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Potassium in PDB 8cxu: Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)

Enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)

All present enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161):
2.1.1.72;

Protein crystallography data

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161), PDB code: 8cxu 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) 44.86 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.446, 161.237, 229.523, 90, 90, 90
R / Rfree (%) 18.7 / 22.1

Potassium Binding Sites:

The binding sites of Potassium atom in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161) (pdb code 8cxu). 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 MC4679 (Compound 161), PDB code: 8cxu:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8cxu

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Potassium binding site 1 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:47.6
occ:1.00
 OE1 A:GLU93 2.7 58.3 1.0
O A:TYR91 2.7 56.8 1.0
O A:LYS89 2.8 43.0 1.0
O A:LYS88 2.9 41.3 1.0
O A:HOH963 3.0 46.4 1.0
O A:HOH960 3.0 55.8 1.0
O A:HOH964 3.2 47.4 1.0
C A:LYS89 3.5 36.6 1.0
CD A:GLU93 3.7 67.1 1.0
CA A:LYS89 3.8 39.3 1.0
C A:TYR91 3.9 46.6 1.0
CB A:GLU93 3.9 44.1 1.0
C A:LYS88 4.0 40.0 1.0
N A:GLU93 4.0 38.7 1.0
N A:TYR91 4.2 34.0 1.0
CG A:GLU93 4.4 48.9 1.0
N A:LYS90 4.4 36.8 1.0
CA A:GLU93 4.4 40.8 1.0
N A:LYS89 4.4 38.0 1.0
C A:LYS90 4.5 43.2 1.0
OE2 A:GLU93 4.5 86.6 1.0
CA A:TYR91 4.6 43.7 1.0
C A:ASP92 4.8 41.5 1.0
N A:ASP92 4.8 53.9 1.0
O A:LYS90 4.9 40.5 1.0
CA A:LYS90 4.9 35.2 1.0
CA A:ASP92 5.0 47.3 1.0

Potassium binding site 2 out of 7 in 8cxu

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Potassium binding site 2 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K704

b:60.1
occ:1.00
 O A:VAL258 2.9 31.5 1.0
O A:GLY249 3.1 50.8 1.0
O A:HOH915 3.2 44.5 1.0
O A:ALA250 3.2 47.8 1.0
OG A:SER259 3.3 29.8 1.0
OD1 A:ASN251 3.4 58.4 1.0
O A:HOH852 3.6 32.0 1.0
C A:VAL258 3.7 28.6 1.0
C A:GLY249 3.7 40.1 1.0
C A:ALA250 3.8 40.9 1.0
O D:HOH116 3.8 42.2 1.0
CG A:ASN251 4.0 73.4 1.0
CA A:ASN251 4.1 48.1 1.0
CA A:SER259 4.1 30.1 1.0
N A:SER259 4.2 23.7 1.0
N A:ASN251 4.2 43.3 1.0
CB A:SER259 4.3 31.8 1.0
CA A:GLY249 4.3 32.2 1.0
O A:HOH838 4.4 32.1 1.0
N A:VAL258 4.4 35.3 1.0
O A:HOH819 4.5 36.8 1.0
N A:ALA250 4.5 33.1 1.0
CA A:SER514 4.6 33.3 1.0
CB A:ASN251 4.6 58.8 1.0
CB A:SER514 4.6 40.2 1.0
CA A:VAL258 4.7 34.4 1.0
CA A:ALA250 4.7 40.1 1.0
N A:LYS515 4.8 32.4 1.0
ND2 A:ASN251 4.8 73.5 1.0
O A:ILE256 5.0 40.0 1.0

Potassium binding site 3 out of 7 in 8cxu

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Potassium binding site 3 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K605

b:50.4
occ:1.00
 OD1 B:ASN251 2.9 66.3 1.0
O B:VAL258 2.9 37.4 1.0
O B:HOH810 2.9 44.0 1.0
OG B:SER259 2.9 30.7 1.0
O B:GLY249 3.0 38.9 1.0
O B:ALA250 3.1 36.2 1.0
O B:HOH840 3.2 33.1 1.0
C B:GLY249 3.6 35.5 1.0
C B:VAL258 3.6 30.2 1.0
C B:ALA250 3.7 36.8 1.0
CG B:ASN251 3.8 52.1 1.0
CA B:SER259 3.9 33.9 1.0
CB B:SER259 4.0 30.0 1.0
N B:SER259 4.0 25.1 1.0
O F:HOH210 4.0 37.0 1.0
CA B:ASN251 4.1 43.2 1.0
CA B:GLY249 4.1 35.6 1.0
N B:ASN251 4.2 37.0 1.0
CA B:SER514 4.3 31.9 1.0
N B:ALA250 4.3 40.2 1.0
O B:HOH736 4.4 38.5 1.0
CB B:SER514 4.5 29.0 1.0
N B:VAL258 4.5 31.0 1.0
CB B:ASN251 4.6 43.2 1.0
O B:HOH798 4.6 40.4 1.0
CA B:ALA250 4.6 35.6 1.0
N B:LYS515 4.6 33.4 1.0
O B:HOH712 4.6 31.3 1.0
CA B:VAL258 4.7 30.4 1.0
ND2 B:ASN251 4.7 49.8 1.0
C B:SER514 4.9 34.6 1.0
O B:MET513 4.9 35.4 1.0
O B:LEU248 5.0 32.1 1.0

