Atomistry » Iron » PDB 8fhc-8gbk » 8gb2
Atomistry »
  Iron »
    PDB 8fhc-8gbk »
      8gb2 »

Iron in PDB 8gb2: Crystal Structure of Apo-SAMHD1

Protein crystallography data

The structure of Crystal Structure of Apo-SAMHD1, PDB code: 8gb2 was solved by M.Egleston, L.Dong, A.H.Howlader, S.Bhat, B.Orris, M.A.Bianchet, M.M.Greenberg, J.T.Stivers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.61 / 3.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 202.574, 81.884, 154.026, 90, 118.52, 90
R / Rfree (%) 19.7 / 25

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Apo-SAMHD1 (pdb code 8gb2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Apo-SAMHD1, PDB code: 8gb2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8gb2

Go back to Iron Binding Sites List in 8gb2
Iron binding site 1 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe701

b:201.6
occ:1.00
OD2 D:ASP311 1.9 89.1 1.0
HE1 D:HIS206 2.0 101.1 1.0
NE2 D:HIS167 2.3 76.1 1.0
CE1 D:HIS206 2.4 84.1 1.0
HD2 D:HIS167 2.5 95.0 1.0
CD2 D:HIS167 2.7 79.0 1.0
OD1 D:ASP311 2.7 88.6 1.0
HD1 D:HIS206 2.8 100.1 1.0
CG D:ASP311 2.8 88.6 1.0
OD2 D:ASP207 2.8 81.6 1.0
ND1 D:HIS206 2.8 83.2 1.0
OD1 D:ASP207 2.9 82.0 1.0
CG D:ASP207 3.1 79.5 1.0
NE2 D:HIS206 3.5 94.0 1.0
CE1 D:HIS167 3.5 76.6 1.0
HH12 D:ARG164 3.8 86.7 1.0
HG21 D:VAL171 3.9 88.8 1.0
CG D:HIS206 4.0 79.1 1.0
HE1 D:HIS167 4.0 92.1 1.0
CG D:HIS167 4.0 73.0 1.0
HD2 D:TYR315 4.0 87.1 1.0
HH11 D:ARG164 4.2 86.7 1.0
NH1 D:ARG164 4.3 72.1 1.0
CD2 D:HIS206 4.3 81.2 1.0
CB D:ASP311 4.3 98.2 1.0
HB2 D:ASP207 4.4 91.1 1.0
ND1 D:HIS167 4.4 72.0 1.0
CB D:ASP207 4.4 75.7 1.0
HB3 D:TYR315 4.5 82.9 1.0
HB2 D:ASP311 4.5 118.1 1.0
CG2 D:VAL171 4.7 73.9 1.0
HG23 D:VAL171 4.7 88.8 1.0
HD3 D:ARG164 4.8 83.8 1.0
HB3 D:ASP311 4.8 118.1 1.0
HA D:ASP311 4.8 99.0 1.0
CD2 D:TYR315 4.8 72.4 1.0
HB2 D:HIS206 4.9 93.7 1.0
HE22 D:GLN149 5.0 84.9 1.0
HB3 D:ASP207 5.0 91.1 1.0

Iron binding site 2 out of 4 in 8gb2

Go back to Iron Binding Sites List in 8gb2
Iron binding site 2 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe701

b:76.9
occ:1.00
OD1 A:ASP311 1.9 74.0 1.0
HE1 A:HIS167 1.9 96.3 1.0
NE2 A:HIS206 2.1 93.0 1.0
CE1 A:HIS167 2.2 80.1 1.0
HE2 A:HIS167 2.6 88.5 1.0
NE2 A:HIS167 2.6 73.6 1.0
HD2 A:HIS206 2.6 99.0 1.0
CG A:ASP311 2.6 75.0 1.0
CD2 A:HIS206 2.7 82.4 1.0
OD2 A:ASP311 2.7 75.2 1.0
OD2 A:ASP207 2.8 85.4 1.0
ND1 A:HIS167 3.2 66.5 1.0
CE1 A:HIS206 3.3 123.0 1.0
HH11 A:ARG164 3.4 75.1 1.0
CG A:ASP207 3.6 83.2 1.0
CD2 A:HIS167 3.7 62.2 1.0
HE1 A:HIS206 3.7 147.8 1.0
HH12 A:ARG164 3.7 75.1 1.0
HD2 A:TYR315 3.8 79.6 1.0
HG21 A:VAL171 3.9 74.0 1.0
OD1 A:ASP207 3.9 78.5 1.0
NH1 A:ARG164 3.9 62.4 1.0
CG A:HIS206 3.9 82.5 1.0
CG A:HIS167 4.0 61.4 1.0
CB A:ASP311 4.1 73.2 1.0
ND1 A:HIS206 4.2 111.0 1.0
HB3 A:TYR315 4.3 74.5 1.0
HD2 A:HIS167 4.4 74.8 1.0
HB2 A:ASP311 4.4 88.0 1.0
HG23 A:VAL171 4.5 74.0 1.0
HB2 A:ASP207 4.5 95.2 1.0
HA A:ASP311 4.5 82.4 1.0
CD2 A:TYR315 4.5 66.2 1.0
CG2 A:VAL171 4.6 61.5 1.0
O A:ASP311 4.7 65.9 1.0
HB3 A:ASP311 4.7 88.0 1.0
CB A:ASP207 4.7 79.1 1.0
CA A:ASP311 4.8 68.5 1.0
HE1 A:HIS210 4.9 76.1 1.0
HD3 A:ARG164 4.9 73.7 1.0
HE22 A:GLN149 5.0 69.5 1.0

