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Potassium in PDB 8cy4: Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)

Enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)

All present enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181):
2.1.1.72;

Protein crystallography data

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181), PDB code: 8cy4 was solved by J.Zhou, J.R.Horton, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.10 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.313, 161.764, 229.946, 90, 90, 90
R / Rfree (%) 17.3 / 20.7

Potassium Binding Sites:

The binding sites of Potassium atom in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) (pdb code 8cy4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181), PDB code: 8cy4:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8cy4

Go back to Potassium Binding Sites List in 8cy4
Potassium binding site 1 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:45.5
occ:1.00
 O A:TYR91 2.7 53.8 1.0
OE1 A:GLU93 2.8 64.8 1.0
O A:LYS89 2.9 48.3 1.0
O A:LYS88 2.9 46.5 1.0
O A:HOH928 3.0 46.3 1.0
O A:HOH927 3.3 56.2 1.0
CD A:GLU93 3.3 69.4 1.0
C A:LYS89 3.5 43.7 1.0
CB A:GLU93 3.8 44.7 1.0
OE2 A:GLU93 3.8 84.2 1.0
O A:HOH793 3.8 59.2 1.0
C A:TYR91 3.9 57.8 1.0
CA A:LYS89 3.9 40.8 1.0
N A:GLU93 4.0 49.0 1.0
C A:LYS88 4.0 44.6 1.0
CG A:GLU93 4.2 53.4 1.0
N A:TYR91 4.3 44.5 1.0
CA A:GLU93 4.3 48.4 1.0
N A:LYS90 4.4 45.7 1.0
C A:LYS90 4.4 47.1 1.0
N A:LYS89 4.5 40.0 1.0
CA A:TYR91 4.7 52.0 1.0
C A:ASP92 4.7 47.8 1.0
O A:LYS90 4.8 48.0 1.0
N A:ASP92 4.8 56.5 1.0
CA A:LYS90 4.9 40.9 1.0
CA A:ASP92 4.9 51.9 1.0

Potassium binding site 2 out of 7 in 8cy4

Go back to Potassium Binding Sites List in 8cy4
Potassium binding site 2 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:61.6
occ:1.00
 O A:HOH884 2.9 45.6 1.0
O A:VAL258 2.9 31.1 1.0
OD1 A:ASN251 3.0 60.7 1.0
O A:GLY249 3.0 53.2 1.0
O A:ALA250 3.1 44.8 1.0
OG A:SER259 3.3 36.1 1.0
O A:HOH766 3.5 31.2 1.0
C A:GLY249 3.6 44.6 1.0
O D:HOH122 3.7 51.8 1.0
C A:VAL258 3.7 36.5 1.0
C A:ALA250 3.8 51.7 1.0
CG A:ASN251 3.9 70.6 1.0
CA A:ASN251 4.1 48.5 1.0
CA A:SER259 4.1 35.1 1.0
O A:HOH831 4.2 51.8 1.0
N A:SER259 4.2 29.9 1.0
CA A:GLY249 4.2 35.1 1.0
N A:ASN251 4.2 48.1 1.0
CB A:SER259 4.2 33.9 1.0
O A:HOH790 4.3 42.0 1.0
N A:ALA250 4.4 40.0 1.0
O A:HOH730 4.5 37.6 1.0
N A:VAL258 4.5 32.3 1.0
CA A:SER514 4.6 33.1 1.0
CB A:ASN251 4.6 63.9 1.0
CA A:ALA250 4.7 40.6 1.0
CB A:SER514 4.7 35.2 1.0
CA A:VAL258 4.7 32.7 1.0
N A:LYS515 4.8 38.2 1.0
ND2 A:ASN251 4.8 69.9 1.0
O A:LEU248 5.0 35.0 1.0

