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Sodium 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
Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6hae

Go back to Sodium Binding Sites List in 6hae
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:27.0
occ:1.00
O A:HOH503 3.0 32.4 1.0
O A:HOH673 3.3 36.1 1.0
N A:GLU56 3.4 22.5 1.0
N A:ASP55 3.7 20.2 1.0
CB A:ASP55 3.8 27.2 1.0
CG A:GLU56 3.8 39.6 1.0
CB A:GLU56 3.9 26.5 1.0
CG1 A:VAL54 3.9 20.8 1.0
CA A:ASP55 4.1 23.2 1.0
C A:ASP55 4.2 26.1 1.0
CA A:GLU56 4.2 23.6 1.0
CD A:GLU56 4.4 60.4 1.0
C A:VAL54 4.4 24.1 1.0
OE1 A:GLU56 4.5 44.2 1.0
CG A:ASP55 4.6 51.0 1.0
OD2 A:ASP55 4.7 60.8 1.0
CA A:VAL54 4.8 16.0 1.0
O A:HOH761 4.8 29.8 1.0
CD1 A:ILE233 5.0 20.1 1.0

Sodium binding site 2 out of 2 in 6hae

Go back to Sodium Binding Sites List in 6hae
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:28.8
occ:1.00
O K:HOH681 3.0 27.2 1.0
N K:GLU56 3.2 23.8 1.0
N K:ASP55 3.5 24.9 1.0
CB K:GLU56 3.6 24.2 1.0
O K:HOH629 3.6 42.9 1.0
CB K:ASP55 3.7 29.2 1.0
CG1 K:VAL54 3.7 16.9 1.0
CA K:ASP55 4.0 25.8 1.0
CA K:GLU56 4.1 24.2 1.0
C K:ASP55 4.1 27.8 1.0
C K:VAL54 4.2 25.6 1.0
CG K:ASP55 4.4 56.8 1.0
OD2 K:ASP55 4.6 67.2 1.0
CA K:VAL54 4.6 16.7 1.0
OE2 K:GLU56 4.6 49.8 1.0
CB K:VAL54 4.8 18.3 1.0
CG K:GLU56 4.9 44.0 1.0
CD1 K:ILE233 4.9 31.0 1.0
O K:VAL54 5.0 22.3 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: Tue Oct 8 09:16:13 2024

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