Iron binding site 3 out of 4 in 8gb2

Go back to Iron Binding Sites List in 8gb2
Iron binding site 3 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe701

b:111.8
occ:1.00
HE2 B:HIS167 1.5 132.2 1.0
OD1 B:ASP311 1.8 110.6 1.0
NE2 B:HIS167 2.1 110.0 1.0
NE2 B:HIS206 2.5 123.9 1.0
HD2 B:HIS167 2.6 125.9 1.0
HD2 B:HIS206 2.6 138.2 1.0
CD2 B:HIS167 2.6 104.7 1.0
OD2 B:ASP207 2.7 126.8 1.0
CD2 B:HIS206 2.7 115.0 1.0
CG B:ASP311 2.9 108.2 1.0
HH12 B:ARG164 3.1 135.4 1.0
CE1 B:HIS167 3.3 105.8 1.0
OD2 B:ASP311 3.3 110.3 1.0
HH11 B:ARG164 3.5 135.4 1.0
CE1 B:HIS206 3.6 137.6 1.0
CG B:ASP207 3.6 130.0 1.0
NH1 B:ARG164 3.7 112.7 1.0
HE1 B:HIS167 3.7 127.2 1.0
CG B:HIS167 3.9 102.2 1.0
CG B:HIS206 3.9 116.0 1.0
OD1 B:ASP207 4.0 124.2 1.0
HE1 B:HIS206 4.1 165.3 1.0
ND1 B:HIS167 4.1 100.0 1.0
CB B:ASP311 4.1 105.5 1.0
HB2 B:ASP311 4.2 126.8 1.0
HD2 B:TYR315 4.2 137.7 1.0
HG21 B:VAL171 4.2 115.7 1.0
ND1 B:HIS206 4.3 129.9 1.0
HG22 B:VAL171 4.3 115.7 1.0
HE22 B:GLN149 4.4 131.5 1.0
HB3 B:TYR315 4.4 132.0 1.0
HB2 B:ASP207 4.5 142.5 1.0
HA B:ASP311 4.6 126.3 1.0
HD3 B:ARG164 4.6 135.3 1.0
CB B:ASP207 4.7 118.6 1.0
CG2 B:VAL171 4.8 96.2 1.0
HB3 B:HIS206 4.8 134.8 1.0
HB3 B:ASP311 4.8 126.8 1.0
CA B:ASP311 4.9 105.1 1.0
CZ B:ARG164 4.9 115.7 1.0
CD2 B:TYR315 5.0 114.6 1.0

Iron binding site 4 out of 4 in 8gb2

Go back to Iron Binding Sites List in 8gb2
Iron binding site 4 out of 4 in the Crystal Structure of Apo-SAMHD1


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 Apo-SAMHD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe701

b:163.1
occ:1.00
HE1 C:HIS167 1.9 172.7 1.0
OD1 C:ASP311 1.9 153.1 1.0
OD2 C:ASP311 2.1 154.6 1.0
CG C:ASP311 2.3 151.6 1.0
ND1 C:HIS206 2.4 173.0 1.0
CE1 C:HIS167 2.6 143.8 1.0
HB2 C:HIS206 2.8 213.3 1.0
OD2 C:ASP207 2.8 227.8 1.0
HD1 C:HIS167 2.9 175.0 1.0
ND1 C:HIS167 3.1 145.7 1.0
HH11 C:ARG164 3.3 190.0 1.0
CG C:HIS206 3.3 178.7 1.0
HH12 C:ARG164 3.4 190.0 1.0
CE1 C:HIS206 3.4 171.1 1.0
CB C:HIS206 3.5 177.6 1.0
HE1 C:HIS206 3.6 205.6 1.0
NH1 C:ARG164 3.7 158.2 1.0
CG C:ASP207 3.7 230.9 1.0
NE2 C:HIS167 3.8 140.2 1.0
HG21 C:VAL171 3.9 186.5 1.0
CB C:ASP311 3.9 147.4 1.0
HB3 C:HIS206 3.9 213.3 1.0
OD1 C:ASP207 4.2 235.9 1.0
HA C:ASP311 4.2 174.0 1.0
HB2 C:ASP311 4.3 177.1 1.0
HG23 C:VAL171 4.3 186.5 1.0
HB3 C:ASP311 4.3 177.1 1.0
CG C:HIS167 4.4 142.9 1.0
HB2 C:TYR315 4.4 171.6 1.0
CD2 C:HIS206 4.5 179.9 1.0
NE2 C:HIS206 4.5 175.1 1.0
CG2 C:VAL171 4.5 155.2 1.0
CA C:ASP311 4.6 144.8 1.0
CD2 C:HIS167 4.7 139.9 1.0
CA C:HIS206 4.7 179.3 1.0
HB2 C:ASP207 4.7 272.1 1.0
C C:HIS206 4.7 188.8 1.0
HG11 C:VAL171 4.8 202.2 1.0
CB C:ASP207 4.9 226.6 1.0
CZ C:ARG164 4.9 145.0 1.0
N C:ASP207 5.0 232.9 1.0
HD3 C:ARG164 5.0 176.9 1.0

Reference:

M.Egleston, L.Dong, A.H.Howlader, S.Bhat, B.Orris, M.A.Bianchet, M.M.Greenberg, J.T.Stivers. Deoxyguanosine-Linked Bifunctional Inhibitor of SAMHD1 Dntpase Activity and Nucleic Acid Binding. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37233733
DOI: 10.1021/ACSCHEMBIO.3C00118
Page generated: Sat Aug 10 04:42:38 2024

Last articles

Ca in 5JXN
Ca in 5JYY
Ca in 5JYI
Ca in 5JXP
Ca in 5JXH
Ca in 5JXG
Ca in 5JXJ
Ca in 5JUH
Ca in 5JXI
Ca in 5JX2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy