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Iron in PDB 6xu1: Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg

Protein crystallography data

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg, PDB code: 6xu1 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) 107.30 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 137.369, 171.860, 179.572, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.2

Other elements in 6xu1:

The structure of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg also contains other interesting chemical elements:

Magnesium (Mg) 25 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg (pdb code 6xu1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg, PDB code: 6xu1:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6xu1

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Iron binding site 1 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:15.0
occ:1.00
OD1 A:ASP311 2.0 13.7 1.0
NE2 A:HIS206 2.2 13.5 1.0
O1A A:DZ4705 2.2 13.6 1.0
OD2 A:ASP207 2.2 12.3 1.0
O A:HOH866 2.2 15.7 1.0
NE2 A:HIS167 2.2 11.0 1.0
CG A:ASP207 3.0 13.2 1.0
CG A:ASP311 3.1 13.9 1.0
CD2 A:HIS206 3.1 13.4 1.0
CD2 A:HIS167 3.2 11.6 1.0
CE1 A:HIS206 3.2 13.3 1.0
CE1 A:HIS167 3.2 11.6 1.0
PA A:DZ4705 3.3 14.4 1.0
OD1 A:ASP207 3.4 13.5 1.0
OD2 A:ASP311 3.5 14.1 1.0
MG A:MG702 3.7 8.2 1.0
O2A A:DZ4705 3.8 15.1 1.0
NH2 A:ARG164 3.8 14.6 1.0
N3A A:DZ4705 3.8 14.0 1.0
CB A:ASP207 4.2 13.3 1.0
CG A:HIS206 4.3 13.4 1.0
ND1 A:HIS206 4.3 13.1 1.0
CB A:ASP311 4.3 13.6 1.0
ND1 A:HIS167 4.3 11.5 1.0
CG A:HIS167 4.3 11.9 1.0
O5' A:DZ4705 4.6 14.3 1.0
O A:HOH845 4.7 11.1 1.0
CG2 A:VAL171 4.8 13.5 1.0
O A:HOH865 4.9 11.1 1.0
O A:HOH884 5.0 18.1 1.0

Iron binding site 2 out of 8 in 6xu1

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Iron binding site 2 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp 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 H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:13.9
occ:1.00
O1A B:DZ4705 2.0 14.6 1.0
O B:HOH822 2.0 11.7 1.0
OD1 B:ASP311 2.1 13.3 1.0
NE2 B:HIS206 2.2 14.3 1.0
NE2 B:HIS167 2.2 11.1 1.0
OD2 B:ASP207 2.2 13.2 1.0
CG B:ASP207 3.0 14.2 1.0
CG B:ASP311 3.1 14.2 1.0
CD2 B:HIS206 3.1 14.7 1.0
CD2 B:HIS167 3.2 11.3 1.0
CE1 B:HIS206 3.2 14.9 1.0
CE1 B:HIS167 3.2 11.3 1.0
PA B:DZ4705 3.2 14.8 1.0
OD1 B:ASP207 3.4 14.2 1.0
OD2 B:ASP311 3.5 15.4 1.0
MG B:MG702 3.7 9.6 1.0
O2A B:DZ4705 3.7 16.8 1.0
NH1 B:ARG164 3.9 13.5 1.0
N3A B:DZ4705 3.9 14.8 1.0
CB B:ASP207 4.2 14.1 1.0
CG B:HIS206 4.3 14.9 1.0
ND1 B:HIS206 4.3 15.4 1.0
CB B:ASP311 4.3 13.9 1.0
ND1 B:HIS167 4.3 10.9 1.0
CG B:HIS167 4.3 11.5 1.0
O5' B:DZ4705 4.6 13.7 1.0
CG2 B:VAL171 4.8 13.8 1.0
O B:HOH850 4.8 11.9 1.0
O B:HOH901 4.9 22.2 1.0

Iron binding site 3 out of 8 in 6xu1

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Iron binding site 3 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe702

b:13.4
occ:1.00
OD1 C:ASP311 2.1 13.5 1.0
O C:HOH825 2.1 18.6 1.0
OD2 C:ASP207 2.1 12.5 1.0
NE2 C:HIS167 2.1 11.4 1.0
NE2 C:HIS206 2.2 11.5 1.0
O1A C:DZ4706 2.2 13.6 1.0
CG C:ASP207 3.0 13.4 1.0
CG C:ASP311 3.1 14.1 1.0
CD2 C:HIS167 3.1 11.5 1.0
CD2 C:HIS206 3.1 11.8 1.0
CE1 C:HIS167 3.2 11.3 1.0
CE1 C:HIS206 3.2 11.8 1.0
PA C:DZ4706 3.3 14.2 1.0
OD1 C:ASP207 3.4 13.1 1.0
OD2 C:ASP311 3.5 15.4 1.0
MG C:MG703 3.7 9.2 1.0
O2A C:DZ4706 3.7 14.0 1.0
NH2 C:ARG164 3.8 15.0 1.0
N3A C:DZ4706 3.9 13.8 1.0
CB C:ASP207 4.2 13.5 1.0
CG C:HIS167 4.3 12.1 1.0
CB C:ASP311 4.3 14.3 1.0
CG C:HIS206 4.3 12.4 1.0
ND1 C:HIS206 4.3 11.8 1.0
ND1 C:HIS167 4.3 11.1 1.0
O5' C:DZ4706 4.6 14.1 1.0
CG2 C:VAL171 4.7 12.1 1.0
O C:HOH841 4.9 13.1 1.0
O C:HOH832 4.9 13.7 1.0

Iron binding site 4 out of 8 in 6xu1

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Iron binding site 4 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe702

b:15.5
occ:1.00
OD1 D:ASP311 2.0 16.3 1.0
OD2 D:ASP207 2.2 13.8 1.0
NE2 D:HIS206 2.2 16.3 1.0
O1A D:DZ4706 2.2 13.7 1.0
O D:HOH847 2.2 13.6 1.0
NE2 D:HIS167 2.2 13.5 1.0
CG D:ASP207 3.0 15.3 1.0
CG D:ASP311 3.0 16.6 1.0
CD2 D:HIS206 3.1 16.3 1.0
CD2 D:HIS167 3.2 14.2 1.0
CE1 D:HIS167 3.2 14.0 1.0
CE1 D:HIS206 3.2 16.4 1.0
PA D:DZ4706 3.3 15.0 1.0
OD1 D:ASP207 3.4 15.3 1.0
OD2 D:ASP311 3.5 17.5 1.0
MG D:MG703 3.7 8.9 1.0
O2A D:DZ4706 3.8 14.1 1.0
NH1 D:ARG164 3.9 15.5 1.0
N3A D:DZ4706 3.9 15.5 1.0
CB D:ASP207 4.2 15.4 1.0
CG D:HIS206 4.3 16.4 1.0
CB D:ASP311 4.3 15.6 1.0
ND1 D:HIS206 4.3 16.7 1.0
ND1 D:HIS167 4.3 13.9 1.0
CG D:HIS167 4.3 13.7 1.0
O5' D:DZ4706 4.6 14.4 1.0
CG2 D:VAL171 4.7 14.9 1.0
O D:HOH840 4.9 14.1 1.0

Iron binding site 5 out of 8 in 6xu1

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Iron binding site 5 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe701

b:17.7
occ:1.00
OD1 E:ASP311 2.0 20.1 1.0
O1A E:DZ4705 2.1 20.1 1.0
NE2 E:HIS206 2.2 16.2 1.0
OD2 E:ASP207 2.2 18.1 1.0
NE2 E:HIS167 2.2 15.6 1.0
O E:HOH837 2.3 23.4 1.0
CG E:ASP311 3.0 20.8 1.0
CG E:ASP207 3.0 18.6 1.0
CD2 E:HIS206 3.1 17.2 1.0
CE1 E:HIS206 3.2 16.3 1.0
PA E:DZ4705 3.2 19.4 1.0
CE1 E:HIS167 3.2 15.4 1.0
CD2 E:HIS167 3.2 15.0 1.0
OD1 E:ASP207 3.4 18.3 1.0
OD2 E:ASP311 3.4 20.9 1.0
MG E:MG702 3.6 15.5 1.0
O2A E:DZ4705 3.7 19.7 1.0
NH2 E:ARG164 3.8 18.0 1.0
N3A E:DZ4705 3.9 21.1 1.0
CB E:ASP311 4.2 20.3 1.0
CG E:HIS206 4.3 17.5 1.0
CB E:ASP207 4.3 17.9 1.0
ND1 E:HIS206 4.3 16.8 1.0
ND1 E:HIS167 4.3 14.9 1.0
CG E:HIS167 4.4 14.9 1.0
O5' E:DZ4705 4.6 18.6 1.0
O E:HOH862 4.7 25.8 1.0
CG2 E:VAL171 4.8 16.1 1.0
O E:HOH826 4.8 14.6 1.0

