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Potassium in PDB 7rfn: Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158

Enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158

All present enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158:
2.1.1.72;

Protein crystallography data

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158, PDB code: 7rfn was solved by J.R.Horton, X.Cheng, J.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.03 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.831, 161.354, 229.908, 90, 90, 90
R / Rfree (%) 19.5 / 23.2

Other elements in 7rfn:

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158 (pdb code 7rfn). 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 SGC8158, PDB code: 7rfn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 1 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:76.8
occ:1.00
 OE1 A:GLU93 2.6 74.7 1.0
O A:LYS89 2.7 55.0 1.0
O A:HOH817 2.9 63.2 1.0
O A:HOH818 2.9 62.5 1.0
O A:TYR91 2.9 79.4 1.0
CD A:GLU93 3.5 89.9 1.0
C A:LYS89 3.6 49.6 1.0
OE2 A:GLU93 3.6 85.0 1.0
O A:HOH806 3.7 52.9 1.0
O A:LYS88 3.8 58.1 1.0
C A:TYR91 3.9 63.1 1.0
C A:LYS90 4.1 55.6 1.0
N A:TYR91 4.1 48.1 1.0
O A:LYS90 4.2 54.9 1.0
CA A:LYS89 4.3 48.0 1.0
N A:LYS90 4.4 64.4 1.0
CA A:TYR91 4.4 48.9 1.0
CA A:LYS90 4.6 51.6 1.0
C A:LYS88 4.8 50.9 1.0
N A:ASP92 4.8 54.6 1.0
N A:GLU93 4.8 61.2 1.0
CG A:GLU93 4.9 59.8 1.0

Potassium binding site 2 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 2 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:80.1
occ:1.00
 O A:GLY249 3.0 66.5 1.0
O A:VAL258 3.0 74.1 1.0
O A:ALA250 3.1 67.4 1.0
ND2 A:ASN251 3.1 87.3 1.0
CG A:ASN251 3.5 78.6 1.0
C A:ALA250 3.5 66.7 1.0
CA A:ASN251 3.7 86.3 1.0
C A:GLY249 3.7 51.4 1.0
N A:ASN251 3.8 66.5 1.0
OD1 A:ASN251 3.9 85.4 1.0
OG A:SER259 3.9 55.1 1.0
C A:VAL258 3.9 64.0 1.0
CB A:ASN251 4.1 72.8 1.0
O A:HOH702 4.4 47.4 1.0
N A:ALA250 4.4 55.7 1.0
N A:VAL258 4.4 75.4 1.0
CA A:GLY249 4.5 53.4 1.0
CA A:ALA250 4.5 58.5 1.0
N A:SER259 4.6 51.5 1.0
CA A:SER259 4.6 37.4 1.0
CB A:SER514 4.8 54.1 1.0
O A:ILE256 4.8 79.3 1.0
CB A:SER259 4.8 52.4 1.0
CA A:SER514 4.8 43.1 1.0
CA A:VAL258 4.8 78.1 1.0
N A:LYS515 4.9 44.5 1.0
C A:ASN251 4.9 81.7 1.0

Potassium binding site 3 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 3 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K606

b:68.0
occ:1.00
 OD1 B:ASN251 2.8 74.6 1.0
O B:GLY249 2.8 50.3 1.0
OG B:SER259 3.0 44.1 1.0
O B:VAL258 3.1 53.8 1.0
O B:ALA250 3.1 55.2 1.0
O B:HOH795 3.3 53.5 1.0
O B:HOH804 3.3 52.1 1.0
C B:GLY249 3.5 45.6 1.0
C B:ALA250 3.6 43.0 1.0
C B:VAL258 3.8 47.7 1.0
CG B:ASN251 3.9 69.5 1.0
CA B:SER259 4.0 41.3 1.0
CB B:SER259 4.0 42.1 1.0
CA B:ASN251 4.1 53.7 1.0
N B:ASN251 4.1 52.5 1.0
CA B:GLY249 4.1 46.4 1.0
N B:SER259 4.1 39.6 1.0
N B:ALA250 4.2 52.1 1.0
O F:HOH205 4.3 50.3 1.0
CA B:SER514 4.3 38.5 1.0
CB B:SER514 4.5 42.5 1.0
CA B:ALA250 4.5 47.3 1.0
N B:LYS515 4.6 51.9 1.0
CB B:ASN251 4.6 55.0 1.0
O B:HOH720 4.6 57.7 1.0
O B:HOH710 4.7 46.8 1.0
N B:VAL258 4.7 46.5 1.0
C B:SER514 4.8 48.5 1.0
ND2 B:ASN251 4.8 68.8 1.0
CA B:VAL258 4.9 42.9 1.0
O B:MET513 4.9 56.1 1.0
O B:LEU248 5.0 48.8 1.0

