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Potassium in PDB 8fs2: Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)

Enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)

All present enzymatic activity of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907):
2.1.1.72;

Protein crystallography data

The structure of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907), PDB code: 8fs2 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) 45.83 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.263, 161.245, 229.602, 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 11B (YD907) (pdb code 8fs2). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907), PDB code: 8fs2:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 8fs2

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Potassium binding site 1 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:61.6
occ:1.00
 O A:TYR91 2.8 69.9 1.0
O A:LYS89 2.9 65.4 1.0
O A:LYS88 3.0 69.4 1.0
OE1 A:GLU93 3.2 76.8 1.0
O A:HOH841 3.3 61.8 1.0
O A:HOH838 3.3 44.4 1.0
CD A:GLU93 3.4 85.4 1.0
OE2 A:GLU93 3.5 97.2 1.0
C A:LYS89 3.5 62.2 1.0
CB A:GLU93 3.8 59.9 1.0
CA A:LYS89 3.8 62.4 1.0
C A:TYR91 4.0 66.7 1.0
N A:GLU93 4.0 66.8 1.0
C A:LYS88 4.0 60.0 1.0
CG A:GLU93 4.2 74.5 1.0
CA A:GLU93 4.3 62.8 1.0
N A:TYR91 4.4 58.9 1.0
N A:LYS89 4.4 60.3 1.0
N A:LYS90 4.5 60.3 1.0
C A:LYS90 4.6 64.0 1.0
C A:ASP92 4.7 64.6 1.0
CA A:TYR91 4.8 59.3 1.0
N A:ASP92 4.9 71.3 1.0
CA A:LYS90 5.0 60.2 1.0
CA A:ASP92 5.0 67.9 1.0

Potassium binding site 2 out of 9 in 8fs2

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Potassium binding site 2 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:82.9
occ:1.00
 O A:VAL258 3.1 56.6 1.0
O A:GLY249 3.2 66.3 1.0
ND2 A:ASN251 3.2 84.0 1.0
OG A:SER259 3.4 49.4 1.0
O A:ALA250 3.4 65.6 1.0
O D:HOH218 3.6 68.7 1.0
O A:HOH726 3.6 48.8 1.0
C A:GLY249 3.7 55.5 1.0
C A:VAL258 3.8 52.5 1.0
CG A:ASN251 3.9 92.5 1.0
C A:ALA250 3.9 64.3 1.0
CA A:ASN251 4.2 67.2 1.0
CA A:GLY249 4.2 48.1 1.0
CA A:SER259 4.3 41.8 1.0
N A:ASN251 4.3 61.2 1.0
N A:SER259 4.3 44.0 1.0
CB A:SER514 4.4 52.4 1.0
OD1 A:ASN251 4.4 89.4 1.0
CB A:SER259 4.4 43.4 1.0
CA A:SER514 4.4 53.1 1.0
N A:VAL258 4.4 52.8 1.0
N A:ALA250 4.5 58.6 1.0
O A:HOH708 4.5 52.4 1.0
N A:LYS515 4.6 52.5 1.0
CB A:ASN251 4.6 77.7 1.0
CA A:VAL258 4.7 51.0 1.0
CA A:ALA250 4.8 56.8 1.0

Potassium binding site 3 out of 9 in 8fs2

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Potassium binding site 3 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K606

b:68.0
occ:1.00
 OG B:SER259 2.9 41.5 1.0
O B:GLY249 3.0 53.1 1.0
O B:VAL258 3.0 51.4 1.0
OD1 B:ASN251 3.1 89.3 1.0
O B:ALA250 3.2 52.1 1.0
O B:HOH784 3.2 48.9 1.0
O B:HOH799 3.4 66.9 1.0
C B:GLY249 3.5 51.2 1.0
C B:ALA250 3.7 56.2 1.0
C B:VAL258 3.7 44.7 1.0
CG B:ASN251 3.8 85.0 1.0
CA B:SER259 3.9 42.4 1.0
CB B:SER259 3.9 41.1 1.0
N B:SER259 4.1 44.4 1.0
CA B:GLY249 4.1 53.2 1.0
CA B:ASN251 4.1 60.3 1.0
N B:ASN251 4.1 57.2 1.0
CA B:SER514 4.2 44.5 1.0
N B:ALA250 4.2 59.5 1.0
O F:HOH210 4.3 60.0 1.0
CB B:SER514 4.3 49.6 1.0
O B:HOH706 4.4 47.7 1.0
ND2 B:ASN251 4.5 70.0 1.0
O B:HOH778 4.5 53.9 1.0
N B:LYS515 4.5 49.1 1.0
CA B:ALA250 4.5 53.7 1.0
CB B:ASN251 4.6 64.7 1.0
O B:HOH743 4.6 50.1 1.0
N B:VAL258 4.7 43.5 1.0
CA B:VAL258 4.8 41.6 1.0
O B:MET513 4.8 50.4 1.0
C B:SER514 4.8 47.4 1.0
O B:LEU248 4.9 41.7 1.0

