1523 2.2 78.3 1.0
O B:HOH203 2.2 78.3 1.0
OP2 B:A-3 2.7 61.2 1.0
O A:ARG800 2.8 72.6 1.0
C A:ARG800 4.0 69.8 1.0
OP2 B:U-4 4.1 69.8 1.0
O A:HOH1511 4.2 52.9 1.0
OD1 A:ASN802 4.2 61.9 1.0
P B:A-3 4.2 67.2 1.0
OP1 B:U-4 4.3 78.4 1.0
OD1 A:ASP792 4.3 64.0 1.0
O5' B:U-4 4.4 74.0 1.0
P B:U-4 4.5 69.6 1.0
CA A:PRO801 4.5 61.9 1.0
C5' B:A-3 4.5 63.5 1.0
C A:PRO801 4.6 63.5 1.0
N A:PRO801 4.7 64.9 1.0
C3' B:U-4 4.7 69.0 1.0
N A:ASN802 4.8 53.7 1.0
N7 B:A-3 4.9 63.0 1.0
O3' B:U-4 4.9 66.4 1.0
O5' B:A-3 5.0 67.5 1.0
C8 B:A-3 5.0 62.2 1.0
N A:ARG800 5.0 74.0 1.0
NZ A:LYS791 5.0 63.9 1.0

Magnesium binding site 5 out of 9 in 6i1l

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Magnesium binding site 5 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:85.0
occ:1.00
 O B:HOH210 2.2 85.0 1.0
O A:HOH1529 2.2 85.0 1.0
O B:HOH206 2.2 85.0 1.0
O B:HOH201 2.2 85.0 1.0
O B:HOH204 2.2 85.0 1.0
O B:HOH208 2.2 85.0 1.0
OP2 B:A-17 4.0 81.8 1.0
O4 B:U-16 4.1 57.5 1.0
OP2 B:U-12 4.2 56.0 1.0
NH2 A:ARG872 4.5 46.3 1.0
OP2 B:A-11 4.7 58.5 1.0
OD1 A:ASP870 4.7 70.0 1.0
OP1 B:A-17 4.8 81.0 1.0
P B:A-17 4.9 81.9 1.0
C4 B:U-16 4.9 57.9 1.0

Magnesium binding site 6 out of 9 in 6i1l

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Magnesium binding site 6 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1401

b:86.5
occ:1.00
 O D:HOH1510 2.2 86.5 1.0
O D:HOH1519 2.2 86.5 1.0
O D:HOH1522 2.2 86.5 1.0
O D:ASP616 2.8 82.2 1.0
OD1 D:ASN602 2.9 76.7 1.0
OG1 D:THR604 2.9 81.6 1.0
CG D:ASN602 3.6 75.9 1.0
ND2 D:ASN602 3.7 70.4 1.0
C D:ASP616 3.8 80.0 1.0
CG2 D:THR604 3.9 74.5 1.0
CB D:THR604 3.9 81.0 1.0
CA D:ASP616 4.1 79.0 1.0
O3 D:CIT1406 4.1 0.9 1.0
CB D:ASP616 4.2 80.2 1.0
N D:THR604 4.3 88.1 1.0
CA D:THR604 4.6 82.1 1.0
OD2 D:ASP616 4.6 99.3 1.0
OG D:SER603 4.7 79.4 1.0
C5 D:CIT1406 4.8 0.9 1.0
O4 D:CIT1406 4.8 0.9 1.0
N D:SER603 4.9 77.0 1.0
C D:THR604 4.9 80.7 1.0
CB D:ASN602 5.0 75.6 1.0
CG D:ASP616 5.0 93.5 1.0
N D:ASN617 5.0 86.8 1.0

Magnesium binding site 7 out of 9 in 6i1l

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Magnesium binding site 7 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1402

b:86.8
occ:1.00
 O D:HOH1507 2.2 86.8 1.0
O E:HOH201 2.2 86.8 1.0
O D:HOH1515 2.2 86.8 1.0
O E:HOH204 2.2 86.8 1.0
OP2 E:A-3 2.8 68.7 1.0
O D:ARG800 2.8 76.2 1.0
OD1 D:ASP792 3.8 72.1 1.0
C D:ARG800 3.9 73.7 1.0
OD1 D:ASN802 4.0 75.1 1.0
OP2 E:U-4 4.1 71.0 1.0
P E:A-3 4.1 74.7 1.0
OP1 E:U-4 4.3 80.1 1.0
P E:U-4 4.5 71.0 1.0
O5' E:A-3 4.5 74.7 1.0
CA D:PRO801 4.5 72.4 1.0
C D:PRO801 4.6 74.7 1.0
O5' E:U-4 4.6 75.6 1.0
N D:ARG800 4.7 79.3 1.0
N D:ASN802 4.7 66.2 1.0
N D:PRO801 4.7 76.6 1.0
CG D:ASP792 4.8 68.6 1.0
CG D:ASN802 4.9 72.2 1.0
CA D:ARG800 4.9 75.1 1.0
N7 E:A-3 4.9 70.2 1.0
C3' E:U-4 5.0 70.9 1.0
C8 E:A-3 5.0 69.5 1.0

Magnesium binding site 8 out of 9 in 6i1l

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Magnesium binding site 8 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna 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 FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1403

b:0.6
occ:1.00
 O D:HOH1506 2.2 0.6 1.0
O D:HOH1505 2.2 0.6 1.0
O D:HOH1526 2.2 0.6 1.0
O D:HOH1525 2.2 0.6 1.0
O D:HOH1502 2.2 0.6 1.0
O E:HOH210 2.2 0.6 1.0
NZ D:LYS994 4.1 87.3 1.0
CE D:LYS994 4.2 82.6 1.0
NE2 D:HIS990 4.4 71.5 1.0
NH2 D:ARG800 4.4 0.4 1.0

Magnesium binding site 9 out of 9 in 6i1l

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Magnesium binding site 9 out of 9 in the Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of FNCAS12A in Complex with A Crrna Guide and Ssdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg101

b:91.7
occ:1.00
 O E:HOH206 2.2 91.7 1.0
O E:HOH211 2.2 91.7 1.0
O E:HOH203 2.2 91.7 1.0
O E:HOH202 2.2 91.7 1.0
O D:HOH1524 2.2 91.7 1.0
O E:HOH207 2.2 91.7 1.0
OP2 E:U-12 4.1 69.9 1.0
O E:HOH208 4.3 91.3 1.0
OP2 E:A-17 4.3 84.8 1.0
O4 E:U-16 4.5 65.8 1.0
OP2 E:A-11 4.6 70.2 1.0
OP1 E:A-17 4.8 84.3 1.0
NH2 D:ARG872 4.9 53.6 1.0
OD1 D:ASP870 4.9 77.4 1.0

Reference:

D.C.Swarts, M.Jinek. Mechanistic Insights Into the Cis- and Trans-Acting Dnase Activities of CAS12A. Mol. Cell V. 73 589 2019.
ISSN: ISSN 1097-4164
PubMed: 30639240
DOI: 10.1016/J.MOLCEL.2018.11.021
Page generated: Tue Oct 1 02:55:54 2024

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