Iron in PDB 8qmk: Enzymatically-Produced Complex-B Bound Tmhyde Structure

Protein crystallography data

The structure of Enzymatically-Produced Complex-B Bound Tmhyde Structure, PDB code: 8qmk was solved by J.Omeiri, L.Martin, A.Usclat, M.V.Cherrier, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.96 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 63.83, 83.56, 70.84, 90, 90, 90
R / Rfree (%) 14.3 / 16.8

Other elements in 8qmk:

The structure of Enzymatically-Produced Complex-B Bound Tmhyde Structure also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Enzymatically-Produced Complex-B Bound Tmhyde Structure (pdb code 8qmk). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Enzymatically-Produced Complex-B Bound Tmhyde Structure, PDB code: 8qmk:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 8qmk

Go back to Iron Binding Sites List in 8qmk
Iron binding site 1 out of 5 in the Enzymatically-Produced Complex-B Bound Tmhyde Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Enzymatically-Produced Complex-B Bound Tmhyde Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.5
occ:0.84
 C A:CMO503 1.8 13.4 0.9
C A:CMO502 1.8 13.9 0.9
C A:CYN504 1.8 15.8 1.0
N A:CYS511 2.0 15.5 1.0
O A:CYS511 2.1 19.0 1.0
SG A:CYS511 2.4 15.1 1.0
H A:CYS511 2.7 18.6 1.0
CA A:CYS511 2.8 16.9 1.0
C A:CYS511 2.9 20.7 1.0
O A:CMO503 2.9 14.9 0.9
O A:CMO502 3.0 15.3 0.9
N A:CYN504 3.0 16.1 1.0
CB A:CYS511 3.2 16.9 1.0
HA A:CYS511 3.7 20.2 1.0
HB3 A:CYS511 3.7 20.3 1.0
HB2 A:CYS511 3.9 20.3 1.0
HD12 A:ILE291 3.9 17.2 1.0
HD21 A:LEU157 4.1 22.6 1.0
OXT A:CYS511 4.1 23.0 1.0
HE22 A:GLN107 4.1 13.2 1.0
OG1 A:THR269 4.3 10.3 0.6
NH2 A:ARG159 4.5 15.9 1.0
O A:HOH715 4.5 21.0 0.5
O A:HOH682 4.6 13.8 1.0
CG2 A:THR268 4.6 11.7 1.0
HD23 A:LEU157 4.7 22.6 1.0
CD2 A:LEU157 4.7 18.8 1.0
HG21 A:ILE291 4.7 14.0 1.0
CD1 A:ILE291 4.7 14.3 1.0
CB A:THR268 4.7 11.3 1.0
HD13 A:ILE291 4.7 17.2 1.0
HD22 A:LEU157 4.8 22.6 1.0
HB A:ILE291 4.9 13.3 1.0
NE2 A:GLN107 4.9 11.0 1.0
N A:THR269 5.0 13.3 0.6

Iron binding site 2 out of 5 in 8qmk

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Iron binding site 2 out of 5 in the Enzymatically-Produced Complex-B Bound Tmhyde Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Enzymatically-Produced Complex-B Bound Tmhyde Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:11.4
occ:1.00
 FE1 A:SF4506 0.0 11.4 1.0
S3 A:SF4506 2.2 11.8 1.0
S2 A:SF4506 2.3 11.7 1.0
SG A:CYS70 2.3 11.2 1.0
S4 A:SF4506 2.3 12.1 1.0
FE2 A:SF4506 2.7 11.7 1.0
FE3 A:SF4506 2.7 11.4 1.0
FE4 A:SF4506 2.9 12.6 1.0
CB A:CYS70 3.1 10.4 1.0
S1 A:SF4506 3.9 12.5 1.0
HB2 A:CYS67 4.0 14.4 1.0
CB A:LEU72 4.3 10.7 1.0
HD22 A:LEU305 4.3 18.0 1.0
SD A:SAH507 4.3 14.8 1.0
CA A:CYS70 4.5 10.8 1.0
HD23 A:LEU305 4.7 18.0 1.0
SG A:CYS67 4.8 12.1 1.0
CB A:CYS67 4.8 12.0 1.0
OXT A:SAH507 4.8 12.7 1.0
SG A:CYS63 4.8 11.4 1.0
N A:ARG73 4.8 10.9 1.0
N A:LEU72 4.8 10.2 1.0
N A:SAH507 4.8 12.1 1.0
CG A:LEU72 4.9 15.5 1.0
C A:LEU72 4.9 11.8 1.0
CD2 A:LEU305 4.9 15.0 1.0
CA A:LEU72 4.9 10.9 1.0
HB2 A:CYS63 5.0 13.2 1.0

