Atomistry » Iron » PDB 6bpu-6cdh » 6bxl
Atomistry »
  Iron »
    PDB 6bpu-6cdh »
      6bxl »

Iron in PDB 6bxl: Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam

Enzymatic activity of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam

All present enzymatic activity of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam:
2.5.1.108;

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam, PDB code: 6bxl was solved by A.T.Torelli, M.K.Fenwick, Y.Zhang, M.Dong, V.Kathiresan, J.D.Carantoa, B.Dzikovski, K.M.Lancaster, J.H.Freed, B.M.Hoffman, H.Lin, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.54 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.035, 80.904, 161.058, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam (pdb code 6bxl). 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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam, PDB code: 6bxl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 1 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:86.4
occ:0.80
 FE1 A:SF4402 0.0 86.4 0.8
S4 A:SF4402 2.2 80.9 0.8
SG A:CYS59 2.3 53.4 1.0
S2 A:SF4402 2.3 91.6 0.8
S3 A:SF4402 2.3 89.7 0.8
FE4 A:SF4402 2.7 0.9 0.8
FE3 A:SF4402 2.8 94.9 0.8
FE2 A:SF4402 2.8 87.8 0.8
CB A:CYS59 3.5 41.8 1.0
NE2 A:GLN241 3.8 47.6 1.0
S1 A:SF4402 3.9 90.2 0.8
N A:SAM401 4.1 82.8 0.8
O A:TYR56 4.6 50.6 0.5
CA A:GLY57 4.7 44.6 1.0
CD A:GLN241 4.7 77.2 1.0
CA A:CYS59 4.7 45.4 1.0
N A:CYS59 4.7 42.8 1.0
NH2 A:ARG153 4.8 59.2 1.0
CG A:GLN241 4.8 69.8 1.0
CB A:CYS287 4.9 76.0 1.0
SG A:CYS287 4.9 87.2 1.0
SG A:CYS163 5.0 81.3 1.0

Iron binding site 2 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 2 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:87.8
occ:0.80
 FE2 A:SF4402 0.0 87.8 0.8
S3 A:SF4402 2.3 89.7 0.8
SG A:CYS163 2.3 81.3 1.0
S4 A:SF4402 2.3 80.9 0.8
S1 A:SF4402 2.3 90.2 0.8
FE4 A:SF4402 2.8 0.9 0.8
FE3 A:SF4402 2.8 94.9 0.8
FE1 A:SF4402 2.8 86.4 0.8
CB A:CYS163 3.2 70.3 1.0
N A:CYS163 3.8 43.9 1.0
S2 A:SF4402 3.9 91.6 0.8
NH2 A:ARG153 4.0 59.2 1.0
CA A:CYS163 4.1 57.8 1.0
N A:SAM401 4.5 82.8 0.8
O A:SAM401 4.6 70.3 0.8
SG A:CYS59 4.7 53.4 1.0
C A:GLY162 4.8 44.7 1.0
N A:GLY162 4.8 47.1 1.0
CB A:LEU161 4.8 48.4 1.0
CD1 A:ILE323 4.9 61.9 1.0
CD1 A:LEU161 4.9 45.5 1.0
SG A:CYS287 4.9 87.2 1.0

Iron binding site 3 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 3 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:94.9
occ:0.80
 FE3 A:SF4402 0.0 94.9 0.8
S2 A:SF4402 2.2 91.6 0.8
S1 A:SF4402 2.2 90.2 0.8
S4 A:SF4402 2.3 80.9 0.8
SG A:CYS287 2.4 87.2 1.0
FE4 A:SF4402 2.8 0.9 0.8
FE2 A:SF4402 2.8 87.8 0.8
FE1 A:SF4402 2.8 86.4 0.8
CB A:CYS287 3.1 76.0 1.0
S3 A:SF4402 3.9 89.7 0.8
CA A:CYS287 4.0 71.4 1.0
C8 A:SAM401 4.0 73.8 0.8
NE2 A:GLN241 4.4 47.6 1.0
N7 A:SAM401 4.4 74.8 0.8
CD A:PRO288 4.6 80.0 1.0
C A:CYS287 4.7 76.0 1.0
CG A:SAM401 4.7 83.8 0.8
CB A:ARG289 4.7 58.0 1.0
CB A:CYS163 4.8 70.3 1.0
SG A:CYS59 4.8 53.4 1.0
SG A:CYS163 4.8 81.3 1.0
N A:PRO288 4.9 79.9 1.0

