Magnesium in PDB 8h7a: Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna

Enzymatic activity of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna

All present enzymatic activity of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna, PDB code: 8h7a was solved by Z.Wang, Y.Cao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.23 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.007, 40.06, 81.252, 90.12, 89.99, 113.88
R / Rfree (%) 19.5 / 23.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna (pdb code 8h7a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna, PDB code: 8h7a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8h7a

Go back to Magnesium Binding Sites List in 8h7a
Magnesium binding site 1 out of 4 in the Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg101

b:43.9
occ:1.00
 O C:HOH206 1.8 48.4 1.0
O C:HOH205 1.8 50.5 1.0
O C:HOH212 1.8 53.7 1.0
O C:HOH201 1.8 46.5 1.0
O C:HOH221 1.9 51.1 1.0
N7 C:DG1 2.1 50.0 1.0
C8 C:DG1 2.9 51.5 1.0
C5 C:DG1 3.2 43.5 1.0
O6 C:DG1 3.7 42.3 1.0
C6 C:DG1 3.9 42.7 1.0
N9 C:DG1 4.1 50.7 1.0
C4 C:DG1 4.3 46.2 1.0
O5' C:DG1 4.6 64.1 1.0
O6 C:DG2 4.7 42.6 1.0

Magnesium binding site 2 out of 4 in 8h7a

Go back to Magnesium Binding Sites List in 8h7a
Magnesium binding site 2 out of 4 in the Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:44.3
occ:1.00
 O D:HOH202 1.8 45.6 1.0
O D:HOH208 1.8 50.4 1.0
O D:HOH209 1.8 50.9 1.0
O D:HOH201 1.9 46.9 1.0
N7 D:DG1 1.9 48.0 1.0
O D:HOH223 2.0 50.5 1.0
C8 D:DG1 2.8 48.1 1.0
C5 D:DG1 3.1 41.1 1.0
O6 D:DG1 3.6 39.8 1.0
C6 D:DG1 3.7 39.6 1.0
N9 D:DG1 4.1 49.4 1.0
C4 D:DG1 4.2 45.9 1.0
O6 D:DG2 4.8 41.3 1.0

Magnesium binding site 3 out of 4 in 8h7a

Go back to Magnesium Binding Sites List in 8h7a
Magnesium binding site 3 out of 4 in the Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg101

b:48.0
occ:1.00
 N7 G:DG1 1.8 53.8 1.0
O G:HOH201 1.8 49.9 1.0
O G:HOH212 1.9 52.4 1.0
O G:HOH221 1.9 58.7 1.0
O G:HOH202 2.1 54.3 1.0
O G:HOH217 2.1 58.5 1.0
C8 G:DG1 2.4 53.9 1.0
C5 G:DG1 3.1 46.5 1.0
N9 G:DG1 3.7 52.9 1.0
C6 G:DG1 3.9 42.9 1.0
O6 G:DG1 4.0 42.7 1.0
C4 G:DG1 4.0 48.3 1.0
O6 G:DG2 4.5 43.7 1.0
C1' G:DG1 4.9 55.6 1.0

Magnesium binding site 4 out of 4 in 8h7a

Go back to Magnesium Binding Sites List in 8h7a
Magnesium binding site 4 out of 4 in the Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Dimer Form KAT6A Wh Domain with Its Bound Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg101

b:42.8
occ:1.00
 O H:HOH201 1.8 43.8 1.0
O H:HOH204 1.8 49.9 1.0
O H:HOH203 1.8 47.5 1.0
O H:HOH210 1.9 53.5 1.0
N7 H:DG1 2.0 49.7 1.0
O H:HOH221 2.0 53.5 1.0
C8 H:DG1 2.8 48.8 1.0
C5 H:DG1 3.1 43.6 1.0
O6 H:DG1 3.6 43.4 1.0
C6 H:DG1 3.7 42.7 1.0
N9 H:DG1 4.1 50.3 1.0
C4 H:DG1 4.2 46.4 1.0
O6 H:DG2 4.7 42.7 1.0

Reference:

L.M.Weber, Y.Jia, B.Stielow, S.S.Gisselbrecht, Y.Cao, Y.Ren, I.Rohner, J.King, E.Rothman, S.Fischer, C.Simon, I.Forne, A.Nist, T.Stiewe, M.L.Bulyk, Z.Wang, R.Liefke. The Histone Acetyltransferase KAT6A Is Recruited to Unmethylated Cpg Islands Via A Dna Binding Winged Helix Domain Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAC1188
Page generated: Fri Oct 4 04:25:58 2024

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