Atomistry » Manganese » PDB 7uuh-7x9i » 7wl0
Atomistry »
  Manganese »
    PDB 7uuh-7x9i »
      7wl0 »

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

Go back to Manganese Binding Sites List in 7wl0
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

Go back to Manganese Binding Sites List in 7wl0
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

Go back to Manganese Binding Sites List in 7wl0
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

Go back to Manganese Binding Sites List in 7wl0
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: Sun Oct 6 11:01:31 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy