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Magnesium in PDB 6i1k: Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target

Enzymatic activity of Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target

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

Protein crystallography data

The structure of Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target, PDB code: 6i1k 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) 47.61 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.172, 141.681, 89.478, 90.00, 97.43, 90.00
R / Rfree (%) 24.8 / 26.4

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target (pdb code 6i1k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target, PDB code: 6i1k:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 6i1k

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Magnesium binding site 1 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1401

b:0.3
occ:1.00
 O A:HOH1502 2.2 0.3 1.0
O B:HOH201 2.2 0.3 1.0
O B:HOH203 2.2 0.3 1.0
O A:HOH1507 2.2 0.3 1.0
O A:ARG800 2.8 0.2 1.0
OP2 B:A-3 2.9 0.0 1.0
OP2 B:U-4 3.6 0.7 1.0
OD1 A:ASP792 3.7 0.1 1.0
C A:ARG800 3.8 0.3 1.0
O5' B:U-4 4.1 0.4 1.0
NZ A:LYS791 4.1 0.1 1.0
P B:U-4 4.2 0.2 1.0
OP1 B:U-4 4.3 1.0 1.0
P B:A-3 4.4 0.9 1.0
CA A:PRO801 4.4 96.3 1.0
N A:ARG800 4.4 1.0 1.0
OD1 A:ASN802 4.4 92.5 1.0
C A:GLY799 4.5 0.9 1.0
N A:PRO801 4.5 97.2 1.0
C3' B:U-4 4.6 0.9 1.0
C A:PRO801 4.6 95.3 1.0
N A:ASN802 4.7 90.3 1.0
CA A:ARG800 4.7 0.4 1.0
CE A:LYS791 4.8 0.6 1.0
CG A:ASP792 4.8 98.6 1.0
O A:GLY799 4.8 0.3 1.0
O3' B:U-4 4.9 0.1 1.0
CA A:GLY799 4.9 0.4 1.0

Magnesium binding site 2 out of 11 in 6i1k

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Magnesium binding site 2 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1402

b:0.4
occ:1.00
 O A:HOH1524 2.2 0.4 1.0
O A:HOH1530 2.2 0.4 1.0
O B:HOH204 2.2 0.4 1.0
O A:HOH1545 2.2 0.4 1.0
O A:HOH1519 2.2 0.4 1.0
O A:HOH1517 2.2 0.4 1.0
O A:ASN395 4.1 0.8 1.0
N A:LYS447 4.2 0.2 1.0
O1 B:EDO106 4.3 0.2 1.0
ND2 A:ASN395 4.5 0.8 1.0
OP2 B:A19 4.6 0.8 1.0
CA A:LYS447 4.8 0.6 1.0
CG A:ASN395 5.0 0.1 1.0

Magnesium binding site 3 out of 11 in 6i1k

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Magnesium binding site 3 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1403

b:0.9
occ:1.00
 O D:HOH103 2.2 0.9 1.0
O A:HOH1529 2.2 0.9 1.0
O D:HOH105 2.2 0.9 1.0
O D:HOH106 2.2 0.9 1.0
O D:HOH101 2.2 0.9 1.0
ND2 A:ASN700 3.0 96.4 1.0
OP2 D:DA4 4.0 0.2 1.0
N7 D:DA4 4.1 0.1 1.0
N6 D:DA5 4.3 0.3 1.0
CG A:ASN700 4.3 97.3 1.0
C8 D:DA4 4.4 0.9 1.0
CB A:ASN700 4.8 95.7 1.0
N7 D:DA5 4.9 0.3 1.0

Magnesium binding site 4 out of 11 in 6i1k

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Magnesium binding site 4 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1404

b:76.5
occ:1.00
 O A:HOH1501 2.2 76.5 1.0
O A:HOH1516 2.2 76.5 1.0
O A:HOH1536 2.2 76.5 1.0
O A:HOH1539 2.2 76.5 1.0
O A:HOH1540 2.2 76.5 1.0
OE1 A:GLU827 3.5 70.5 1.0
NZ A:LYS180 4.3 76.1 1.0
O B:HOH215 4.3 64.9 1.0
NZ A:LYS597 4.4 69.5 1.0
O A:HOH1522 4.4 75.2 1.0
O A:HOH1537 4.5 71.1 1.0
CE A:LYS597 4.5 70.4 1.0
ND2 A:ASN607 4.6 69.6 1.0
CD A:GLU827 4.8 70.1 1.0
CE A:LYS180 4.8 76.1 1.0
OD1 A:ASN607 4.9 71.7 1.0

Magnesium binding site 5 out of 11 in 6i1k

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Magnesium binding site 5 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1405

b:0.1
occ:1.00
 O A:HOH1512 2.2 0.1 1.0
OD1 A:ASN270 2.9 0.6 1.0
O A:SER67 3.0 0.8 1.0
OH A:TYR248 3.1 0.3 1.0
O A:LEU66 3.1 0.8 1.0
O A:VAL69 3.1 0.4 1.0
CG A:ASN270 3.2 0.8 1.0
ND2 A:ASN270 3.2 0.1 1.0
C A:SER67 3.3 0.9 1.0
CA A:SER67 3.4 0.2 1.0
O A:ASN270 3.9 0.6 1.0
C A:LEU66 4.0 99.8 1.0
CZ A:TYR248 4.1 0.8 1.0
N A:SER67 4.2 0.1 1.0
N A:SER68 4.2 0.7 1.0
C A:VAL69 4.3 0.6 1.0
OG A:SER67 4.4 0.2 1.0
CB A:ASN270 4.4 0.2 1.0
N A:VAL69 4.4 0.1 1.0
C A:ASN270 4.4 0.8 1.0
CB A:SER67 4.5 0.6 1.0
C A:SER68 4.6 0.2 1.0
CE2 A:TYR248 4.6 0.5 1.0
CA A:SER68 4.8 0.6 1.0
CA A:VAL69 4.9 0.9 1.0
CA A:ASN270 4.9 0.1 1.0
CE1 A:TYR248 4.9 0.8 1.0

Magnesium binding site 6 out of 11 in 6i1k

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Magnesium binding site 6 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1406

b:88.3
occ:1.00
 O D:HOH102 2.2 88.3 1.0
O A:HOH1521 2.2 88.3 1.0
O D:HOH104 2.2 88.3 1.0
OD1 A:ASN602 3.0 77.3 1.0
NZ A:LYS635 3.1 95.6 1.0
O A:ASP616 3.2 83.2 1.0
OG1 A:THR604 3.2 74.7 1.0
CB A:THR604 3.8 72.9 1.0
OP2 D:DC-4 4.0 0.5 1.0
CE A:LYS635 4.0 97.7 1.0
CG A:ASN602 4.1 77.3 1.0
C A:ASP616 4.2 83.2 1.0
N A:THR604 4.3 72.8 1.0
OG A:SER603 4.4 78.3 1.0
CA A:ASP616 4.5 84.0 1.0
ND2 A:ASN602 4.6 77.0 1.0
CB A:ASP616 4.7 84.0 1.0
CA A:THR604 4.7 71.2 1.0
N A:SER603 4.9 77.7 1.0
CG2 A:THR604 5.0 72.3 1.0

Magnesium binding site 7 out of 11 in 6i1k

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Magnesium binding site 7 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1407

b:0.3
occ:1.00
 O A:HOH1546 2.2 0.3 1.0
O B:HOH216 2.2 0.3 1.0
O A:HOH1533 2.2 0.3 1.0
O A:HOH1532 2.2 0.3 1.0
O A:HOH1528 2.2 0.3 1.0
O A:HOH1527 2.2 0.3 1.0
OH A:TYR591 4.2 0.9 1.0
CE1 A:PHE873 4.5 0.7 1.0
CD1 A:PHE873 4.7 0.2 1.0
CZ A:PHE873 4.8 0.2 1.0
CZ A:TYR591 4.8 0.1 1.0
OE2 A:GLU594 4.8 0.6 1.0
CE2 A:TYR591 4.8 0.1 1.0
OE1 A:GLU594 4.8 0.3 1.0
CD A:GLU594 5.0 0.7 1.0

Magnesium binding site 8 out of 11 in 6i1k

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Magnesium binding site 8 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1408

b:0.3
occ:1.00
 O A:PHE153 2.1 0.8 1.0
O A:ILE159 2.8 0.1 1.0
O A:THR160 2.9 0.1 1.0
O A:ASN156 3.2 0.3 1.0
C A:PHE153 3.3 0.4 1.0
C A:THR160 3.8 0.2 1.0
C A:ILE159 4.0 0.1 1.0
CA A:LYS154 4.0 0.1 1.0
N A:LYS154 4.0 0.1 1.0
CA A:THR160 4.1 0.3 1.0
O A:LYS154 4.1 0.7 1.0
C A:LYS154 4.2 0.2 1.0
CB A:PHE153 4.2 0.3 1.0
C A:ASN156 4.4 0.8 1.0
CA A:PHE153 4.4 0.3 1.0
N A:THR160 4.5 0.3 1.0
N A:ASP161 4.9 0.7 1.0
CA A:SER157 4.9 0.4 1.0
N A:ALA155 5.0 0.6 1.0

Magnesium binding site 9 out of 11 in 6i1k

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Magnesium binding site 9 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna 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 Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1409

b:88.2
occ:1.00
 O A:GLU601 3.1 89.5 1.0
O D:HOH104 3.2 88.3 1.0
CZ2 A:TRP175 3.6 85.4 1.0
CE2 A:TRP175 3.6 85.4 1.0
NE1 A:TRP175 3.6 85.8 1.0
N A:SER603 3.6 77.7 1.0
C A:GLU601 3.9 88.6 1.0
CA A:ASN602 3.9 78.0 1.0
N A:ASN602 4.2 78.8 1.0
CE A:LYS635 4.3 97.7 1.0
C A:ASN602 4.3 75.0 1.0
OG A:SER603 4.3 78.3 1.0
CH2 A:TRP175 4.4 84.2 1.0
CD1 A:TRP175 4.4 85.9 1.0
CB A:SER603 4.4 77.5 1.0
CD2 A:TRP175 4.4 85.0 1.0
OP1 D:DC-4 4.4 0.2 1.0
OP2 D:DC-4 4.5 0.5 1.0
CA A:SER603 4.6 77.2 1.0
CG A:TRP175 4.8 86.1 1.0
P D:DC-4 4.9 0.3 1.0
OD1 A:ASN602 4.9 77.3 1.0
CD A:LYS635 5.0 97.9 1.0
CA A:GLU601 5.0 88.4 1.0

Magnesium binding site 10 out of 11 in 6i1k

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Magnesium binding site 10 out of 11 in the Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Catalytically Inactive FNCAS12A in Complex with A Crrna Guide and A Dsdna Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:0.4
occ:1.00
 O B:HOH202 2.2 0.4 1.0
O A:HOH1525 2.2 0.4 1.0
O B:HOH208 2.2 0.4 1.0
O B:HOH205 2.2 0.4 1.0
O A:HOH1543 2.2 0.4 1.0
O B:HOH213 2.2 0.4 1.0
OP1 B:A-17 4.0 0.9 1.0
OP2 B:U-12 4.1 0.1 1.0
O4 B:U-16 4.2 0.2 1.0
OP2 B:A-11 4.4 0.3 1.0
N7 B:A-11 4.9 0.0 1.0
C5' B:A-18 4.9 1.0 1.0
NH2 A:ARG872 5.0 0.1 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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