Atomistry » Potassium » PDB 6hae-6i4g » 6hae
Atomistry »
  Potassium »
    PDB 6hae-6i4g »
      6hae »

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 Aug 12 16:21:52 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy