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Manganese in PDB 6yom: Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg

Protein crystallography data

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg, PDB code: 6yom was solved by E.R.Morris, S.Kunzelmann, S.J.Caswell, L.H.Arnold, A.G.Purkiss, G.Kelly, I.A.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.72 / 3.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.298, 105.298, 195.629, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 23.6

Other elements in 6yom:

The structure of Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg (pdb code 6yom). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg, PDB code: 6yom:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6yom

Go back to Manganese Binding Sites List in 6yom
Manganese binding site 1 out of 2 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg


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 Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:57.8
occ:1.00
O1A A:0KX705 2.1 62.2 1.0
OD1 A:ASP207 2.2 52.0 1.0
NE2 A:HIS233 2.2 68.6 1.0
CE1 A:HIS233 3.2 71.3 1.0
PA A:0KX705 3.2 60.6 1.0
CD2 A:HIS233 3.3 67.9 1.0
CG A:ASP207 3.3 53.7 1.0
FE A:FE701 3.6 53.3 1.0
N3A A:0KX705 3.6 62.5 1.0
OD2 A:ASP207 3.7 52.2 1.0
CD2 A:HIS206 3.7 64.4 1.0
O1B A:0KX705 3.8 66.4 1.0
O2A A:0KX705 3.9 58.9 1.0
O A:HIS206 4.1 62.0 1.0
OD2 A:ASP311 4.2 71.9 1.0
PB A:0KX705 4.2 62.9 1.0
NE2 A:HIS206 4.2 65.5 1.0
OE2 A:GLU234 4.2 82.3 1.0
NE2 A:HIS210 4.2 74.5 1.0
ND1 A:HIS233 4.3 68.5 1.0
CG A:HIS233 4.4 65.5 1.0
CG A:GLU234 4.5 71.0 1.0
CD A:GLU234 4.5 76.4 1.0
O5' A:0KX705 4.6 57.6 1.0
CB A:ASP207 4.7 57.2 1.0
CD2 A:HIS210 4.8 73.4 1.0
O2B A:0KX705 4.8 64.2 1.0
CA A:ASP207 4.9 60.9 1.0
CG A:HIS206 4.9 59.7 1.0
C A:HIS206 4.9 63.1 1.0
CG A:ASP311 4.9 65.9 1.0

Manganese binding site 2 out of 2 in 6yom

Go back to Manganese Binding Sites List in 6yom
Manganese binding site 2 out of 2 in the Crystal Structure of Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg


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 Tetrameric Human D137N-SAMHD1 (Residues 109-626) with Xtp, Datp, Dcmpnpp, Mn and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn703

b:61.7
occ:1.00
OD1 B:ASP207 2.2 66.1 1.0
O1A B:0KX706 2.4 68.8 1.0
NE2 B:HIS233 2.4 74.0 1.0
PA B:0KX706 3.2 66.6 1.0
CG B:ASP207 3.3 63.9 1.0
CE1 B:HIS233 3.4 74.9 1.0
FE B:FE702 3.4 60.6 1.0
N3A B:0KX706 3.4 69.4 1.0
CD2 B:HIS233 3.4 75.1 1.0
OD2 B:ASP207 3.6 62.8 1.0
CD2 B:HIS206 3.6 68.4 1.0
O2A B:0KX706 3.8 64.0 1.0
O1B B:0KX706 3.9 71.7 1.0
NE2 B:HIS206 4.0 68.3 1.0
PB B:0KX706 4.0 70.3 1.0
OD2 B:ASP311 4.0 77.8 1.0
O B:HIS206 4.2 73.0 1.0
NE2 B:HIS210 4.2 73.5 1.0
O2B B:0KX706 4.4 69.4 1.0
OE2 B:GLU234 4.4 80.6 1.0
ND1 B:HIS233 4.5 73.6 1.0
CG B:HIS233 4.6 72.6 1.0
O5' B:0KX706 4.6 61.5 1.0
CB B:ASP207 4.6 63.7 1.0
CG B:GLU234 4.7 82.4 1.0
CD B:GLU234 4.8 84.6 1.0
CG B:ASP311 4.8 68.1 1.0
CG B:HIS206 4.8 67.9 1.0
CD2 B:HIS210 4.8 72.6 1.0
OD1 B:ASP311 4.8 64.5 1.0
CA B:ASP207 4.9 66.5 1.0
C B:HIS206 4.9 71.8 1.0

Reference:

E.R.Morris, S.Kunzelmann, S.J.Caswell, L.H.Arnold, A.G.Purkiss, G.Kelly, I.A.Taylor. Crystal Structures of SAMHD1 Inhibitor Complexes Reveal the Mechanism of Water-Mediated Dntp Hydrolysis Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-020-16983-2
Page generated: Sun Oct 6 07:54:02 2024

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