Phosphorus in PDB 10mh: Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target

Enzymatic activity of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target

All present enzymatic activity of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target:
2.1.1.73;

Protein crystallography data

The structure of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target, PDB code: 10mh was solved by G.Sheikhnejad, A.Brank, J.K.Christman, A.Goddard, E.Alvarez, H.Ford Junior, V.E.Marquez, C.J.Marasco, J.R.Sufrin, M.O'gara, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.30 / 2.55
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 99.860, 99.860, 325.200, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Phosphorus atom in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target (pdb code 10mh). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 24 binding sites of Phosphorus where determined in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target, PDB code: 10mh:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 24 in 10mh

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Phosphorus binding site 1 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P402

b:57.0
occ:1.00
P B:DC402 0.0 57.0 1.0
OP2 B:DC402 1.5 55.8 1.0
OP1 B:DC402 1.5 57.6 1.0
O5' B:DC402 1.7 49.8 1.0
C5' B:DC402 2.7 40.4 1.0
O4' B:DC402 3.5 32.4 1.0
C4' B:DC402 3.7 35.3 1.0
C6 B:DC402 4.2 15.5 1.0
C3' B:DC402 4.6 35.8 1.0
C1' B:DC402 4.8 25.9 1.0
C5 B:DC402 4.9 15.1 1.0
O A:HOH385 4.9 41.7 1.0
N1 B:DC402 5.0 14.8 1.0

Phosphorus binding site 2 out of 24 in 10mh

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Phosphorus binding site 2 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P403

b:38.6
occ:1.00
P B:DC403 0.0 38.6 1.0
OP1 B:DC403 1.5 37.6 1.0
OP2 B:DC403 1.5 36.0 1.0
O5' B:DC403 1.6 28.0 1.0
O3' B:DC402 1.6 38.1 1.0
C3' B:DC402 2.7 35.8 1.0
C5' B:DC403 2.7 16.9 1.0
C2' B:DC402 3.6 28.1 1.0
C4' B:DC402 3.9 35.3 1.0
C4' B:DC403 4.0 11.3 1.0
O4' B:DC403 4.0 10.7 1.0
OE1 A:GLN297 4.1 12.7 1.0
C5' B:DC402 4.4 40.4 1.0
CB A:SER296 4.4 16.2 1.0
OG A:SER296 4.4 25.5 1.0
C3' B:DC403 4.6 13.0 1.0
O A:HOH429 4.6 46.7 1.0
O A:HOH385 4.8 41.7 1.0
OG A:SER294 4.8 10.0 1.0
C1' B:DC402 4.9 25.9 1.0
O4' B:DC402 4.9 32.4 1.0
CD A:GLN297 5.0 8.1 1.0
CG A:GLN297 5.0 2.0 1.0

Phosphorus binding site 3 out of 24 in 10mh

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Phosphorus binding site 3 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P404

b:21.6
occ:1.00
P B:DA404 0.0 21.6 1.0
OP1 B:DA404 1.5 16.8 1.0
OP2 B:DA404 1.5 23.7 1.0
O5' B:DA404 1.6 22.2 1.0
O3' B:DC403 1.7 18.2 1.0
C5' B:DA404 2.8 18.8 1.0
C3' B:DC403 2.9 13.0 1.0
C2' B:DC403 3.4 10.5 1.0
C4' B:DA404 4.0 15.4 1.0
C4' B:DC403 4.1 11.3 1.0
O4' B:DA404 4.1 16.9 1.0
C3' B:DA404 4.6 12.8 1.0
C1' B:DC403 4.7 7.5 1.0
O4' B:DC403 4.9 10.7 1.0
C5' B:DC403 5.0 16.9 1.0

Phosphorus binding site 4 out of 24 in 10mh

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Phosphorus binding site 4 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P405

b:22.4
occ:1.00
P B:DT405 0.0 22.4 1.0
OP1 B:DT405 1.5 24.7 1.0
OP2 B:DT405 1.5 21.4 1.0
O5' B:DT405 1.6 15.6 1.0
O3' B:DA404 1.6 18.0 1.0
C5' B:DT405 2.6 13.2 1.0
C3' B:DA404 2.8 12.8 1.0
C2' B:DA404 3.5 14.4 1.0
O A:HOH361 3.7 25.1 1.0
C4' B:DA404 4.0 15.4 1.0
C4' B:DT405 4.0 13.5 1.0
O B:HOH415 4.2 44.1 1.0
CD1 A:ILE258 4.2 8.7 1.0
C3' B:DT405 4.3 12.6 1.0
C2' B:DT405 4.6 13.9 1.0
O4' B:DT405 4.7 15.2 1.0
C1' B:DA404 4.7 10.4 1.0
O4' B:DA404 4.9 16.9 1.0
C5' B:DA404 4.9 18.8 1.0

Phosphorus binding site 5 out of 24 in 10mh

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Phosphorus binding site 5 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P406

b:21.3
occ:1.00
P B:DG406 0.0 21.3 1.0
OP1 B:DG406 1.5 24.6 1.0
OP2 B:DG406 1.5 26.9 1.0
O5' B:DG406 1.6 18.2 1.0
O3' B:DT405 1.7 17.8 1.0
C5' B:DG406 2.8 19.4 1.0
C3' B:DT405 2.8 12.6 1.0
C4' B:DT405 3.8 13.5 1.0
C2' B:DT405 4.0 13.9 1.0
C4' B:DG406 4.1 19.2 1.0
O A:HOH364 4.1 11.9 1.0
O4' B:DG406 4.3 17.0 1.0
NH1 A:ARG209 4.4 31.2 1.0
C1' B:DT405 4.6 9.5 1.0
C2' B:DG406 4.6 19.4 1.0
C3' B:DG406 4.7 19.6 1.0
O4' B:DT405 4.7 15.2 1.0
NH2 A:ARG209 4.7 33.3 1.0
C5' B:DT405 4.8 13.2 1.0

Phosphorus binding site 6 out of 24 in 10mh

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Phosphorus binding site 6 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P407

b:31.5
occ:1.00
P B:5CM407 0.0 31.5 1.0
OP2 B:5CM407 1.5 29.1 1.0
OP1 B:5CM407 1.5 33.3 1.0
O5' B:5CM407 1.6 29.4 1.0
O3' B:DG406 1.7 26.6 1.0
C5' B:5CM407 2.6 28.8 1.0
C3' B:DG406 2.8 19.6 1.0
C2' B:DG406 3.7 19.4 1.0
C4' B:5CM407 4.1 28.6 1.0
C4' B:DG406 4.2 19.2 1.0
O B:HOH419 4.3 42.5 1.0
O4' B:5CM407 4.3 24.6 1.0
NZ A:LYS234 4.4 44.9 1.0
CE A:LYS234 4.5 45.0 1.0
C1' B:DG406 4.5 13.1 1.0
O A:HOH358 4.5 19.1 1.0
CD A:LYS234 4.6 39.0 1.0
O4' B:DG406 5.0 17.0 1.0

Phosphorus binding site 7 out of 24 in 10mh

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Phosphorus binding site 7 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P408

b:44.8
occ:1.00
P B:DG408 0.0 44.8 1.0
OP1 B:DG408 1.5 44.1 1.0
OP2 B:DG408 1.5 36.8 1.0
O5' B:DG408 1.6 41.6 1.0
O3' B:5CM407 1.6 36.6 1.0
C3' B:5CM407 2.6 28.0 1.0
C5' B:DG408 2.7 41.2 1.0
C4' B:5CM407 3.7 28.6 1.0
C4' B:DG408 3.8 40.1 1.0
C2' B:DG408 3.8 36.6 1.0
C2' B:5CM407 3.9 23.2 1.0
C3' B:DG408 4.0 41.1 1.0
C5' B:5CM407 4.1 28.8 1.0
O4' B:DG408 4.3 35.0 1.0
O4' B:5CM407 4.7 24.6 1.0
C1' B:DG408 4.7 30.8 1.0
C1' B:5CM407 4.9 20.2 1.0

