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Potassium 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:

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

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6hae

Go back to Potassium Binding Sites List in 6hae
Potassium binding site 1 out of 4 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 Potassium with other atoms in the K 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:K413

b:44.4
occ:1.00
O A:LEU51 2.2 20.1 1.0
O A:ILE57 2.2 23.1 1.0
O A:VAL54 2.5 22.4 1.0
O A:HOH653 2.6 50.7 1.0
O A:HOH698 2.7 30.9 1.0
C A:LEU51 3.2 21.3 1.0
C A:ILE57 3.4 26.9 1.0
C A:VAL54 3.5 24.1 1.0
O A:LEU50 3.7 21.9 1.0
CA A:LEU51 3.8 21.9 1.0
O A:ASP55 3.8 25.4 1.0
N A:ILE57 4.0 22.2 1.0
C A:ASP55 4.1 26.1 1.0
CA A:ILE57 4.1 20.2 1.0
CA A:ASP55 4.2 23.2 1.0
N A:ASP55 4.2 20.2 1.0
N A:VAL54 4.3 20.8 1.0
CB A:ILE57 4.3 23.3 1.0
N A:HIS52 4.3 19.7 1.0
N A:ASP58 4.4 23.8 1.0
CA A:VAL54 4.4 16.0 1.0
CD1 A:LEU51 4.4 21.6 1.0
CA A:ASP58 4.6 25.9 1.0
O A:HOH764 4.6 63.7 1.0
CA A:HIS52 4.6 20.1 1.0
C A:LEU50 4.6 21.1 1.0
C A:HIS52 4.7 27.1 1.0
O A:HOH738 4.7 58.4 1.0
O A:HOH781 4.7 51.9 1.0
N A:LEU51 4.8 21.7 1.0
CG A:LEU51 4.8 25.2 1.0
CG2 A:ILE57 4.9 23.2 1.0
N A:GLU56 4.9 22.5 1.0
CB A:LEU51 4.9 21.8 1.0
N A:LEU53 4.9 23.8 1.0
CB A:VAL54 5.0 18.7 1.0
C A:GLU56 5.0 28.6 1.0

Potassium binding site 2 out of 4 in 6hae

Go back to Potassium Binding Sites List in 6hae
Potassium binding site 2 out of 4 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 Potassium with other atoms in the K 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
A:K414

b:54.0
occ:1.00
O A:HOH774 2.3 56.0 1.0
OE2 A:GLU125 2.8 58.0 1.0
N A:VAL131 3.0 23.7 1.0
CA A:LYS130 3.5 24.9 1.0
O A:VAL131 3.7 32.3 1.0
C A:LYS130 3.7 28.6 1.0
O A:HOH647 3.7 55.8 1.0
CD A:GLU125 3.8 63.8 1.0
CG2 A:VAL131 3.8 29.7 1.0
CG A:GLU125 4.0 33.0 1.0
CB A:LYS130 4.0 26.9 1.0
CA A:VAL131 4.0 23.8 1.0
C A:VAL131 4.3 30.1 1.0
CG A:LYS130 4.3 35.3 1.0
CB A:VAL131 4.5 27.4 1.0
O A:LEU129 4.6 30.8 1.0
S A:SCN409 4.7 77.5 1.0
N A:LYS130 4.8 22.7 1.0
O A:LYS130 4.9 24.2 1.0
C A:SCN409 4.9 78.1 1.0
OE1 A:GLU125 5.0 74.2 1.0
CG1 A:VAL131 5.0 25.7 1.0

Potassium binding site 3 out of 4 in 6hae

Go back to Potassium Binding Sites List in 6hae
Potassium binding site 3 out of 4 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 Potassium with other atoms in the K binding site number 3 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:K412

b:41.8
occ:1.00
O K:LEU51 2.3 21.8 1.0
O K:ILE57 2.3 25.0 1.0
O K:VAL54 2.4 22.3 1.0
O K:HOH702 2.4 33.0 1.0
O K:HOH664 2.5 45.0 1.0
C K:VAL54 3.3 25.6 1.0
C K:LEU51 3.4 22.5 1.0
C K:ILE57 3.4 26.1 1.0
O K:ASP55 3.7 29.7 1.0
O K:LEU50 3.8 24.7 1.0
C K:ASP55 3.9 27.8 1.0
N K:ILE57 3.9 22.9 1.0
CA K:ASP55 4.0 25.8 1.0
CA K:LEU51 4.0 18.5 1.0
N K:ASP55 4.0 24.9 1.0
CA K:ILE57 4.1 22.4 1.0
N K:VAL54 4.2 19.7 1.0
CB K:ILE57 4.3 21.7 1.0
CA K:VAL54 4.3 16.7 1.0
N K:HIS52 4.4 21.6 1.0
N K:ASP58 4.5 24.2 1.0
CD1 K:LEU51 4.6 21.5 1.0
CA K:HIS52 4.6 22.1 1.0
CA K:ASP58 4.7 27.6 1.0
C K:HIS52 4.7 26.5 1.0
N K:GLU56 4.7 23.8 1.0
C K:LEU50 4.8 25.1 1.0
C K:GLU56 4.9 30.6 1.0
N K:LEU53 4.9 22.1 1.0
CB K:VAL54 4.9 18.3 1.0
N K:LEU51 4.9 19.4 1.0
CG2 K:ILE57 5.0 21.9 1.0

Potassium binding site 4 out of 4 in 6hae

Go back to Potassium Binding Sites List in 6hae
Potassium binding site 4 out of 4 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 Potassium with other atoms in the K binding site number 4 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:K413

b:58.6
occ:1.00
O K:HOH512 2.2 37.7 1.0
O K:ASP164 2.3 28.5 1.0
NH1 K:ARG192 2.9 22.3 1.0
C K:ASP164 3.3 26.1 1.0
CZ K:ARG192 3.6 34.7 1.0
CA K:ASP164 3.8 23.4 1.0
O K:ILE166 4.0 23.8 1.0
NH2 K:ARG192 4.2 24.1 1.0
NE K:ARG192 4.3 27.7 1.0
N K:ALA165 4.5 27.3 1.0
CD K:ARG192 4.5 20.6 1.0
CB K:ASP164 4.5 27.7 1.0
O K:VAL163 4.7 25.5 1.0
N K:ILE166 4.9 23.8 1.0
CA K:ALA165 4.9 26.7 1.0
C K:ALA165 5.0 29.0 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: Mon Dec 14 00:40:00 2020

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