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Potassium in PDB 8cy2: Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)

Enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)

All present enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168):
2.1.1.72;

Protein crystallography data

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168), PDB code: 8cy2 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) 45.17 / 2.81
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.531, 161.814, 230.342, 90, 90, 90
R / Rfree (%) 17.1 / 22.2

Potassium Binding Sites:

The binding sites of Potassium atom in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168) (pdb code 8cy2). 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 Apnea (Compound 168), PDB code: 8cy2:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8cy2

Go back to Potassium Binding Sites List in 8cy2
Potassium binding site 1 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:60.5
occ:1.00
 OE1 A:GLU93 2.7 88.5 1.0
O A:TYR91 2.7 69.9 1.0
O A:LYS89 2.9 55.7 1.0
O A:LYS88 3.0 57.5 1.0
O A:HOH782 3.3 44.1 1.0
CD A:GLU93 3.3 90.7 1.0
O A:HOH780 3.4 56.1 1.0
C A:LYS89 3.5 52.5 1.0
OE2 A:GLU93 3.7 97.4 1.0
C A:TYR91 3.9 63.4 1.0
CA A:LYS89 3.9 52.6 1.0
CB A:GLU93 4.0 61.7 1.0
C A:LYS88 4.1 49.3 1.0
N A:GLU93 4.2 60.7 1.0
N A:TYR91 4.2 57.2 1.0
CG A:GLU93 4.2 63.4 1.0
N A:LYS90 4.3 55.1 1.0
C A:LYS90 4.4 58.4 1.0
N A:LYS89 4.5 50.3 1.0
CA A:GLU93 4.5 64.6 1.0
CA A:TYR91 4.6 53.8 1.0
CA A:LYS90 4.8 53.8 1.0
O A:LYS90 4.8 60.3 1.0
C A:ASP92 4.8 56.5 1.0
N A:ASP92 4.9 67.1 1.0

Potassium binding site 2 out of 7 in 8cy2

Go back to Potassium Binding Sites List in 8cy2
Potassium binding site 2 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:92.9
occ:1.00
 ND2 A:ASN251 3.1 86.7 1.0
O A:GLY249 3.3 56.5 1.0
O A:VAL258 3.4 42.9 1.0
O A:ALA250 3.6 59.5 1.0
CG A:ASN251 3.6 92.1 1.0
OG A:SER259 3.7 47.5 1.0
OD1 A:ASN251 4.0 85.3 1.0
C A:ALA250 4.0 58.3 1.0
C A:GLY249 4.1 54.3 1.0
C A:VAL258 4.1 42.3 1.0
CA A:ASN251 4.1 57.4 1.0
N A:ASN251 4.3 58.2 1.0
CB A:SER514 4.3 45.5 1.0
CB A:ASN251 4.4 82.9 1.0
N A:VAL258 4.4 45.4 1.0
CA A:SER514 4.5 44.8 1.0
N A:SER259 4.6 37.0 1.0
N A:LYS515 4.7 42.2 1.0
CA A:GLY249 4.7 41.9 1.0
CA A:SER259 4.7 33.0 1.0
O A:ILE256 4.8 48.0 1.0
CB A:SER259 4.8 34.9 1.0
N A:ALA250 4.8 52.0 1.0
CA A:VAL258 4.9 42.2 1.0
O A:HOH710 5.0 42.9 1.0
CA A:ALA250 5.0 43.9 1.0

Potassium binding site 3 out of 7 in 8cy2

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Potassium binding site 3 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:60.0
occ:1.00
 O B:GLY249 3.1 46.4 1.0
O B:ALA250 3.1 49.9 1.0
OG B:SER259 3.2 37.2 1.0
O B:VAL258 3.2 38.2 1.0
ND2 B:ASN251 3.2 80.8 1.0
O B:HOH772 3.4 38.3 1.0
CG B:ASN251 3.7 82.0 1.0
C B:ALA250 3.7 46.4 1.0
C B:GLY249 3.7 46.1 1.0
C B:VAL258 3.9 30.1 1.0
OD1 B:ASN251 4.0 72.0 1.0
CA B:ASN251 4.0 48.6 1.0
N B:ASN251 4.1 47.9 1.0
CA B:SER259 4.1 35.1 1.0
CB B:SER259 4.2 35.4 1.0
N B:SER259 4.3 34.8 1.0
CA B:SER514 4.4 33.2 1.0
N B:ALA250 4.4 52.5 1.0
CB B:SER514 4.4 39.3 1.0
CB B:ASN251 4.4 56.7 1.0
CA B:GLY249 4.4 46.4 1.0
CA B:ALA250 4.6 41.9 1.0
N B:LYS515 4.6 41.8 1.0
O B:HOH726 4.7 39.7 1.0
N B:VAL258 4.7 34.9 1.0
O B:HOH703 4.8 40.9 1.0
CA B:VAL258 4.9 28.0 1.0
C B:SER514 5.0 40.0 1.0

