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Manganese in PDB 4wmb: Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp

Enzymatic activity of Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp

All present enzymatic activity of Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp:
3.4.21.22;

Protein crystallography data

The structure of Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp, PDB code: 4wmb was solved by H.Yu, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.48 / 2.05
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 89.468, 89.468, 42.934, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp (pdb code 4wmb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp, PDB code: 4wmb:

Manganese binding site 1 out of 1 in 4wmb

Go back to Manganese Binding Sites List in 4wmb
Manganese binding site 1 out of 1 in the Crystal Structure of Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp


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 Mouse Xyloside Xylosyltransferase 1 Complexed with Manganese, Acceptor Ligand and Udp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:27.0
occ:1.00
 O3B A:UDP402 1.9 30.3 1.0
OD1 A:ASP227 2.1 29.6 1.0
NE2 A:HIS382 2.1 30.0 1.0
O1A A:UDP402 2.3 32.8 1.0
OD2 A:ASP225 2.3 23.1 1.0
OD2 A:ASP227 2.4 28.6 1.0
CG A:ASP227 2.6 30.2 1.0
CD2 A:HIS382 3.0 29.9 1.0
CE1 A:HIS382 3.2 27.9 1.0
CG A:ASP225 3.2 24.8 1.0
PB A:UDP402 3.3 33.6 1.0
PA A:UDP402 3.5 33.0 1.0
CB A:ASP225 3.5 25.5 1.0
O3A A:UDP402 3.8 31.4 1.0
O3' A:UDP402 3.9 30.4 1.0
CB A:ASP227 4.1 30.8 1.0
CB A:ASN384 4.1 30.5 1.0
O2B A:UDP402 4.2 33.9 1.0
CG A:HIS382 4.3 29.2 1.0
ND1 A:HIS382 4.3 27.8 1.0
C5' A:UDP402 4.3 31.9 1.0
O1B A:UDP402 4.4 35.0 1.0
OD1 A:ASP225 4.4 24.3 1.0
CA A:ASN384 4.4 31.6 1.0
O5' A:UDP402 4.5 33.4 1.0
O A:HOH512 4.5 35.0 1.0
O2A A:UDP402 4.6 35.3 1.0
C3' A:UDP402 4.7 32.2 1.0
N A:ASP227 4.8 31.9 1.0
C4' A:UDP402 4.9 32.2 1.0
CA A:ASP227 4.9 32.1 1.0
N A:ASN384 4.9 31.6 1.0
CA A:ASP225 5.0 25.6 1.0

Reference:

H.Yu, M.Takeuchi, J.Lebarron, J.Kantharia, E.London, H.Bakker, R.S.Haltiwanger, H.Li, H.Takeuchi. Notch-Modifying Xylosyltransferase Structures Support An Sni-Like Retaining Mechanism. Nat.Chem.Biol. V. 11 847 2015.
ISSN: ESSN 1552-4469
PubMed: 26414444
DOI: 10.1038/NCHEMBIO.1927
Page generated: Sat Oct 5 22:50:57 2024

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