Potassium binding site 4 out of 9 in 8fs2

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Potassium binding site 4 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K607

b:62.4
occ:1.00
 O B:TYR91 2.6 64.2 1.0
O B:LYS89 2.9 59.6 1.0
OE1 B:GLU93 3.0 74.7 1.0
O B:LYS88 3.2 49.2 1.0
O2 B:EDO604 3.2 54.3 1.0
C2 B:EDO604 3.4 47.2 1.0
C1 B:EDO604 3.4 48.7 1.0
C B:LYS89 3.6 58.4 1.0
C B:TYR91 3.7 47.6 1.0
O1 B:EDO604 4.0 58.8 1.0
CA B:LYS89 4.0 53.4 1.0
N B:GLU93 4.1 57.0 1.0
CD B:GLU93 4.1 81.1 1.0
N B:TYR91 4.2 55.2 1.0
C B:LYS88 4.2 54.1 1.0
CB B:GLU93 4.3 59.7 1.0
C B:LYS90 4.4 55.2 1.0
N B:LYS90 4.5 54.5 1.0
CA B:TYR91 4.5 52.1 1.0
N B:LYS89 4.6 53.7 1.0
N B:ASP92 4.7 53.7 1.0
CA B:GLU93 4.7 62.3 1.0
C B:ASP92 4.7 60.0 1.0
CA B:ASP92 4.8 60.5 1.0
O B:LYS90 4.8 53.8 1.0
CG B:GLU93 4.8 65.4 1.0
CA B:LYS90 4.9 50.3 1.0
OE2 B:GLU93 4.9 79.5 1.0

Potassium binding site 5 out of 9 in 8fs2

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Potassium binding site 5 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K608

b:93.0
occ:1.00
 OD1 B:ASP370 2.9 92.5 1.0
O B:LEU365 2.9 71.2 1.0
O B:VAL368 3.3 69.4 1.0
C B:LEU365 3.9 69.0 1.0
CG B:ASP370 4.0 80.7 1.0
CA B:ASN366 4.3 72.7 1.0
CD1 B:LEU373 4.4 60.4 1.0
OD2 B:ASP370 4.4 96.7 1.0
N B:ASN366 4.5 69.8 1.0
C B:VAL368 4.6 70.6 1.0
OD1 B:ASN366 4.7 73.5 1.0
O B:ASN366 4.8 76.5 1.0
C B:ASN366 4.8 71.8 1.0
CB B:LEU365 4.9 67.0 1.0
N B:ASP370 4.9 72.3 1.0
CA B:LEU365 5.0 72.7 1.0

Potassium binding site 6 out of 9 in 8fs2

Go back to Potassium Binding Sites List in 8fs2
Potassium binding site 6 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:75.5
occ:1.00
 OD1 C:ASN251 2.9 82.9 1.0
OG C:SER259 2.9 53.6 1.0
O C:VAL258 3.0 66.4 1.0
O C:GLY249 3.1 67.3 1.0
O C:ALA250 3.2 69.3 1.0
CG C:ASN251 3.6 79.5 1.0
C C:VAL258 3.7 61.1 1.0
C C:ALA250 3.7 68.2 1.0
C C:GLY249 3.8 59.4 1.0
CA C:ASN251 3.9 66.5 1.0
N C:ASN251 4.0 66.8 1.0
CA C:SER259 4.0 54.5 1.0
CB C:SER259 4.0 57.5 1.0
N C:SER259 4.1 56.8 1.0
CB C:ASN251 4.3 69.3 1.0
ND2 C:ASN251 4.3 75.7 1.0
CB C:SER514 4.4 48.6 1.0
CA C:GLY249 4.4 57.7 1.0
N C:ALA250 4.4 65.4 1.0
CA C:SER514 4.4 54.4 1.0
N C:VAL258 4.5 57.7 1.0
CA C:ALA250 4.6 69.6 1.0
CA C:VAL258 4.7 57.6 1.0
N C:LYS515 4.7 57.8 1.0

