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Iron in PDB 6hux: Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution

Enzymatic activity of Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution

All present enzymatic activity of Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution:
1.12.98.2;

Protein crystallography data

The structure of Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution, PDB code: 6hux was solved by T.Watanabe, T.Wagner, G.Huang, J.Kahnt, K.Ataka, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.97 / 2.50
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 124.281, 124.281, 150.086, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 21.9

Other elements in 6hux:

The structure of Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution (pdb code 6hux). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution, PDB code: 6hux:

Iron binding site 1 out of 1 in 6hux

Go back to Iron Binding Sites List in 6hux
Iron binding site 1 out of 1 in the Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hmdii From Methanocaldococcus Jannaschii Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydromethanopterin at 2.5 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe410

b:98.2
occ:1.00
FE A:FE9410 0.0 98.2 1.0
C2F A:FE9410 1.8 93.9 1.0
C1F A:FE9410 1.8 94.2 1.0
C8 A:FE9410 1.9 85.1 1.0
N1 A:FE9410 2.0 93.4 1.0
SG A:CYS127 2.7 55.2 1.0
O18 A:FE9410 2.7 73.7 1.0
C6 A:FE9410 2.8 91.8 1.0
C7 A:FE9410 2.9 90.0 1.0
O2F A:FE9410 3.0 91.6 1.0
O1F A:FE9410 3.0 88.2 1.0
C2 A:FE9410 3.0 84.8 1.0
O2 A:FE9410 3.3 81.4 1.0
CB A:CYS127 3.6 49.4 1.0
OH4 A:E4M412 3.8 52.6 1.0
C10 A:E4M412 4.0 58.5 1.0
C5 A:FE9410 4.3 90.2 1.0
N5 A:E4M412 4.3 59.3 1.0
C3 A:FE9410 4.4 86.6 1.0
N10 A:E4M412 4.5 55.3 1.0
C9M A:E4M412 4.6 47.0 1.0
C4 A:E4M412 4.6 50.1 1.0
CZ A:PHE99 4.7 46.5 1.0
CA A:CYS127 4.8 46.6 1.0
C4A A:E4M412 4.8 50.6 1.0
N A:CYS127 4.8 45.4 1.0
O A:ALA158 4.9 49.9 1.0
C4 A:FE9410 4.9 90.1 1.0
OH A:TYR25 4.9 56.2 1.0
C6 A:E4M412 5.0 56.1 1.0
C9 A:E4M412 5.0 54.1 1.0

Reference:

T.Watanabe, T.Wagner, G.Huang, J.Kahnt, K.Ataka, U.Ermler, S.Shima. The Bacterial [Fe]-Hydrogenase Paralog Hmdii Uses Tetrahydrofolate Derivatives As Substrates. Angew. Chem. Int. Ed. Engl. V. 58 3506 2019.
ISSN: ESSN 1521-3773
PubMed: 30600878
DOI: 10.1002/ANIE.201813465
Page generated: Sun Dec 13 16:29:11 2020

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