Iron binding site 3 out of 5 in 8qmk

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Iron binding site 3 out of 5 in the Enzymatically-Produced Complex-B Bound Tmhyde Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Enzymatically-Produced Complex-B Bound Tmhyde Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:11.7
occ:1.00
 FE2 A:SF4506 0.0 11.7 1.0
SG A:CYS63 2.2 11.4 1.0
S4 A:SF4506 2.3 12.1 1.0
S3 A:SF4506 2.3 11.8 1.0
S1 A:SF4506 2.3 12.5 1.0
FE1 A:SF4506 2.7 11.4 1.0
FE3 A:SF4506 2.7 11.4 1.0
FE4 A:SF4506 2.9 12.6 1.0
CB A:CYS63 3.3 11.0 1.0
HB2 A:CYS63 3.3 13.2 1.0
HB3 A:CYS63 3.4 13.2 1.0
S2 A:SF4506 3.9 11.7 1.0
N A:SAH507 4.1 12.1 1.0
CB A:LYS65 4.2 12.7 1.0
N A:GLU110 4.5 11.1 1.0
CA A:GLY109 4.6 11.5 1.0
CA A:CYS63 4.7 11.4 1.0
HA A:CYS63 4.8 13.6 1.0
SG A:CYS67 4.8 12.1 1.0
N A:LYS65 4.8 11.9 1.0
SG A:CYS70 4.8 11.2 1.0
H A:CYS67 4.8 14.1 1.0
OXT A:SAH507 4.8 12.7 1.0
O A:LYS65 4.9 12.8 1.0
CA A:LYS65 4.9 12.2 1.0
C A:LYS65 4.9 13.0 1.0
CB A:LEU72 4.9 10.7 1.0

Iron binding site 4 out of 5 in 8qmk

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Iron binding site 4 out of 5 in the Enzymatically-Produced Complex-B Bound Tmhyde Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Enzymatically-Produced Complex-B Bound Tmhyde Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:11.4
occ:1.00
 FE3 A:SF4506 0.0 11.4 1.0
S1 A:SF4506 2.3 12.5 1.0
S2 A:SF4506 2.3 11.7 1.0
S4 A:SF4506 2.3 12.1 1.0
SG A:CYS67 2.3 12.1 1.0
FE1 A:SF4506 2.7 11.4 1.0
FE2 A:SF4506 2.7 11.7 1.0
HB2 A:CYS67 2.9 14.4 1.0
FE4 A:SF4506 2.9 12.6 1.0
CB A:CYS67 3.2 12.0 1.0
H A:CYS67 3.5 14.1 1.0
HH21 A:ARG172 3.6 16.3 1.0
HB3 A:CYS67 3.8 14.4 1.0
S3 A:SF4506 3.9 11.8 1.0
O A:HOH688 3.9 18.1 1.0
OXT A:SAH507 4.2 12.7 1.0
HE A:ARG172 4.3 14.7 1.0
N A:CYS67 4.3 11.7 1.0
CA A:CYS67 4.4 9.9 1.0
CB A:LYS65 4.4 12.7 1.0
CB A:CYS70 4.5 10.4 1.0
NH2 A:ARG172 4.5 13.6 1.0
OH A:TYR69 4.7 13.2 1.0
SG A:CYS70 4.7 11.2 1.0
SG A:CYS63 4.7 11.4 1.0
CE1 A:TYR69 4.8 9.8 1.0
HA A:CYS67 4.9 11.9 1.0
HH22 A:ARG172 5.0 16.3 1.0
N A:SAH507 5.0 12.1 1.0
O A:HOH712 5.0 14.8 1.0
CZ A:TYR69 5.0 10.5 1.0

Iron binding site 5 out of 5 in 8qmk

Go back to Iron Binding Sites List in 8qmk
Iron binding site 5 out of 5 in the Enzymatically-Produced Complex-B Bound Tmhyde Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Enzymatically-Produced Complex-B Bound Tmhyde Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe506

b:12.6
occ:1.00
 FE4 A:SF4506 0.0 12.6 1.0
OXT A:SAH507 2.2 12.7 1.0
N A:SAH507 2.3 12.1 1.0
S2 A:SF4506 2.3 11.7 1.0
S3 A:SF4506 2.4 11.8 1.0
S1 A:SF4506 2.4 12.5 1.0
FE1 A:SF4506 2.9 11.4 1.0
FE2 A:SF4506 2.9 11.7 1.0
FE3 A:SF4506 2.9 11.4 1.0
C A:SAH507 3.0 12.4 1.0
CA A:SAH507 3.1 11.4 1.0
SD A:SAH507 3.1 14.8 1.0
CG A:SAH507 3.6 13.8 1.0
CB A:SAH507 3.9 14.1 1.0
O A:HOH688 4.1 18.1 1.0
O A:HOH712 4.1 14.8 1.0
S4 A:SF4506 4.1 12.1 1.0
O A:SAH507 4.2 12.6 1.0
SG A:CYS63 4.7 11.4 1.0
C5' A:SAH507 4.8 15.7 1.0
HH21 A:ARG172 4.8 16.3 1.0
SG A:CYS70 4.9 11.2 1.0

Reference:

J.Omeiri, L.Martin, A.Usclat, M.V.Cherrier, Y.Nicolet. Maturation of the [Fefe]-Hydrogenase: Direct Transfer of the ( Kappa 3-Cysteinate)Feii(Cn)(Co)2 Complex-B From Hydg to Hyde. Angew.Chem.Int.Ed.Engl. 14819 2023.
ISSN: ESSN 1521-3773
PubMed: 37962296
DOI: 10.1002/ANIE.202314819
Page generated: Sat Aug 10 15:30:36 2024

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