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Iron 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
Manganese (Mn) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6yom

Go back to Iron Binding Sites List in 6yom
Iron 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 Iron with other atoms in the Fe 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:Fe701

b:53.3
occ:1.00
O2A A:0KX705 2.0 58.9 1.0
OD1 A:ASP311 2.1 61.8 1.0
NE2 A:HIS206 2.1 65.5 1.0
OD2 A:ASP207 2.2 52.2 1.0
NE2 A:HIS167 2.4 47.0 1.0
CG A:ASP311 2.9 65.9 1.0
CG A:ASP207 3.0 53.7 1.0
CD2 A:HIS206 3.0 64.4 1.0
PA A:0KX705 3.0 60.6 1.0
OD2 A:ASP311 3.2 71.9 1.0
CE1 A:HIS206 3.2 62.0 1.0
CE1 A:HIS167 3.3 50.9 1.0
OD1 A:ASP207 3.3 52.0 1.0
CD2 A:HIS167 3.4 46.6 1.0
O1A A:0KX705 3.5 62.2 1.0
N3A A:0KX705 3.6 62.5 1.0
MN A:MN702 3.6 57.8 1.0
NH2 A:ARG164 4.1 53.6 1.0
CG A:HIS206 4.2 59.7 1.0
CB A:ASP311 4.2 64.0 1.0
CB A:ASP207 4.2 57.2 1.0
ND1 A:HIS206 4.2 60.3 1.0
O5' A:0KX705 4.4 57.6 1.0
ND1 A:HIS167 4.4 48.3 1.0
CG A:HIS167 4.5 48.9 1.0
CG2 A:VAL171 4.7 51.6 1.0
CA A:ASP311 4.9 58.4 1.0
C5' A:0KX705 5.0 59.4 1.0

Iron binding site 2 out of 2 in 6yom

Go back to Iron Binding Sites List in 6yom
Iron 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 Iron with other atoms in the Fe 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:Fe702

b:60.6
occ:1.00
O2A B:0KX706 2.0 64.0 1.0
OD2 B:ASP207 2.1 62.8 1.0
NE2 B:HIS206 2.2 68.3 1.0
OD1 B:ASP311 2.2 64.5 1.0
NE2 B:HIS167 2.4 59.1 1.0
CG B:ASP207 3.0 63.9 1.0
CG B:ASP311 3.0 68.1 1.0
CD2 B:HIS206 3.0 68.4 1.0
PA B:0KX706 3.0 66.6 1.0
OD2 B:ASP311 3.2 77.8 1.0
CE1 B:HIS206 3.2 68.8 1.0
OD1 B:ASP207 3.3 66.1 1.0
CE1 B:HIS167 3.3 58.3 1.0
MN B:MN703 3.4 61.7 1.0
CD2 B:HIS167 3.4 61.6 1.0
O1A B:0KX706 3.5 68.8 1.0
N3A B:0KX706 3.5 69.4 1.0
NH1 B:ARG164 4.0 64.4 1.0
CB B:ASP207 4.2 63.7 1.0
CG B:HIS206 4.2 67.9 1.0
ND1 B:HIS206 4.3 66.7 1.0
CB B:ASP311 4.3 65.0 1.0
ND1 B:HIS167 4.5 59.4 1.0
O5' B:0KX706 4.5 61.5 1.0
CG B:HIS167 4.5 61.5 1.0
CG2 B:VAL171 4.8 60.6 1.0
CA B:ASP311 5.0 61.5 1.0
PB B:0KX706 5.0 70.3 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: Wed Aug 7 16:41:48 2024

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