Potassium binding site 4 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 4 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K607

b:63.1
occ:1.00
 O B:TYR91 2.7 79.1 1.0
O B:LYS89 2.8 57.0 1.0
O B:HOH702 2.8 66.0 1.0
O B:HOH823 2.8 70.1 1.0
O B:LYS88 3.0 52.9 1.0
O B:HOH826 3.1 39.5 1.0
C B:LYS89 3.4 54.3 1.0
OE1 B:GLU93 3.7 97.1 1.0
CA B:LYS89 3.7 49.9 1.0
C B:TYR91 3.9 54.1 1.0
C B:LYS88 4.0 52.8 1.0
CB B:GLU93 4.1 68.4 1.0
N B:GLU93 4.1 61.3 1.0
N B:TYR91 4.3 41.5 1.0
N B:LYS90 4.3 55.8 1.0
N B:LYS89 4.4 41.4 1.0
C B:LYS90 4.5 51.7 1.0
CA B:GLU93 4.5 63.5 1.0
CA B:TYR91 4.7 49.3 1.0
CD B:GLU93 4.7 92.7 1.0
C B:ASP92 4.8 63.5 1.0
N B:ASP92 4.8 54.3 1.0
O B:LYS90 4.8 45.3 1.0
CA B:LYS90 4.9 53.4 1.0
CA B:ASP92 4.9 52.4 1.0

Potassium binding site 5 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 5 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K608

b:86.9
occ:1.00
 O B:LEU365 2.8 73.1 1.0
OD1 B:ASP370 2.9 67.7 1.0
O B:VAL368 3.1 51.1 1.0
C B:LEU365 3.8 62.4 1.0
CD1 B:LEU373 4.0 43.8 1.0
CG B:ASP370 4.1 75.7 1.0
CA B:ASN366 4.2 84.5 1.0
C B:VAL368 4.3 52.0 1.0
N B:ASN366 4.4 75.6 1.0
OD2 B:ASP370 4.6 87.0 1.0
CB B:LEU365 4.6 73.4 1.0
C B:ASN366 4.7 78.4 1.0
O B:ASN366 4.7 73.0 1.0
CA B:LEU365 4.8 79.3 1.0
N B:ASP370 4.8 56.6 1.0
OD1 B:ASN366 4.9 84.3 1.0
N B:VAL368 5.0 67.3 1.0

Potassium binding site 6 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 6 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:86.9
occ:1.00
 OD1 C:ASN251 2.7 71.4 1.0
O C:ALA250 3.0 77.8 1.0
O C:VAL258 3.0 88.3 1.0
O C:GLY249 3.0 63.1 1.0
OG C:SER259 3.4 63.7 1.0
C C:ALA250 3.5 73.5 1.0
C C:GLY249 3.7 53.2 1.0
C C:VAL258 3.7 81.1 1.0
CG C:ASN251 3.8 78.2 1.0
CA C:ASN251 3.8 82.1 1.0
N C:ASN251 3.9 79.1 1.0
CA C:SER259 4.1 59.2 1.0
N C:SER259 4.2 76.6 1.0
CB C:SER259 4.3 55.6 1.0
O C:HOH701 4.3 64.1 1.0
N C:ALA250 4.3 67.3 1.0
CB C:ASN251 4.3 84.7 1.0
CA C:GLY249 4.4 63.1 1.0
CA C:ALA250 4.4 74.2 1.0
N C:VAL258 4.5 84.2 1.0
CB C:SER514 4.7 45.6 1.0
CA C:SER514 4.7 48.1 1.0
CA C:VAL258 4.7 82.5 1.0
ND2 C:ASN251 4.8 80.6 1.0
O C:ILE256 4.9 97.8 1.0
N C:LYS515 4.9 58.6 1.0

Potassium binding site 7 out of 7 in 7rfn

Go back to Potassium Binding Sites List in 7rfn
Potassium binding site 7 out of 7 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor SGC8158


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 SGC8158 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K605

b:85.3
occ:1.00
 O C:LEU365 2.8 60.5 1.0
OD1 C:ASP370 2.9 87.9 1.0
O C:VAL368 2.9 76.7 1.0
C C:LEU365 3.7 66.1 1.0
CG C:ASP370 4.0 81.7 1.0
C C:VAL368 4.1 61.4 1.0
CD1 C:LEU373 4.1 51.1 1.0
CA C:ASN366 4.3 75.6 1.0
N C:ASN366 4.4 71.5 1.0
CB C:LEU365 4.5 67.6 1.0
OD2 C:ASP370 4.6 95.8 1.0
N C:ASP370 4.7 70.6 1.0
CA C:LEU365 4.7 68.3 1.0
C C:ASN366 4.8 66.5 1.0
N C:VAL368 4.8 58.9 1.0
C C:ASP369 4.9 69.1 1.0
O C:ASN366 4.9 71.0 1.0
CA C:VAL368 5.0 64.5 1.0
CA C:ASP370 5.0 62.5 1.0
OD1 C:ASN366 5.0 101.5 1.0

Reference:

J.Zhou, J.R.Horton, D.Yu, R.M.Blumenthal, X.Zhang, X.Cheng. Repurposing Epigenetic Inhibitors to Target the Clostridioides Difficile-Specific Dna Adenine Methyltransferase and Sporulation Regulator Cama To Be Published.
Page generated: Mon Aug 12 20:54:09 2024

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