Potassium binding site 3 out of 7 in 8cy4

Go back to Potassium Binding Sites List in 8cy4
Potassium binding site 3 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K808

b:48.4
occ:1.00
 O B:VAL258 2.8 33.0 1.0
OD1 B:ASN251 2.9 59.8 1.0
O B:GLY249 3.0 45.7 1.0
OG B:SER259 3.0 31.6 1.0
O B:ALA250 3.0 41.9 1.0
O B:HOH1061 3.1 37.1 1.0
O B:HOH1065 3.2 43.4 1.0
C B:VAL258 3.6 28.2 1.0
C B:GLY249 3.6 39.8 1.0
C B:ALA250 3.7 43.4 1.0
CG B:ASN251 3.8 54.6 1.0
CA B:SER259 3.9 37.3 1.0
CB B:SER259 4.0 31.8 1.0
N B:SER259 4.1 29.4 1.0
O F:HOH206 4.1 41.4 1.0
CA B:ASN251 4.1 48.8 1.0
N B:ASN251 4.2 45.9 1.0
CA B:GLY249 4.2 37.7 1.0
O B:HOH1001 4.3 41.3 1.0
CA B:SER514 4.3 32.3 1.0
N B:ALA250 4.4 41.6 1.0
O B:HOH989 4.4 42.0 1.0
CB B:SER514 4.4 32.4 1.0
N B:VAL258 4.5 30.9 1.0
ND2 B:ASN251 4.6 48.8 1.0
CB B:ASN251 4.6 48.7 1.0
CA B:ALA250 4.6 39.0 1.0
O B:HOH935 4.6 39.0 1.0
N B:LYS515 4.6 35.9 1.0
CA B:VAL258 4.6 29.9 1.0
O B:MET513 4.9 36.1 1.0
C B:SER514 5.0 38.9 1.0

Potassium binding site 4 out of 7 in 8cy4

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Potassium binding site 4 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K809

b:49.6
occ:1.00
 O B:TYR91 2.6 58.1 1.0
O B:LYS89 2.8 51.7 1.0
O1 B:EDO805 3.0 54.7 1.0
O2 B:EDO805 3.0 59.0 1.0
O B:LYS88 3.1 38.8 1.0
O B:HOH1121 3.1 57.7 1.0
OE1 B:GLU93 3.4 78.0 1.0
O B:HOH1027 3.4 60.8 1.0
C B:LYS89 3.5 47.8 1.0
C1 B:EDO805 3.6 50.6 1.0
C B:TYR91 3.8 42.6 1.0
C2 B:EDO805 3.8 53.5 1.0
CA B:LYS89 3.9 44.2 1.0
N B:GLU93 4.0 46.5 1.0
CB B:GLU93 4.0 51.1 1.0
C B:LYS88 4.1 44.5 1.0
CD B:GLU93 4.3 81.8 1.0
N B:TYR91 4.3 44.3 1.0
N B:LYS90 4.4 45.0 1.0
C B:LYS90 4.5 47.5 1.0
N B:LYS89 4.5 44.1 1.0
CA B:GLU93 4.5 59.1 1.0
CA B:TYR91 4.6 46.6 1.0
N B:ASP92 4.7 42.2 1.0
C B:ASP92 4.7 47.1 1.0
CA B:ASP92 4.7 51.8 1.0
CG B:GLU93 4.8 57.3 1.0
O B:LYS90 4.8 42.0 1.0
CA B:LYS90 4.9 41.8 1.0

Potassium binding site 5 out of 7 in 8cy4

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Potassium binding site 5 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K810

b:76.7
occ:1.00
 OD1 B:ASP370 2.8 73.0 1.0
O B:HOH1133 2.8 64.8 1.0
O B:LEU365 2.9 67.5 1.0
O B:VAL368 2.9 64.8 1.0
C B:LEU365 3.9 62.3 1.0
CG B:ASP370 3.9 73.1 1.0
CD1 B:LEU373 4.1 46.1 1.0
C B:VAL368 4.2 60.3 1.0
CA B:ASN366 4.2 70.5 1.0
N B:ASN366 4.5 63.6 1.0
OD2 B:ASP370 4.5 88.2 1.0
C B:ASN366 4.6 67.1 1.0
O B:ASN366 4.6 65.5 1.0
N B:ASP370 4.6 54.8 1.0
N B:VAL368 4.8 61.6 1.0
OD1 B:ASN366 4.9 66.7 1.0
C B:ASP369 4.9 53.2 1.0
CA B:ASP370 4.9 53.8 1.0
CA B:VAL368 5.0 56.6 1.0
CB B:LEU365 5.0 63.4 1.0
CA B:LEU365 5.0 66.7 1.0

