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Sodium in PDB 6hav: Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution

Enzymatic activity of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution

All present enzymatic activity of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution:
1.12.98.2;

Protein crystallography data

The structure of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution, PDB code: 6hav 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) 45.24 / 1.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.648, 66.246, 167.599, 90.00, 90.00, 90.00
R / Rfree (%) 11.8 / 13.4

Other elements in 6hav:

The structure of Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution (pdb code 6hav). 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 and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution, PDB code: 6hav:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6hav

Go back to Sodium Binding Sites List in 6hav
Sodium binding site 1 out of 2 in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution


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 and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:11.8
occ:1.00
O A:LEU51 2.2 11.5 1.0
O A:VAL54 2.3 11.6 1.0
O A:ILE57 2.3 13.1 1.0
C A:VAL54 3.3 11.4 1.0
C A:LEU51 3.3 10.6 1.0
C A:ILE57 3.5 12.6 1.0
O A:LEU50 3.8 11.5 1.0
CA A:ASP55 3.8 13.2 0.5
CA A:ASP55 3.9 11.7 0.5
N A:ASP55 4.0 12.1 1.0
CA A:LEU51 4.0 10.7 1.0
C A:ASP55 4.0 13.2 1.0
O A:ASP55 4.0 16.4 1.0
N A:ILE57 4.0 12.2 1.0
N A:VAL54 4.1 11.0 1.0
CA A:ILE57 4.2 12.5 1.0
N A:HIS52 4.2 10.4 1.0
CA A:VAL54 4.3 11.6 1.0
CB A:ILE57 4.4 11.8 1.0
N A:ASP58 4.5 12.8 1.0
CA A:HIS52 4.5 10.8 1.0
C A:HIS52 4.5 10.9 1.0
CD1 A:LEU51 4.5 15.1 1.0
C A:LEU50 4.7 10.6 1.0
N A:GLU56 4.8 13.4 1.0
CA A:ASP58 4.8 14.2 1.0
N A:LEU53 4.8 10.7 1.0
O A:HIS52 4.8 13.3 1.0
N A:LEU51 4.9 10.3 1.0
CB A:VAL54 4.9 11.6 1.0
C A:LEU53 4.9 11.5 1.0
CG2 A:ILE57 5.0 11.9 1.0

Sodium binding site 2 out of 2 in 6hav

Go back to Sodium Binding Sites List in 6hav
Sodium binding site 2 out of 2 in the Crystal Structure of [Fe]-Hydrogenase (Hmd) From Methanococcus Aeolicus in Complex with Fegp and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution


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 and Methenyl-Tetrahydromethanopterin (Close Form A) at 1.06 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:22.6
occ:1.00
O A:HOH989 2.7 41.5 0.5
O A:HOH842 3.1 36.9 1.0
C A:VAL127 3.4 11.9 1.0
CE1 A:HIS52 3.4 12.1 1.0
O A:VAL127 3.5 12.4 1.0
NE2 A:HIS52 3.5 11.7 1.0
N A:GLY128 3.6 12.4 1.0
CA A:VAL127 3.8 12.4 1.0
CA A:GLY128 3.8 12.8 1.0
CD1 A:ILE34 3.9 14.0 1.0
O A:HOH608 3.9 38.2 1.0
O A:LYS126 4.0 17.4 1.0
N A:VAL127 4.6 12.1 1.0
C A:LYS126 4.6 13.7 1.0
ND1 A:HIS52 4.6 11.3 1.0
CG2 A:ILE34 4.6 12.5 1.0
CG1 A:ILE34 4.8 13.3 1.0
CD2 A:HIS52 4.8 11.2 1.0
CB A:VAL127 4.9 12.6 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: Tue Dec 15 12:20:03 2020

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