Iron in PDB 6hae: Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B)

Enzymatic activity of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B)

All present enzymatic activity of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B):
1.12.98.2;

Protein crystallography data

The structure of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B), PDB code: 6hae was solved by G.Huang, T.Wagner, M.D.Wodrich, K.Ataka, E.Bill, U.Ermler, X.Hu, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.56 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.015, 156.480, 53.654, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.2

Other elements in 6hae:

The structure of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B) also contains other interesting chemical elements:

Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B) (pdb code 6hae). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B), PDB code: 6hae:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6hae

Go back to Iron Binding Sites List in 6hae
Iron binding site 1 out of 2 in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B)


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 [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe415

b:30.5
occ:1.00
FE A:FE9415 0.0 30.5 1.0
C1F A:FE9415 1.8 31.7 1.0
C2F A:FE9415 1.8 34.4 1.0
C8 A:FE9415 1.9 27.8 1.0
N1 A:FE9415 2.0 26.7 1.0
SG A:CYS176 2.4 23.6 1.0
O18 A:FE9415 2.7 25.9 1.0
C6 A:FE9415 2.8 23.9 1.0
C7 A:FE9415 2.9 22.0 1.0
C2 A:FE9415 3.0 28.9 1.0
O1F A:FE9415 3.0 38.0 1.0
O2F A:FE9415 3.0 31.7 1.0
O2 A:FE9415 3.2 28.4 1.0
CB A:CYS176 3.5 21.1 1.0
C10 A:E4M402 3.9 24.2 1.0
OH4 A:E4M402 4.0 21.3 1.0
CZ2 A:TRP148 4.2 22.9 1.0
C5 A:FE9415 4.2 21.8 1.0
CH2 A:TRP148 4.2 23.6 1.0
C3 A:FE9415 4.3 24.1 1.0
N5 A:E4M402 4.5 22.1 1.0
N10 A:E4M402 4.5 27.4 1.0
C15 A:E4M402 4.5 20.2 1.0
O A:CYS204 4.6 19.4 1.0
C4 A:E4M402 4.7 19.1 1.0
CA A:CYS176 4.7 20.2 1.0
N A:CYS176 4.8 18.4 1.0
C4 A:FE9415 4.8 24.6 1.0
C4A A:E4M402 4.9 19.6 1.0
C14 A:E4M402 4.9 18.2 1.0

Iron binding site 2 out of 2 in 6hae

Go back to Iron Binding Sites List in 6hae
Iron binding site 2 out of 2 in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B)


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 [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp Cofactor and Methenyl- Tetrahydromethanopterin (Close Form B) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe415

b:30.3
occ:1.00
FE K:FE9415 0.0 30.3 1.0
C1F K:FE9415 1.8 26.4 1.0
C2F K:FE9415 1.8 30.1 1.0
C8 K:FE9415 1.9 22.8 1.0
N1 K:FE9415 2.0 24.4 1.0
SG K:CYS176 2.4 21.8 1.0
O18 K:FE9415 2.7 26.3 1.0
C6 K:FE9415 2.9 27.0 1.0
O1F K:FE9415 2.9 33.5 1.0
O2F K:FE9415 2.9 26.6 1.0
C7 K:FE9415 3.0 19.3 1.0
C2 K:FE9415 3.0 23.2 1.0
O2 K:FE9415 3.1 30.0 1.0
CB K:CYS176 3.6 18.3 1.0
C10 K:E4M402 3.9 25.3 1.0
OH4 K:E4M402 4.0 21.9 1.0
CH2 K:TRP148 4.2 20.4 1.0
CZ2 K:TRP148 4.2 21.1 1.0
C5 K:FE9415 4.3 25.3 1.0
C3 K:FE9415 4.3 25.1 1.0
N5 K:E4M402 4.5 21.6 1.0
N10 K:E4M402 4.5 22.0 1.0
O K:CYS204 4.5 22.6 1.0
C15 K:E4M402 4.5 18.1 1.0
C4 K:E4M402 4.6 20.1 1.0
CA K:CYS176 4.7 18.3 1.0
N K:CYS176 4.8 17.5 1.0
C4A K:E4M402 4.8 18.0 1.0
C4 K:FE9415 4.9 22.1 1.0
C14 K:E4M402 4.9 17.6 1.0

Reference:

G.Huang, T.Wagner, M.D.Wodrich, K.Ataka, E.Bill, U.Ermler, X.Hu, S.Shima. The Atomic-Resolution Crystal Structure of Activated [Fe]-Hydrogenase Nat Catal 2019.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-019-0289-4
Page generated: Sun Dec 13 16:28:25 2020

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