Potassium in PDB 8cxw: Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)

Enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)

All present enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164):
2.1.1.72;

Protein crystallography data

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164), PDB code: 8cxw was solved by J.R.Horton, J.Zhou, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.80 / 2.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.326, 161.634, 229.602, 90, 90, 90
R / Rfree (%) 18.5 / 22.7

Other elements in 8cxw:

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164) also contains other interesting chemical elements:

Iodine (I) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164) (pdb code 8cxw). 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 MC4682 (Compound 164), PDB code: 8cxw:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8cxw

Go back to Potassium Binding Sites List in 8cxw
Potassium binding site 1 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K601

b:58.6
occ:1.00
 O A:TYR91 2.8 73.8 1.0
OE1 A:GLU93 2.8 76.5 1.0
O A:LYS89 2.9 63.2 1.0
O A:HOH796 3.1 35.4 1.0
O A:LYS88 3.2 69.8 1.0
CD A:GLU93 3.5 80.7 1.0
O A:HOH791 3.5 39.9 1.0
C A:LYS89 3.6 61.8 1.0
OE2 A:GLU93 3.9 87.4 1.0
C A:TYR91 3.9 73.7 1.0
CA A:LYS89 4.0 61.7 1.0
CB A:GLU93 4.1 68.8 1.0
C A:LYS88 4.2 51.7 1.0
N A:GLU93 4.3 60.1 1.0
N A:TYR91 4.3 59.9 1.0
CG A:GLU93 4.3 66.6 1.0
N A:LYS90 4.5 59.7 1.0
C A:LYS90 4.6 56.8 1.0
CA A:GLU93 4.6 62.1 1.0
N A:LYS89 4.6 54.1 1.0
CA A:TYR91 4.7 60.9 1.0
N A:ASP92 4.9 70.7 1.0
C A:ASP92 4.9 66.9 1.0
CA A:LYS90 5.0 58.4 1.0
O A:LYS90 5.0 54.4 1.0

Potassium binding site 2 out of 7 in 8cxw

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Potassium binding site 2 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:73.0
occ:1.00
 O A:GLY249 3.1 53.6 1.0
O A:VAL258 3.2 45.8 1.0
ND2 A:ASN251 3.3 76.9 1.0
O A:ALA250 3.5 58.9 1.0
OG A:SER259 3.6 41.4 1.0
O A:HOH725 3.7 43.6 1.0
O D:HOH316 3.7 51.6 1.0
CG A:ASN251 3.8 82.6 1.0
C A:GLY249 3.8 41.3 1.0
C A:VAL258 3.9 40.1 1.0
C A:ALA250 3.9 53.4 1.0
CA A:ASN251 4.0 60.3 1.0
N A:ASN251 4.2 51.4 1.0
OD1 A:ASN251 4.2 79.3 1.0
N A:VAL258 4.4 44.6 1.0
CA A:GLY249 4.4 42.6 1.0
CB A:SER514 4.4 46.8 1.0
N A:SER259 4.4 35.4 1.0
CA A:SER259 4.4 33.0 1.0
CA A:SER514 4.5 41.6 1.0
CB A:ASN251 4.5 63.3 1.0
N A:LYS515 4.5 39.4 1.0
CB A:SER259 4.6 35.1 1.0
N A:ALA250 4.6 43.1 1.0
CA A:VAL258 4.7 41.7 1.0
CA A:ALA250 4.8 44.8 1.0
O A:ILE256 4.9 58.2 1.0
O A:HOH701 4.9 43.3 1.0
C A:SER514 5.0 39.4 1.0

Potassium binding site 3 out of 7 in 8cxw

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Potassium binding site 3 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K601

b:60.5
occ:1.00
 ND2 B:ASN251 2.9 50.9 1.0
O B:VAL258 3.0 44.9 1.0
O B:GLY249 3.0 52.1 1.0
O B:ALA250 3.0 54.7 1.0
OG B:SER259 3.2 38.7 1.0
C B:ALA250 3.6 48.5 1.0
C B:GLY249 3.6 45.1 1.0
C B:VAL258 3.7 40.0 1.0
CG B:ASN251 4.0 71.5 1.0
CA B:SER259 4.1 36.8 1.0
CA B:ASN251 4.1 46.9 1.0
N B:ASN251 4.1 46.7 1.0
N B:SER259 4.1 39.6 1.0
CB B:SER259 4.2 34.7 1.0
CA B:GLY249 4.3 41.5 1.0
N B:ALA250 4.3 49.6 1.0
CA B:SER514 4.4 35.8 1.0
CB B:SER514 4.5 37.0 1.0
CA B:ALA250 4.5 42.0 1.0
N B:LYS515 4.5 40.9 1.0
N B:VAL258 4.5 39.6 1.0
CB B:ASN251 4.6 47.8 1.0
CA B:VAL258 4.7 40.7 1.0
C B:SER514 4.9 43.3 1.0
O B:HOH710 4.9 47.0 1.0
OD1 B:ASN251 4.9 83.1 1.0
O B:MET513 5.0 42.2 1.0

Potassium binding site 4 out of 7 in 8cxw

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Potassium binding site 4 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:58.0
occ:1.00
 O B:TYR91 2.7 60.6 1.0
O B:LYS89 2.9 52.2 1.0
O B:HOH815 3.0 39.9 1.0
O B:LYS88 3.1 44.1 1.0
C B:LYS89 3.6 44.7 1.0
C B:TYR91 3.9 40.5 1.0
N B:GLU93 4.0 55.3 1.0
CB B:GLU93 4.0 54.5 1.0
CA B:LYS89 4.1 47.5 1.0
C B:LYS88 4.2 46.5 1.0
CG B:GLU93 4.3 67.7 1.0
N B:TYR91 4.4 51.0 1.0
CA B:GLU93 4.4 58.2 1.0
C B:LYS90 4.5 50.0 1.0
N B:LYS90 4.6 46.3 1.0
N B:LYS89 4.7 41.8 1.0
CA B:TYR91 4.7 46.3 1.0
C B:ASP92 4.7 55.3 1.0
N B:ASP92 4.8 49.4 1.0
O B:LYS90 4.8 50.9 1.0
CA B:ASP92 4.8 56.1 1.0
CD B:GLU93 4.9 94.1 1.0

Potassium binding site 5 out of 7 in 8cxw

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Potassium binding site 5 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:85.8
occ:1.00
 OD1 B:ASP370 3.0 81.2 1.0
O B:LEU365 3.0 73.2 1.0
O B:VAL368 3.7 61.0 1.0
C B:LEU365 3.8 68.4 1.0
CG B:ASP370 4.1 68.9 1.0
CA B:ASN366 4.1 70.0 1.0
N B:ASN366 4.3 72.0 1.0
CD1 B:LEU373 4.4 54.6 1.0
OD2 B:ASP370 4.4 69.0 1.0
OD1 B:ASN366 4.5 78.3 1.0
CB B:LEU365 4.6 69.3 1.0
C B:ASN366 4.7 67.9 1.0
O B:ASN366 4.8 67.8 1.0
CA B:LEU365 4.8 68.0 1.0
C B:VAL368 5.0 61.5 1.0

Potassium binding site 6 out of 7 in 8cxw

Go back to Potassium Binding Sites List in 8cxw
Potassium binding site 6 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:72.0
occ:1.00
 OD1 C:ASN251 2.8 85.9 1.0
OG C:SER259 3.1 59.6 1.0
O C:GLY249 3.1 66.6 1.0
O C:VAL258 3.2 65.3 1.0
O C:ALA250 3.3 64.3 1.0
C C:ALA250 3.7 70.0 1.0
C C:VAL258 3.8 56.2 1.0
CG C:ASN251 3.8 81.1 1.0
C C:GLY249 3.8 55.8 1.0
CA C:ASN251 3.9 71.8 1.0
N C:ASN251 4.0 72.1 1.0
CA C:SER259 4.1 52.5 1.0
N C:SER259 4.1 56.5 1.0
CB C:SER259 4.1 57.5 1.0
CB C:ASN251 4.4 72.4 1.0
CA C:GLY249 4.5 56.6 1.0
N C:ALA250 4.5 58.9 1.0
CA C:SER514 4.5 48.3 1.0
N C:VAL258 4.5 57.5 1.0
CA C:ALA250 4.7 71.8 1.0
CB C:SER514 4.7 51.2 1.0
N C:LYS515 4.7 55.3 1.0
CA C:VAL258 4.7 50.9 1.0
ND2 C:ASN251 4.8 84.5 1.0
O C:MET513 5.0 60.2 1.0

Potassium binding site 7 out of 7 in 8cxw

Go back to Potassium Binding Sites List in 8cxw
Potassium binding site 7 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4682 (Compound 164)


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 MC4682 (Compound 164) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:89.3
occ:1.00
 OD1 C:ASP370 2.9 92.9 1.0
O C:LEU365 2.9 61.2 1.0
O C:VAL368 3.5 66.9 1.0
C C:LEU365 3.8 67.6 1.0
CG C:ASP370 3.9 92.4 1.0
OD2 C:ASP370 4.3 111.4 1.0
CA C:ASN366 4.4 60.3 1.0
N C:ASN366 4.4 60.4 1.0
CD1 C:LEU373 4.4 44.0 1.0
CB C:LEU365 4.6 60.6 1.0
C C:VAL368 4.7 64.9 1.0
CA C:LEU365 4.8 58.5 1.0
OD1 C:ASN366 4.9 87.0 1.0
C C:ASN366 4.9 58.5 1.0
O C:ASN366 4.9 72.4 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: Wed Apr 5 10:37:21 2023

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