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Iron in PDB 6huy: Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A

Enzymatic activity of Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A

All present enzymatic activity of Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A:
1.12.98.2;

Protein crystallography data

The structure of Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A, PDB code: 6huy 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) 24.98 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.769, 131.829, 168.263, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.2

Iron Binding Sites:

The binding sites of Iron atom in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A (pdb code 6huy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A, PDB code: 6huy:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6huy

Go back to Iron Binding Sites List in 6huy
Iron binding site 1 out of 2 in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:60.8
occ:1.00
 FE A:FE9401 0.0 60.8 1.0
C2F A:FE9401 1.8 62.6 1.0
C1F A:FE9401 1.8 64.9 1.0
C8 A:FE9401 1.9 59.7 1.0
N1 A:FE9401 1.9 60.3 1.0
O18 A:FE9401 2.7 57.5 1.0
SG A:CYS117 2.8 56.5 1.0
C6 A:FE9401 2.8 58.5 1.0
C7 A:FE9401 2.9 58.1 1.0
O1F A:FE9401 2.9 65.4 1.0
O2F A:FE9401 3.0 62.5 1.0
C2 A:FE9401 3.0 58.4 1.0
O2 A:FE9401 3.1 60.2 1.0
CB A:CYS117 3.7 51.2 1.0
O4 A:GUE403 4.1 51.3 1.0
C5 A:FE9401 4.2 56.6 1.0
C3 A:FE9401 4.3 56.1 1.0
N5 A:GUE403 4.7 56.0 1.0
C4 A:GUE403 4.7 51.0 1.0
O A:ALA149 4.8 50.9 1.0
C1 A:GUE403 4.8 57.0 1.0
C4 A:FE9401 4.8 56.7 1.0
CZ A:PHE88 4.8 56.8 1.0
CA A:CYS117 4.9 46.8 1.0
N A:CYS117 4.9 46.4 1.0
OH A:TYR14 4.9 57.1 1.0
C4A A:GUE403 5.0 54.1 1.0

Iron binding site 2 out of 2 in 6huy

Go back to Iron Binding Sites List in 6huy
Iron binding site 2 out of 2 in the Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hmdii From Desulfurobacterium Thermolithotrophum Reconstitued with Fe- Guanylylpyridinol (Fegp) Cofactor and Co-Crystallized with Methenyl- Tetrahydrofolate Form A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:55.8
occ:1.00
 FE C:FE9401 0.0 55.8 1.0
C1F C:FE9401 1.8 59.8 1.0
C2F C:FE9401 1.8 57.6 1.0
N1 C:FE9401 1.9 56.8 1.0
C8 C:FE9401 1.9 53.9 1.0
SG C:CYS117 2.7 51.0 1.0
O18 C:FE9401 2.8 51.5 1.0
C6 C:FE9401 2.9 56.1 1.0
O1F C:FE9401 2.9 60.0 1.0
C2 C:FE9401 2.9 56.8 1.0
O2F C:FE9401 3.0 57.1 1.0
C7 C:FE9401 3.0 53.9 1.0
O2 C:FE9401 3.1 58.7 1.0
CB C:CYS117 3.6 48.0 1.0
O4 C:GUE404 4.0 41.5 1.0
C5 C:FE9401 4.3 56.2 1.0
C3 C:FE9401 4.3 56.6 1.0
C4 C:GUE404 4.6 44.0 1.0
N5 C:GUE404 4.6 46.5 1.0
C1 C:GUE404 4.7 49.6 1.0
O C:ALA149 4.7 46.9 1.0
CA C:CYS117 4.8 44.0 1.0
C4 C:FE9401 4.9 56.9 1.0
C4A C:GUE404 4.9 44.7 1.0
N C:CYS117 4.9 42.7 1.0
CZ C:PHE88 5.0 54.3 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 16:29:14 2020

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