Iron binding site 4 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 4 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:0.9
occ:0.80
 FE4 A:SF4402 0.0 0.9 0.8
S1 A:SF4402 2.2 90.2 0.8
S3 A:SF4402 2.3 89.7 0.8
N A:SAM401 2.3 82.8 0.8
S2 A:SF4402 2.3 91.6 0.8
FE1 A:SF4402 2.7 86.4 0.8
FE2 A:SF4402 2.8 87.8 0.8
FE3 A:SF4402 2.8 94.9 0.8
CG A:SAM401 3.0 83.8 0.8
O A:SAM401 3.1 70.3 0.8
CA A:SAM401 3.1 79.8 0.8
C A:SAM401 3.4 71.8 0.8
CB A:SAM401 3.5 82.7 0.8
S4 A:SF4402 3.8 80.9 0.8
O A:TYR56 4.3 50.6 0.5
SD A:SAM401 4.3 90.9 0.8
OXT A:SAM401 4.3 69.8 0.8
N A:GLY162 4.6 47.1 1.0
SG A:CYS59 4.8 53.4 1.0
SG A:CYS163 4.9 81.3 1.0
CA A:GLY162 5.0 42.5 1.0

Iron binding site 5 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 5 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:94.5
occ:0.80
 FE1 B:SF4402 0.0 94.5 0.8
S4 B:SF4402 2.2 75.4 0.8
S2 B:SF4402 2.3 75.7 0.8
S3 B:SF4402 2.3 98.5 0.8
SG B:CYS59 2.3 60.3 1.0
FE4 B:SF4402 2.7 0.8 0.8
FE3 B:SF4402 2.8 90.2 0.8
FE2 B:SF4402 2.8 98.7 0.8
CB B:CYS59 3.4 52.6 1.0
NE2 B:GLN241 3.7 73.5 1.0
S1 B:SF4402 3.9 0.3 0.8
N B:SAM401 4.5 78.4 0.8
CA B:GLY57 4.6 49.2 1.0
NH2 B:ARG153 4.6 69.7 1.0
O B:TYR56 4.6 61.8 1.0
CA B:CYS59 4.6 53.9 1.0
CD B:GLN241 4.7 73.9 1.0
CG B:GLN241 4.7 66.0 1.0
N B:CYS59 4.7 52.4 1.0
SG B:CYS163 4.7 81.0 1.0
SG B:CYS287 4.8 79.3 1.0

Iron binding site 6 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 6 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:98.7
occ:0.80
 FE2 B:SF4402 0.0 98.7 0.8
S3 B:SF4402 2.3 98.5 0.8
SG B:CYS163 2.3 81.0 1.0
S4 B:SF4402 2.3 75.4 0.8
S1 B:SF4402 2.3 0.3 0.8
FE4 B:SF4402 2.8 0.8 0.8
FE3 B:SF4402 2.8 90.2 0.8
FE1 B:SF4402 2.8 94.5 0.8
CB B:CYS163 3.1 77.0 1.0
N B:CYS163 3.7 57.9 1.0
S2 B:SF4402 3.9 75.7 0.8
CA B:CYS163 4.0 62.2 1.0
NH2 B:ARG153 4.1 69.7 1.0
CB B:LEU161 4.4 62.0 1.0
CD1 B:LEU161 4.4 52.9 1.0
O B:SAM401 4.4 68.8 0.8
N B:GLY162 4.5 59.1 1.0
N B:SAM401 4.6 78.4 0.8
C B:GLY162 4.6 62.5 1.0
CA B:GLY162 4.9 47.7 1.0
CG B:LEU161 4.9 66.3 1.0
SG B:CYS59 4.9 60.3 1.0
SG B:CYS287 5.0 79.3 1.0

