Manganese in PDB 7aua: Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp

All present enzymatic activity of Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp:
2.4.1.223;

The binding sites of Manganese atom in the Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp (pdb code 7aua). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp, PDB code: 7aua:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:85.1 occ:1.00 O2A A:UDP1002 1.8 69.8 1.0 O2B A:UDP1002 2.0 69.8 1.0 OD2 A:ASP746 2.5 64.9 1.0 OD1 A:ASP746 2.9 64.9 1.0 PB A:UDP1002 3.0 69.8 1.0 O3B A:UDP1002 3.0 69.8 1.0 CG A:ASP746 3.1 64.9 1.0 PA A:UDP1002 3.1 69.8 1.0 O3A A:UDP1002 3.4 69.8 1.0 OD2 A:ASP744 4.1 57.6 1.0 O5' A:UDP1002 4.1 69.8 1.0 C5' A:UDP1002 4.2 69.8 1.0 NH1 A:ARG672 4.2 69.1 1.0 O1A A:UDP1002 4.2 69.8 1.0 O1B A:UDP1002 4.3 69.8 1.0 NH2 A:ARG858 4.4 72.3 1.0 CZ A:ARG858 4.5 72.3 1.0 NH1 A:ARG858 4.6 72.3 1.0 CB A:ASP746 4.6 64.9 1.0 CG A:ASP744 4.7 57.6 1.0 CB A:ASP744 4.7 57.6 1.0 NH2 A:ARG672 4.8 69.1 1.0 CZ A:ARG672 5.0 69.1 1.0

Manganese binding site 2 out of 2 in the Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of Human Exostosin-Like 3 (EXTL3) in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:85.1 occ:1.00 O2A B:UDP1002 1.8 69.7 1.0 O2B B:UDP1002 2.0 69.7 1.0 OD2 B:ASP746 2.5 64.9 1.0 OD1 B:ASP746 2.9 64.9 1.0 PB B:UDP1002 3.0 69.7 1.0 O3B B:UDP1002 3.0 69.7 1.0 CG B:ASP746 3.1 64.9 1.0 PA B:UDP1002 3.1 69.7 1.0 O3A B:UDP1002 3.4 69.7 1.0 OD2 B:ASP744 4.1 57.6 1.0 O5' B:UDP1002 4.1 69.7 1.0 C5' B:UDP1002 4.2 69.7 1.0 NH1 B:ARG672 4.2 69.1 1.0 O1A B:UDP1002 4.2 69.7 1.0 O1B B:UDP1002 4.3 69.7 1.0 NH2 B:ARG858 4.4 72.3 1.0 CZ B:ARG858 4.5 72.3 1.0 NH1 B:ARG858 4.6 72.3 1.0 CB B:ASP746 4.6 64.9 1.0 CG B:ASP744 4.7 57.6 1.0 CB B:ASP744 4.7 57.6 1.0 NH2 B:ARG672 4.8 69.1 1.0 CZ B:ARG672 5.0 69.1 1.0

L.F.L.Wilson, T.Dendooven, S.W.Hardwick, A.Echevarria-Poza, T.Tryfona, K.B.R.M.Krogh, D.Y.Chirgadze, B.F.Luisi, D.T.Logan, K.Mani, P.Dupree. The Structure of EXTL3 Helps to Explain the Different Roles of Bi-Domain Exostosins in Heparan Sulfate Synthesis. Nat Commun V. 13 3314 2022.
ISSN: ESSN 2041-1723
PubMed: 35676258
DOI: 10.1038/S41467-022-31048-2