Potassium binding site 6 out of 7 in 8cy4

Go back to Potassium Binding Sites List in 8cy4
Potassium binding site 6 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:55.0
occ:1.00
 O C:HOH796 2.9 52.6 1.0
O C:VAL258 2.9 49.6 1.0
O C:ALA250 2.9 52.0 1.0
O C:GLY249 3.1 48.1 1.0
O C:HOH771 3.1 44.6 1.0
OG C:SER259 3.1 42.0 1.0
OD1 C:ASN251 3.1 69.0 1.0
C C:VAL258 3.6 45.7 1.0
C C:ALA250 3.6 50.9 1.0
C C:GLY249 3.7 45.9 1.0
CG C:ASN251 3.9 55.3 1.0
CA C:SER259 4.0 40.5 1.0
N C:SER259 4.0 46.5 1.0
CA C:ASN251 4.0 54.3 1.0
CB C:SER259 4.1 43.0 1.0
N C:ASN251 4.1 46.1 1.0
O C:HOH736 4.3 46.8 1.0
CA C:GLY249 4.3 40.4 1.0
N C:ALA250 4.3 45.9 1.0
N C:VAL258 4.4 49.2 1.0
O C:HOH713 4.5 48.2 1.0
CA C:SER514 4.5 37.8 1.0
CB C:ASN251 4.5 61.9 1.0
CA C:ALA250 4.6 47.6 1.0
CB C:SER514 4.6 39.0 1.0
CA C:VAL258 4.6 48.4 1.0
ND2 C:ASN251 4.7 58.5 1.0
N C:LYS515 4.7 37.9 1.0

Potassium binding site 7 out of 7 in 8cy4

Go back to Potassium Binding Sites List in 8cy4
Potassium binding site 7 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4761 (Compound 181) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K603

b:69.7
occ:1.00
 OD1 C:ASP370 2.8 72.5 1.0
O C:VAL368 2.8 66.1 1.0
O C:LEU365 2.9 56.8 1.0
O C:HOH819 3.0 63.1 1.0
O C:HOH822 3.1 52.7 1.0
O C:HOH734 3.3 61.3 1.0
C C:LEU365 3.9 59.0 1.0
CG C:ASP370 4.0 82.3 1.0
CD1 C:LEU373 4.0 48.9 1.0
C C:VAL368 4.1 58.2 1.0
N C:ASP370 4.5 54.7 1.0
CA C:ASN366 4.6 58.4 1.0
OD2 C:ASP370 4.6 92.1 1.0
N C:ASN366 4.7 58.7 1.0
C C:ASP369 4.7 53.7 1.0
CA C:ASP370 4.7 53.5 1.0
CB C:LEU365 4.7 56.6 1.0
N C:VAL368 4.9 57.9 1.0
CA C:LEU365 4.9 56.2 1.0
CA C:VAL368 4.9 53.9 1.0
C C:ASN366 4.9 56.9 1.0
CB C:ASP370 5.0 65.4 1.0
CA C:ASP369 5.0 55.9 1.0
N C:ASP369 5.0 59.7 1.0

Reference:

J.Zhou, J.R.Horton, M.Menna, F.Fiorentino, R.Ren, D.Yu, T.Hajian, M.Vedadi, G.Mazzoccanti, A.Ciogli, E.Weinhold, M.Huben, R.M.Blumenthal, X.Zhang, A.Mai, D.Rotili, X.Cheng. Systematic Design of Adenosine Analogs As Inhibitors of A Clostridioides Difficile- Specific Dna Adenine Methyltransferase Required For Normal Sporulation and Persistence. J.Med.Chem. 2022.
ISSN: ISSN 0022-2623
PubMed: 36581322
DOI: 10.1021/ACS.JMEDCHEM.2C01789
Page generated: Mon Aug 12 23:24:37 2024

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