Potassium binding site 7 out of 9 in 8fs2

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Potassium binding site 7 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


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 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K603

b:92.3
occ:1.00
 OD1 C:ASP370 2.8 95.4 1.0
O C:LEU365 2.9 68.9 1.0
O C:VAL368 3.1 76.1 1.0
C C:LEU365 3.9 72.8 1.0
CG C:ASP370 3.9 93.9 1.0
CA C:ASN366 4.3 70.0 1.0
OD2 C:ASP370 4.3 110.1 1.0
C C:VAL368 4.3 68.5 1.0
N C:ASN366 4.4 70.0 1.0
CD1 C:LEU373 4.4 57.1 1.0
CB C:LEU365 4.7 65.5 1.0
OD1 C:ASN366 4.7 86.4 1.0
N C:ASP370 4.7 70.5 1.0
C C:ASN366 4.7 66.9 1.0
O C:ASN366 4.8 72.4 1.0
CA C:LEU365 4.9 69.8 1.0

Potassium binding site 8 out of 9 in 8fs2

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Potassium binding site 8 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K101

b:88.1
occ:1.00
 C5' D:DT10 3.2 74.5 1.0
C3' D:DG9 3.6 72.8 1.0
OP2 D:DT10 3.7 87.0 1.0
C2' D:DG9 3.8 55.5 1.0
O5' D:DG9 4.0 63.8 1.0
C2' D:DT10 4.0 77.3 1.0
C4' D:DT10 4.1 69.2 1.0
C3' D:DT10 4.1 78.6 1.0
C6 D:DT10 4.1 78.7 1.0
O5' D:DT10 4.2 76.1 1.0
OP2 D:DG9 4.3 63.2 1.0
P D:DT10 4.4 83.3 1.0
OP1 D:DG9 4.4 72.9 1.0
O4' D:DT10 4.4 62.5 1.0
P D:DG9 4.4 59.4 1.0
O3' D:DG9 4.5 81.2 1.0
C5' D:DG9 4.6 62.4 1.0
C7 D:DT10 4.7 66.2 1.0
C4' D:DG9 4.7 66.8 1.0
C1' D:DT10 4.7 70.4 1.0
C5 D:DT10 4.9 68.3 1.0
N1 D:DT10 5.0 74.3 1.0

Potassium binding site 9 out of 9 in 8fs2

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Potassium binding site 9 out of 9 in the Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Cama Adenine Methyltransferase Complexed to Cognate Substrate Dna and Inhibitor 11B (YD907) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K101

b:100.9
occ:1.00
 O G:HOH109 3.4 64.2 1.0
O6 G:DG5 3.7 61.8 1.0
O F:HOH210 3.9 60.0 1.0
O4 F:DT10 4.0 54.5 1.0
OD1 B:ASN251 4.4 89.3 1.0
C7 F:DT10 4.5 45.4 1.0
O B:HOH799 4.7 66.9 1.0
C6 G:DG5 4.7 62.6 1.0
O B:ILE256 4.8 58.7 1.0
N7 G:DG4 4.8 69.9 1.0
N7 G:DG5 4.9 53.4 1.0
CG B:ASN251 5.0 85.0 1.0
C4 F:DT10 5.0 57.8 1.0
N4 F:DC11 5.0 62.8 1.0

Reference:

J.Zhou, Y.Deng, I.D.Iyamu, J.R.Horton, D.Yu, T.Hajian, M.Vedadi, D.Rotili, A.Mai, R.M.Blumenthal, X.Zhang, R.Huang, X.Cheng. Comparative Study of Adenosine Analogs As Inhibitors of Protein Arginine Methyltransferases and A Clostridioides Difficile- Specific Dna Adenine Methyltransferase. Acs Chem.Biol. V. 18 734 2023.
ISSN: ESSN 1554-8937
PubMed: 37082867
DOI: 10.1021/ACSCHEMBIO.3C00035
Page generated: Mon Aug 12 23:43:47 2024

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