Potassium binding site 4 out of 7 in 8cy2

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Potassium binding site 4 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K605

b:69.4
occ:1.00
 O B:TYR91 2.7 74.0 1.0
O B:LYS89 2.8 52.6 1.0
O B:LYS88 3.1 48.2 1.0
O B:HOH799 3.3 28.8 1.0
C B:LYS89 3.6 53.0 1.0
C B:TYR91 3.9 44.9 1.0
CA B:LYS89 4.0 51.6 1.0
CB B:GLU93 4.0 57.0 1.0
N B:GLU93 4.1 60.4 1.0
C B:LYS88 4.2 48.6 1.0
N B:TYR91 4.3 52.5 1.0
CA B:GLU93 4.4 58.2 1.0
CG B:GLU93 4.5 69.0 1.0
N B:LYS90 4.5 53.2 1.0
C B:LYS90 4.5 50.4 1.0
N B:LYS89 4.6 44.9 1.0
CA B:TYR91 4.7 47.5 1.0
C B:ASP92 4.7 56.7 1.0
N B:ASP92 4.8 45.4 1.0
CA B:ASP92 4.9 56.1 1.0
O B:LYS90 4.9 45.5 1.0
CA B:LYS90 5.0 47.5 1.0

Potassium binding site 5 out of 7 in 8cy2

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Potassium binding site 5 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K606

b:104.5
occ:1.00
 OD1 B:ASP370 2.9 97.5 1.0
O B:LEU365 2.9 73.2 1.0
O B:VAL368 3.4 62.1 1.0
C B:LEU365 3.8 71.9 1.0
CG B:ASP370 4.0 80.5 1.0
CA B:ASN366 4.2 69.5 1.0
N B:ASN366 4.4 69.7 1.0
CD1 B:LEU373 4.5 47.2 1.0
OD2 B:ASP370 4.5 81.8 1.0
C B:VAL368 4.6 59.0 1.0
OD1 B:ASN366 4.6 77.1 1.0
C B:ASN366 4.7 67.7 1.0
CB B:LEU365 4.7 64.3 1.0
O B:ASN366 4.7 62.9 1.0
CA B:LEU365 4.9 64.4 1.0

Potassium binding site 6 out of 7 in 8cy2

Go back to Potassium Binding Sites List in 8cy2
Potassium binding site 6 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:72.0
occ:1.00
 OD1 C:ASN251 2.8 77.3 1.0
O C:ALA250 3.0 67.6 1.0
O C:VAL258 3.1 62.2 1.0
OG C:SER259 3.1 62.0 1.0
O C:GLY249 3.1 58.1 1.0
C C:VAL258 3.6 54.5 1.0
C C:ALA250 3.6 61.2 1.0
C C:GLY249 3.7 55.4 1.0
CG C:ASN251 3.8 69.8 1.0
CA C:SER259 3.9 54.7 1.0
N C:SER259 3.9 51.3 1.0
CA C:ASN251 4.0 63.5 1.0
CB C:SER259 4.0 54.3 1.0
N C:ASN251 4.1 59.2 1.0
CA C:GLY249 4.4 55.7 1.0
N C:ALA250 4.4 53.7 1.0
N C:VAL258 4.4 50.1 1.0
CB C:ASN251 4.5 60.4 1.0
CA C:SER514 4.5 46.0 1.0
CA C:ALA250 4.6 62.7 1.0
CA C:VAL258 4.6 50.9 1.0
CB C:SER514 4.6 52.3 1.0
ND2 C:ASN251 4.7 63.7 1.0
N C:LYS515 4.8 56.7 1.0

Potassium binding site 7 out of 7 in 8cy2

Go back to Potassium Binding Sites List in 8cy2
Potassium binding site 7 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor Apnea (Compound 168)


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 Apnea (Compound 168) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K603

b:94.1
occ:1.00
 O C:LEU365 2.8 64.3 1.0
O C:HOH727 2.9 58.8 1.0
OD1 C:ASP370 3.0 92.2 1.0
O C:VAL368 3.3 75.1 1.0
C C:LEU365 3.7 67.5 1.0
CG C:ASP370 4.1 96.4 1.0
CA C:ASN366 4.3 60.7 1.0
N C:ASN366 4.3 62.8 1.0
CD1 C:LEU373 4.4 51.3 1.0
CB C:LEU365 4.5 66.1 1.0
C C:VAL368 4.5 68.8 1.0
OD2 C:ASP370 4.6 96.5 1.0
CA C:LEU365 4.7 62.6 1.0
OD1 C:ASN366 4.7 82.0 1.0
C C:ASN366 4.8 62.8 1.0
O C:ASN366 5.0 63.0 1.0
N C:ASP370 5.0 65.9 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 23:24:36 2024

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