Manganese in PDB 7wl0: Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna

Enzymatic activity of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna

All present enzymatic activity of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna:
1.14.11.53;

Protein crystallography data

The structure of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna, PDB code: 7wl0 was solved by S.Kaur, M.A.Mcdonough, C.J.Schofield, W.S.Aik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.67 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.77, 132.37, 77.96, 90, 100.99, 90
R / Rfree (%) 19.6 / 24

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna (pdb code 7wl0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna, PDB code: 7wl0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 7wl0

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Manganese binding site 1 out of 5 in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:54.6
occ:1.00
 O2' A:OGA302 1.9 39.1 1.0
O2 A:OGA302 2.0 46.6 1.0
NE2 A:HIS266 2.1 40.1 1.0
OD1 A:ASP206 2.2 33.4 1.0
NE2 A:HIS204 2.3 38.6 1.0
C2 A:OGA302 2.5 36.5 1.0
C1 A:OGA302 2.5 41.5 1.0
O A:HOH426 2.6 36.9 1.0
CE1 A:HIS266 2.8 36.0 1.0
CG A:ASP206 3.2 36.3 1.0
CE1 A:HIS204 3.2 38.1 1.0
CD2 A:HIS204 3.3 38.0 1.0
CD2 A:HIS266 3.3 33.4 1.0
OD2 A:ASP206 3.4 36.8 1.0
O1 A:OGA302 3.7 42.1 1.0
N1 A:OGA302 3.8 39.7 1.0
C9 B:6MZ4 4.0 37.3 1.0
ND1 A:HIS266 4.0 32.7 1.0
N6 B:6MZ4 4.2 38.4 1.0
NH1 A:ARG283 4.2 36.6 1.0
CG A:HIS266 4.3 35.9 1.0
ND1 A:HIS204 4.3 35.6 1.0
CG A:HIS204 4.4 36.5 1.0
C4 A:OGA302 4.5 42.2 1.0
CB A:ASP206 4.6 32.5 1.0
O A:HOH433 4.6 35.5 1.0
CD1 A:ILE281 4.9 33.7 1.0
CA A:ASP206 4.9 32.6 1.0
N A:ASP206 4.9 35.0 1.0

Manganese binding site 2 out of 5 in 7wl0

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Manganese binding site 2 out of 5 in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:44.4
occ:1.00
 O2' C:OGA302 1.9 51.6 1.0
O2 C:OGA302 1.9 45.0 1.0
O C:HOH401 2.1 38.8 1.0
OD1 C:ASP206 2.3 37.6 1.0
NE2 C:HIS266 2.3 41.9 1.0
NE2 C:HIS204 2.4 38.0 1.0
C1 C:OGA302 2.4 44.0 1.0
C2 C:OGA302 2.5 47.6 1.0
CE1 C:HIS266 3.1 37.0 1.0
CG C:ASP206 3.2 37.0 1.0
CD2 C:HIS204 3.3 37.6 1.0
CE1 C:HIS204 3.4 40.0 1.0
CD2 C:HIS266 3.4 37.0 1.0
OD2 C:ASP206 3.5 34.9 1.0
O1 C:OGA302 3.6 46.4 1.0
N1 C:OGA302 3.7 47.1 1.0
C9 D:6MZ4 4.0 38.2 1.0
NH1 C:ARG283 4.1 37.3 1.0
O C:HOH438 4.1 42.8 1.0
N6 D:6MZ4 4.3 35.0 1.0
ND1 C:HIS266 4.3 33.6 1.0
ND1 C:HIS204 4.5 37.9 1.0
CG C:HIS266 4.5 35.4 1.0
CG C:HIS204 4.5 36.2 1.0
C4 C:OGA302 4.5 48.7 1.0
CB C:ASP206 4.6 40.6 1.0
N C:ASP206 4.9 38.1 1.0
CA C:ASP206 4.9 36.2 1.0
CD1 C:ILE281 5.0 44.4 1.0

Manganese binding site 3 out of 5 in 7wl0

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Manganese binding site 3 out of 5 in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:43.3
occ:1.00
 O2' E:OGA302 1.9 42.8 1.0
O2 E:OGA302 2.0 45.9 1.0
NE2 E:HIS266 2.2 40.5 1.0
O E:HOH418 2.3 35.6 1.0
C2 E:OGA302 2.4 43.7 1.0
OD1 E:ASP206 2.4 33.9 1.0
C1 E:OGA302 2.5 43.9 1.0
NE2 E:HIS204 2.5 36.5 1.0
CE1 E:HIS266 2.9 36.8 1.0
CG E:ASP206 3.3 40.1 1.0
CD2 E:HIS266 3.3 39.0 1.0
CE1 E:HIS204 3.4 39.4 1.0
OD2 E:ASP206 3.5 44.5 1.0
CD2 E:HIS204 3.5 36.0 1.0
N1 E:OGA302 3.6 45.1 1.0
O1 E:OGA302 3.7 43.5 1.0
O E:HOH430 3.9 43.4 1.0
NH1 E:ARG283 4.1 35.8 1.0
ND1 E:HIS266 4.1 37.5 1.0
C9 F:6MZ4 4.2 42.2 1.0
C4 E:OGA302 4.3 46.5 1.0
CG E:HIS266 4.3 38.5 1.0
N6 F:6MZ4 4.5 40.8 1.0
ND1 E:HIS204 4.5 41.1 1.0
CG E:HIS204 4.6 39.1 1.0
CB E:ASP206 4.7 38.2 1.0
CD1 E:ILE281 5.0 40.4 1.0

Manganese binding site 4 out of 5 in 7wl0

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Manganese binding site 4 out of 5 in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn301

b:42.0
occ:1.00
 O2' G:OGA302 2.1 52.2 1.0
NE2 G:HIS266 2.1 40.2 1.0
O2 G:OGA302 2.2 49.5 1.0
OD1 G:ASP206 2.2 37.2 1.0
O G:HOH424 2.4 40.3 1.0
NE2 G:HIS204 2.5 39.6 1.0
C2 G:OGA302 2.5 50.8 1.0
C1 G:OGA302 2.7 51.9 1.0
CE1 G:HIS266 2.7 39.1 1.0
CG G:ASP206 3.2 38.0 1.0
CD2 G:HIS204 3.4 40.7 1.0
OD2 G:ASP206 3.4 37.7 1.0
CD2 G:HIS266 3.4 41.0 1.0
CE1 G:HIS204 3.5 42.6 1.0
N1 G:OGA302 3.7 48.0 1.0
O1 G:OGA302 3.9 49.4 1.0
NH1 G:ARG283 4.0 41.7 1.0
ND1 G:HIS266 4.0 39.1 1.0
C9 H:6MZ4 4.1 52.0 1.0
N6 H:6MZ4 4.2 49.1 1.0
CG G:HIS266 4.3 39.6 1.0
C4 G:OGA302 4.4 51.0 1.0
CG G:HIS204 4.5 42.7 1.0
CB G:ASP206 4.6 37.4 1.0
ND1 G:HIS204 4.6 43.4 1.0
N G:ASP206 4.9 35.3 1.0
CA G:ASP206 4.9 36.2 1.0

Manganese binding site 5 out of 5 in 7wl0

Go back to Manganese Binding Sites List in 7wl0
Manganese binding site 5 out of 5 in the Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human ALKBH5 in Complex with N-Oxalylglycine (Nog) and M6A-Containing Ssrna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn301

b:36.4
occ:1.00
 O2' I:OGA302 1.9 50.1 1.0
OD1 I:ASP206 2.3 46.7 1.0
NE2 I:HIS204 2.3 41.2 1.0
NE2 I:HIS266 2.3 44.1 1.0
C2 I:OGA302 2.7 53.0 1.0
O1 I:OGA302 2.9 46.9 1.0
CE1 I:HIS204 3.1 44.2 1.0
CG I:ASP206 3.1 42.7 1.0
C1 I:OGA302 3.1 49.1 1.0
CE1 I:HIS266 3.2 40.0 1.0
OD2 I:ASP206 3.3 37.7 1.0
CD2 I:HIS266 3.4 38.5 1.0
CD2 I:HIS204 3.4 41.8 1.0
N1 I:OGA302 3.8 54.4 1.0
NH1 I:ARG283 4.0 48.8 1.0
C9 J:6MZ4 4.1 54.1 1.0
ND1 I:HIS204 4.3 44.4 1.0
N6 J:6MZ4 4.3 51.8 1.0
O2 I:OGA302 4.3 50.9 1.0
ND1 I:HIS266 4.4 42.0 1.0
C4 I:OGA302 4.4 54.0 1.0
CG I:HIS204 4.4 43.6 1.0
CG I:HIS266 4.5 38.3 1.0
CB I:ASP206 4.5 42.8 1.0
N I:ASP206 4.9 40.8 1.0
CA I:ASP206 5.0 43.6 1.0

Reference:

S.Kaur, N.Y.Tam, M.A.Mcdonough, C.J.Schofield, W.S.Aik. Mechanisms of Substrate Recognition and N6-Methyladenosine Demethylation Revealed By Crystal Structures of ALKBH5-Rna Complexes. Nucleic Acids Res. V. 50 4148 2022.
ISSN: ESSN 1362-4962
PubMed: 35333330
DOI: 10.1093/NAR/GKAC195
Page generated: Fri Apr 7 12:59:28 2023

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