Phosphorus binding site 8 out of 24 in 10mh

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Phosphorus binding site 8 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P409

b:49.4
occ:1.00
P B:DC409 0.0 49.4 1.0
OP2 B:DC409 1.5 48.8 1.0
OP1 B:DC409 1.5 46.3 1.0
O3' B:DG408 1.6 45.2 1.0
O5' B:DC409 1.6 44.8 1.0
C5' B:DC409 2.6 42.3 1.0
C3' B:DG408 2.7 41.1 1.0
C4' B:DG408 3.6 40.1 1.0
C4' B:DC409 3.8 38.6 1.0
C2' B:DG408 3.9 36.6 1.0
O4' B:DC409 4.0 34.3 1.0
C1' B:DG408 4.4 30.8 1.0
C3' B:DC409 4.5 36.9 1.0
O4' B:DG408 4.5 35.0 1.0
C5' B:DG408 4.7 41.2 1.0
O5' B:DG408 4.9 41.6 1.0
C2' B:DC409 5.0 33.8 1.0

Phosphorus binding site 9 out of 24 in 10mh

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Phosphorus binding site 9 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P410

b:40.5
occ:1.00
P B:DT410 0.0 40.5 1.0
OP2 B:DT410 1.5 35.3 1.0
OP1 B:DT410 1.5 40.9 1.0
O5' B:DT410 1.6 40.0 1.0
O3' B:DC409 1.6 38.5 1.0
C5' B:DT410 2.7 37.8 1.0
C3' B:DC409 2.7 36.9 1.0
C2' B:DC409 3.5 33.8 1.0
C4' B:DC409 4.0 38.6 1.0
C4' B:DT410 4.1 35.5 1.0
C3' B:DT410 4.4 34.0 1.0
C1' B:DC409 4.5 26.8 1.0
O4' B:DT410 4.5 31.6 1.0
C2' B:DT410 4.6 33.4 1.0
C5' B:DC409 4.9 42.3 1.0
O4' B:DC409 4.9 34.3 1.0
C6 B:DT410 5.0 26.5 1.0

Phosphorus binding site 10 out of 24 in 10mh

Go back to Phosphorus Binding Sites List in 10mh
Phosphorus binding site 10 out of 24 in the Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Ternary Structure of Hhai Methyltransferase with Adohcy and Hemimethylated Dna Containing 5,6-Dihydro-5-Azacytosine at the Target within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P411

b:40.0
occ:1.00
P B:DG411 0.0 40.0 1.0
OP2 B:DG411 1.5 33.6 1.0
OP1 B:DG411 1.5 41.0 1.0
O5' B:DG411 1.6 39.3 1.0
O3' B:DT410 1.7 35.7 1.0
C5' B:DG411 2.8 34.9 1.0
C3' B:DT410 2.8 34.0 1.0
C2' B:DT410 3.5 33.4 1.0
NE2 A:GLN90 3.6 34.7 1.0
C4' B:DG411 4.1 30.4 1.0
C4' B:DT410 4.1 35.5 1.0
C3' B:DG411 4.3 29.7 1.0
OE1 A:GLN90 4.3 37.2 1.0
CD A:GLN90 4.4 36.9 1.0
C1' B:DT410 4.6 30.0 1.0
O4' B:DG411 4.7 32.0 1.0
C2' B:DG411 4.8 26.2 1.0
O4' B:DT410 4.9 31.6 1.0

Reference:

G.Sheikhnejad, A.Brank, J.K.Christman, A.Goddard, E.Alvarez, H.Ford Jr., V.E.Marquez, C.J.Marasco, J.R.Sufrin, M.O'gara, X.Cheng. Mechanism of Inhibition of Dna (Cytosine C5)-Methyltransferases By Oligodeoxyribonucleotides Containing 5,6-Dihydro-5-Azacytosine. J.Mol.Biol. V. 285 2021 1999.
ISSN: ISSN 0022-2836
PubMed: 9925782
DOI: 10.1006/JMBI.1998.2426
Page generated: Fri Sep 25 11:06:55 2020

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