Iron binding site 6 out of 8 in 6xu1

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Iron binding site 6 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe701

b:14.3
occ:1.00
OD1 F:ASP311 2.0 14.9 1.0
O1A F:DZ4705 2.1 13.2 1.0
NE2 F:HIS206 2.1 14.2 1.0
O F:HOH869 2.1 12.2 1.0
OD2 F:ASP207 2.2 17.3 1.0
NE2 F:HIS167 2.2 10.8 1.0
CG F:ASP207 3.0 16.2 1.0
CG F:ASP311 3.0 15.1 1.0
CD2 F:HIS206 3.1 14.9 1.0
CE1 F:HIS206 3.1 14.7 1.0
CD2 F:HIS167 3.2 11.4 1.0
CE1 F:HIS167 3.2 11.0 1.0
PA F:DZ4705 3.2 13.6 1.0
OD1 F:ASP207 3.4 16.4 1.0
OD2 F:ASP311 3.5 15.3 1.0
MG F:MG702 3.7 9.8 1.0
O2A F:DZ4705 3.8 13.1 1.0
N3A F:DZ4705 3.8 12.9 1.0
NH1 F:ARG164 3.9 14.8 1.0
CB F:ASP207 4.2 15.6 1.0
CG F:HIS206 4.2 15.0 1.0
ND1 F:HIS206 4.3 14.4 1.0
CB F:ASP311 4.3 15.7 1.0
ND1 F:HIS167 4.3 10.9 1.0
CG F:HIS167 4.3 11.4 1.0
O5' F:DZ4705 4.5 12.9 1.0
CG2 F:VAL171 4.7 18.5 1.0
O F:HOH843 4.8 12.7 1.0
O F:HOH914 4.9 23.6 1.0

Iron binding site 7 out of 8 in 6xu1

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Iron binding site 7 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe702

b:13.1
occ:1.00
OD1 G:ASP311 2.0 16.8 1.0
O1A G:DZ4706 2.1 13.4 1.0
NE2 G:HIS206 2.1 16.0 1.0
O G:HOH847 2.2 12.9 1.0
NE2 G:HIS167 2.2 11.8 1.0
OD2 G:ASP207 2.2 15.2 1.0
CG G:ASP311 3.0 15.9 1.0
CG G:ASP207 3.0 15.1 1.0
CD2 G:HIS206 3.1 16.1 1.0
CE1 G:HIS167 3.2 11.9 1.0
CE1 G:HIS206 3.2 16.5 1.0
CD2 G:HIS167 3.2 12.2 1.0
PA G:DZ4706 3.3 14.5 1.0
OD1 G:ASP207 3.4 15.9 1.0
OD2 G:ASP311 3.5 16.5 1.0
MG G:MG703 3.7 11.5 1.0
O2A G:DZ4706 3.8 13.1 1.0
N3A G:DZ4706 3.8 13.3 1.0
NH2 G:ARG164 3.9 13.9 1.0
CB G:ASP311 4.2 15.4 1.0
CB G:ASP207 4.3 15.3 1.0
CG G:HIS206 4.3 16.8 1.0
ND1 G:HIS206 4.3 16.9 1.0
ND1 G:HIS167 4.3 12.2 1.0
CG G:HIS167 4.3 12.4 1.0
O5' G:DZ4706 4.5 12.8 1.0
CG2 G:VAL171 4.7 16.5 1.0
O G:HOH866 4.8 17.7 1.0
O G:HOH900 4.9 19.1 1.0

Iron binding site 8 out of 8 in 6xu1

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Iron binding site 8 out of 8 in the Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Tetrameric Human H215A-SAMHD1 (Residues 109-626) with Gtp, Dampnpp and Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe702

b:20.5
occ:1.00
OD1 H:ASP311 2.0 22.3 1.0
OD2 H:ASP207 2.2 23.7 1.0
NE2 H:HIS206 2.2 23.9 1.0
O1A H:DZ4706 2.2 23.0 1.0
NE2 H:HIS167 2.2 19.9 1.0
O H:HOH845 2.3 21.9 1.0
CG H:ASP207 3.0 22.4 1.0
CG H:ASP311 3.0 22.1 1.0
CD2 H:HIS206 3.1 23.8 1.0
PA H:DZ4706 3.1 22.4 1.0
CD2 H:HIS167 3.2 19.1 1.0
CE1 H:HIS167 3.2 18.9 1.0
CE1 H:HIS206 3.2 24.6 1.0
OD1 H:ASP207 3.4 21.0 1.0
OD2 H:ASP311 3.5 22.0 1.0
MG H:MG703 3.7 15.4 1.0
O2A H:DZ4706 3.7 22.2 1.0
N3A H:DZ4706 3.8 24.5 1.0
NH1 H:ARG164 3.9 23.1 1.0
CB H:ASP207 4.2 21.5 1.0
CG H:HIS206 4.3 23.1 1.0
CB H:ASP311 4.3 22.2 1.0
ND1 H:HIS206 4.3 24.7 1.0
ND1 H:HIS167 4.3 18.3 1.0
CG H:HIS167 4.4 18.3 1.0
O5' H:DZ4706 4.5 21.6 1.0
CG2 H:VAL171 4.8 19.0 1.0
O H:HOH833 4.9 20.9 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 15:38:37 2024

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