Potassium binding site 4 out of 7 in 8cxu

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Potassium binding site 4 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K606

b:48.6
occ:1.00
 O B:TYR91 2.6 54.2 1.0
O B:LYS89 2.7 45.0 1.0
OE1 B:GLU93 2.8 63.6 1.0
O B:HOH879 2.9 46.3 1.0
O B:HOH878 3.0 34.2 1.0
O B:LYS88 3.1 38.0 1.0
C B:LYS89 3.4 47.7 1.0
C B:TYR91 3.7 39.6 1.0
CD B:GLU93 3.8 79.9 1.0
CA B:LYS89 3.9 40.0 1.0
N B:GLU93 4.0 42.5 1.0
CB B:GLU93 4.1 45.3 1.0
C B:LYS88 4.1 40.5 1.0
N B:TYR91 4.2 36.7 1.0
N B:LYS90 4.4 37.8 1.0
C B:LYS90 4.5 41.6 1.0
N B:LYS89 4.5 36.7 1.0
CA B:TYR91 4.5 44.9 1.0
OE2 B:GLU93 4.5 76.2 1.0
CA B:GLU93 4.6 51.3 1.0
CG B:GLU93 4.6 46.6 1.0
N B:ASP92 4.7 39.8 1.0
C B:ASP92 4.7 46.2 1.0
CA B:ASP92 4.8 50.3 1.0
O B:LYS90 4.9 39.7 1.0
CA B:LYS90 4.9 37.3 1.0

Potassium binding site 5 out of 7 in 8cxu

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Potassium binding site 5 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K607

b:68.0
occ:1.00
 O B:LEU365 2.8 61.5 1.0
OD1 B:ASP370 2.9 72.8 1.0
O B:VAL368 3.0 52.1 1.0
C B:LEU365 3.8 58.8 1.0
CD1 B:LEU373 4.1 49.1 1.0
CG B:ASP370 4.1 64.9 1.0
CA B:ASN366 4.2 63.6 1.0
C B:VAL368 4.2 50.2 1.0
N B:ASN366 4.4 60.4 1.0
C B:ASN366 4.6 60.2 1.0
OD2 B:ASP370 4.6 81.5 1.0
O B:ASN366 4.7 58.2 1.0
CB B:LEU365 4.7 67.3 1.0
N B:ASP370 4.8 59.9 1.0
CA B:LEU365 4.8 64.6 1.0
N B:VAL368 4.9 54.0 1.0
OD1 B:ASN366 4.9 55.9 1.0

Potassium binding site 6 out of 7 in 8cxu

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Potassium binding site 6 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K601

b:53.5
occ:1.00
 OD1 C:ASN251 2.8 70.6 1.0
O C:ALA250 2.9 46.5 1.0
O C:VAL258 2.9 43.4 1.0
O C:GLY249 2.9 43.4 1.0
OG C:SER259 3.0 34.3 1.0
O C:HOH772 3.0 41.1 1.0
O C:HOH779 3.1 39.0 1.0
C C:ALA250 3.6 48.8 1.0
C C:GLY249 3.6 41.7 1.0
C C:VAL258 3.6 39.8 1.0
CG C:ASN251 3.9 63.5 1.0
CA C:SER259 4.0 39.5 1.0
O H:HOH112 4.0 50.3 1.0
CB C:SER259 4.0 38.5 1.0
N C:SER259 4.1 38.8 1.0
CA C:ASN251 4.1 50.3 1.0
N C:ASN251 4.1 50.3 1.0
O C:HOH738 4.3 45.6 1.0
CA C:GLY249 4.3 34.1 1.0
N C:ALA250 4.3 43.9 1.0
CA C:SER514 4.4 33.7 1.0
O C:HOH709 4.5 43.7 1.0
N C:VAL258 4.5 41.5 1.0
CA C:ALA250 4.5 47.9 1.0
CB C:SER514 4.6 38.0 1.0
CB C:ASN251 4.6 59.2 1.0
N C:LYS515 4.7 41.5 1.0
CA C:VAL258 4.7 43.5 1.0
ND2 C:ASN251 4.8 55.1 1.0
O C:LEU248 5.0 39.5 1.0
O C:MET513 5.0 46.0 1.0

Potassium binding site 7 out of 7 in 8cxu

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Potassium binding site 7 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor MC4679 (Compound 161)


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 MC4679 (Compound 161) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:74.6
occ:1.00
 O C:HOH799 2.7 54.9 1.0
O C:LEU365 2.8 52.7 1.0
OD1 C:ASP370 2.8 72.8 1.0
O C:VAL368 2.9 59.5 1.0
C C:LEU365 3.8 56.9 1.0
CG C:ASP370 4.0 69.4 1.0
C C:VAL368 4.1 54.3 1.0
CA C:ASN366 4.3 58.6 1.0
N C:ASN366 4.5 50.8 1.0
CD1 C:LEU373 4.5 41.7 1.0
OD2 C:ASP370 4.5 81.1 1.0
C C:ASN366 4.7 50.7 1.0
N C:ASP370 4.7 47.0 1.0
O C:ASN366 4.7 61.7 1.0
N C:VAL368 4.8 51.0 1.0
CB C:LEU365 4.9 53.1 1.0
CA C:LEU365 4.9 57.7 1.0
OD1 C:ASN366 4.9 73.7 1.0
C C:ASP369 5.0 52.9 1.0
CA C:VAL368 5.0 58.9 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 23:18:03 2024

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