Iron binding site 7 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 7 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:90.2
occ:0.80
 FE3 B:SF4402 0.0 90.2 0.8
S2 B:SF4402 2.2 75.7 0.8
S1 B:SF4402 2.2 0.3 0.8
S4 B:SF4402 2.3 75.4 0.8
SG B:CYS287 2.3 79.3 1.0
FE4 B:SF4402 2.8 0.8 0.8
FE2 B:SF4402 2.8 98.7 0.8
FE1 B:SF4402 2.8 94.5 0.8
CB B:CYS287 3.3 73.3 1.0
S3 B:SF4402 3.9 98.5 0.8
CA B:CYS287 4.0 67.2 1.0
C8 B:SAM401 4.3 70.5 0.8
NE2 B:GLN241 4.4 73.5 1.0
C5' B:SAM401 4.5 71.2 0.8
CD B:PRO288 4.5 85.7 1.0
CG B:ARG289 4.5 92.5 1.0
CB B:CYS163 4.6 77.0 1.0
N7 B:SAM401 4.6 65.0 0.8
C B:CYS287 4.7 66.2 1.0
SG B:CYS163 4.7 81.0 1.0
CD B:ARG289 4.8 96.4 1.0
CB B:ARG289 4.8 85.3 1.0
N B:PRO288 4.9 79.7 1.0
SG B:CYS59 5.0 60.3 1.0

Iron binding site 8 out of 8 in 6bxl

Go back to Iron Binding Sites List in 6bxl
Iron binding site 8 out of 8 in the Crystal Structure of Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam


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 Pyrococcus Horikoshii DPH2 with 4FE-4S Cluster and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:0.8
occ:0.80
 FE4 B:SF4402 0.0 0.8 0.8
S1 B:SF4402 2.2 0.3 0.8
S3 B:SF4402 2.3 98.5 0.8
N B:SAM401 2.3 78.4 0.8
S2 B:SF4402 2.3 75.7 0.8
FE1 B:SF4402 2.7 94.5 0.8
FE2 B:SF4402 2.8 98.7 0.8
FE3 B:SF4402 2.8 90.2 0.8
CA B:SAM401 3.4 78.0 0.8
O B:SAM401 3.4 68.8 0.8
C B:SAM401 3.5 71.7 0.8
S4 B:SF4402 3.8 75.4 0.8
O B:TYR56 3.8 61.8 1.0
CG B:SAM401 4.0 86.5 0.8
SD B:SAM401 4.0 77.7 0.8
CB B:SAM401 4.1 83.2 0.8
C5' B:SAM401 4.3 71.2 0.8
OXT B:SAM401 4.4 73.9 0.8
SG B:CYS59 4.7 60.3 1.0
SG B:CYS287 4.8 79.3 1.0
C B:TYR56 4.9 60.5 1.0
CA B:GLY57 4.9 49.2 1.0
N B:GLY162 4.9 59.1 1.0
SG B:CYS163 5.0 81.0 1.0

Reference:

M.Dong, V.Kathiresan, M.K.Fenwick, A.T.Torelli, Y.Zhang, J.D.Caranto, B.Dzikovski, A.Sharma, K.M.Lancaster, J.H.Freed, S.E.Ealick, B.M.Hoffman, H.Lin. Organometallic and Radical Intermediates Reveal Mechanism of Diphthamide Biosynthesis. Science V. 359 1247 2018.
ISSN: ESSN 1095-9203
PubMed: 29590073
DOI: 10.1126/SCIENCE.AAO6595
Page generated: Tue Aug 6 14:39:10 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy