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Potassium in PDB 6h6v: Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn

Protein crystallography data

The structure of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn, PDB code: 6h6v was solved by K.A.P.Payne, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.20 / 2.66
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.910, 139.250, 136.880, 90.00, 93.74, 90.00
R / Rfree (%) 19.9 / 23.6

Other elements in 6h6v:

The structure of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn also contains other interesting chemical elements:

Manganese (Mn) 6 atoms
Calcium (Ca) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn (pdb code 6h6v). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn, PDB code: 6h6v:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 6h6v

Go back to Potassium Binding Sites List in 6h6v
Potassium binding site 1 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:56.2
occ:1.00
 O5' A:FMN501 2.5 34.5 1.0
OE2 A:GLU210 2.6 43.4 1.0
O3P A:FMN501 2.7 39.8 1.0
O A:SER200 2.7 44.0 1.0
O A:HOH619 2.9 30.1 1.0
O A:VAL148 3.0 37.8 1.0
P A:FMN501 3.1 41.9 1.0
O A:ALA202 3.1 49.4 1.0
O4' A:FMN501 3.2 42.3 1.0
CD A:GLU210 3.4 47.8 1.0
MN A:MN503 3.6 46.0 1.0
O2P A:FMN501 3.7 41.3 1.0
C4' A:FMN501 3.7 36.0 1.0
C5' A:FMN501 3.7 34.7 1.0
C A:SER200 3.8 45.3 1.0
CG A:GLU210 3.9 46.0 1.0
C A:VAL148 4.2 36.6 1.0
C A:ALA202 4.3 53.7 1.0
OE1 A:GLU210 4.3 50.8 1.0
O1P A:FMN501 4.5 36.3 1.0
N A:ALA202 4.5 50.6 1.0
C A:GLN201 4.5 42.4 1.0
CB A:SER149 4.6 38.9 1.0
OD1 A:ASN147 4.6 48.8 1.0
N A:GLN201 4.6 42.6 1.0
CA A:SER149 4.6 37.4 1.0
CA A:SER200 4.6 40.9 1.0
CA A:GLN201 4.6 41.5 1.0
ND2 A:ASN147 4.7 51.4 1.0
N A:SER149 4.9 36.5 1.0
O A:ALA199 4.9 35.8 1.0

Potassium binding site 2 out of 6 in 6h6v

Go back to Potassium Binding Sites List in 6h6v
Potassium binding site 2 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:44.1
occ:1.00
 O B:SER200 2.4 33.6 1.0
O5' B:FMN501 2.6 38.8 1.0
OE2 B:GLU210 2.6 27.4 1.0
O3P B:FMN501 2.7 40.2 1.0
O B:VAL148 2.8 37.5 1.0
O4' B:FMN501 3.1 43.6 1.0
O B:ALA202 3.1 47.6 1.0
O B:HOH624 3.3 42.2 1.0
P B:FMN501 3.3 40.6 1.0
CD B:GLU210 3.4 36.0 1.0
C B:SER200 3.5 34.5 1.0
C4' B:FMN501 3.6 40.7 1.0
MN B:MN503 3.6 35.6 1.0
C5' B:FMN501 3.7 40.7 1.0
CG B:GLU210 3.8 39.4 1.0
O2P B:FMN501 3.9 41.8 1.0
O B:HOH607 4.0 46.8 1.0
C B:VAL148 4.0 39.2 1.0
C B:ALA202 4.3 44.9 1.0
OE1 B:GLU210 4.3 38.7 1.0
CA B:SER200 4.3 36.1 1.0
N B:GLN201 4.4 36.4 1.0
N B:ALA202 4.4 36.5 1.0
C B:GLN201 4.4 33.7 1.0
CA B:GLN201 4.5 37.4 1.0
CA B:SER149 4.5 37.1 1.0
O1P B:FMN501 4.6 42.4 1.0
CB B:SER149 4.6 38.5 1.0
O B:ALA199 4.6 40.0 1.0
N B:SER149 4.8 38.7 1.0
ND2 B:ASN147 4.8 33.5 1.0
OD1 B:ASN147 4.8 28.4 1.0
CB B:GLU210 4.9 40.7 1.0
CA B:ALA202 4.9 39.5 1.0
O B:GLN201 5.0 30.3 1.0

Potassium binding site 3 out of 6 in 6h6v

Go back to Potassium Binding Sites List in 6h6v
Potassium binding site 3 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:53.6
occ:1.00
 OE2 C:GLU210 2.6 41.5 1.0
O C:SER200 2.7 39.9 1.0
O5' C:FMN501 2.7 44.7 1.0
O3P C:FMN501 2.8 43.6 1.0
O C:ALA202 3.0 50.7 1.0
O4' C:FMN501 3.0 38.3 1.0
O C:HOH621 3.0 24.4 1.0
O C:VAL148 3.1 46.8 1.0
P C:FMN501 3.1 45.1 1.0
O2P C:FMN501 3.3 39.9 1.0
MN C:MN503 3.5 42.1 1.0
CD C:GLU210 3.5 48.6 1.0
C4' C:FMN501 3.6 42.2 1.0
C5' C:FMN501 3.7 44.9 1.0
C C:SER200 3.7 42.5 1.0
CG C:GLU210 3.9 50.8 1.0
C C:ALA202 4.2 48.5 1.0
C C:VAL148 4.3 42.6 1.0
N C:ALA202 4.4 43.2 1.0
C C:GLN201 4.4 40.9 1.0
OE1 C:GLU210 4.4 45.9 1.0
N C:GLN201 4.5 43.5 1.0
O1P C:FMN501 4.5 45.4 1.0
CA C:GLN201 4.5 42.2 1.0
CA C:SER200 4.6 40.0 1.0
CB C:SER149 4.7 41.6 1.0
CA C:SER149 4.7 41.2 1.0
OD1 C:ASN147 4.7 30.3 1.0
O C:ALA199 4.8 42.4 1.0
ND2 C:ASN147 4.9 41.1 1.0
O C:GLN201 4.9 43.6 1.0
CA C:ALA202 4.9 45.2 1.0
N C:SER149 5.0 42.1 1.0
C3' C:FMN501 5.0 39.5 1.0

Potassium binding site 4 out of 6 in 6h6v

Go back to Potassium Binding Sites List in 6h6v
Potassium binding site 4 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:58.1
occ:1.00
 OE2 D:GLU210 2.6 48.1 1.0
O3P D:FMN501 2.6 41.1 1.0
O5' D:FMN501 2.6 34.8 1.0
O D:SER200 2.7 44.0 1.0
O D:VAL148 2.9 33.6 1.0
O D:ALA202 3.1 55.5 1.0
P D:FMN501 3.2 42.7 1.0
O D:HOH629 3.2 33.4 1.0
O4' D:FMN501 3.3 32.5 1.0
CD D:GLU210 3.4 50.4 1.0
MN D:MN503 3.5 40.5 1.0
O2P D:FMN501 3.7 38.7 1.0
C4' D:FMN501 3.8 35.0 1.0
C D:SER200 3.8 42.3 1.0
C5' D:FMN501 3.8 33.2 1.0
CG D:GLU210 3.9 50.1 1.0
C D:VAL148 4.1 37.1 1.0
OE1 D:GLU210 4.3 53.2 1.0
C D:ALA202 4.4 62.0 1.0
O1P D:FMN501 4.4 39.4 1.0
N D:ALA202 4.6 54.5 1.0
C D:GLN201 4.6 44.4 1.0
OD1 D:ASN147 4.6 41.1 1.0
CB D:SER149 4.6 37.8 1.0
CA D:SER149 4.6 37.0 1.0
N D:GLN201 4.6 45.7 1.0
CA D:SER200 4.6 39.8 1.0
ND2 D:ASN147 4.7 46.9 1.0
CA D:GLN201 4.7 43.5 1.0
N D:SER149 4.8 36.8 1.0
O D:ALA199 4.9 40.3 1.0
CG D:ASN147 5.0 43.2 1.0

Potassium binding site 5 out of 6 in 6h6v

Go back to Potassium Binding Sites List in 6h6v
Potassium binding site 5 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K502

b:46.7
occ:1.00
 O E:SER200 2.5 48.9 1.0
O5' E:FMN501 2.6 42.5 1.0
OE2 E:GLU210 2.8 57.6 1.0
O3P E:FMN501 2.9 45.3 1.0
O E:VAL148 2.9 44.2 1.0
O4' E:FMN501 3.1 50.4 1.0
O E:ALA202 3.1 59.2 1.0
P E:FMN501 3.3 46.5 1.0
O E:HOH627 3.4 45.4 1.0
C4' E:FMN501 3.5 41.3 1.0
C E:SER200 3.5 47.0 1.0
CD E:GLU210 3.5 58.4 1.0
C5' E:FMN501 3.6 43.5 1.0
MN E:MN503 3.7 47.2 1.0
O2P E:FMN501 3.8 43.0 1.0
CG E:GLU210 3.9 56.4 1.0
C E:VAL148 4.1 46.2 1.0
C E:ALA202 4.2 64.3 1.0
N E:ALA202 4.3 48.1 1.0
C E:GLN201 4.3 41.5 1.0
N E:GLN201 4.4 45.4 1.0
CA E:SER200 4.4 46.0 1.0
CA E:GLN201 4.4 42.3 1.0
OE1 E:GLU210 4.4 54.8 1.0
CA E:SER149 4.5 39.9 1.0
CB E:SER149 4.5 40.1 1.0
O1P E:FMN501 4.6 42.9 1.0
O E:ALA199 4.6 45.4 1.0
N E:SER149 4.8 42.4 1.0
ND2 E:ASN147 4.8 43.5 1.0
OD1 E:ASN147 4.9 52.6 1.0
O E:GLN201 4.9 39.7 1.0
CA E:ALA202 4.9 56.2 1.0
C3' E:FMN501 4.9 39.9 1.0

Potassium binding site 6 out of 6 in 6h6v

Go back to Potassium Binding Sites List in 6h6v
Potassium binding site 6 out of 6 in the Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of the Ubid-Class Enzyme Hmff From Pelotomaculum Thermopropionicum in Complex with Fmn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K502

b:85.5
occ:1.00
 O3P F:FMN501 2.5 78.0 1.0
OE2 F:GLU210 2.6 75.4 1.0
O F:SER200 2.8 59.1 1.0
O F:ALA202 2.9 79.8 1.0
O5' F:FMN501 3.0 68.8 1.0
P F:FMN501 3.1 66.5 1.0
O2P F:FMN501 3.1 58.8 1.0
O F:VAL148 3.2 73.3 1.0
O4' F:FMN501 3.3 56.4 1.0
MN F:MN503 3.4 63.0 1.0
CD F:GLU210 3.5 76.9 1.0
C4' F:FMN501 3.7 58.8 1.0
C F:SER200 3.8 56.9 1.0
C5' F:FMN501 3.9 61.9 1.0
CG F:GLU210 4.0 79.8 1.0
C F:ALA202 4.1 79.7 1.0
N F:ALA202 4.4 67.2 1.0
C F:GLN201 4.4 58.8 1.0
C F:VAL148 4.4 75.3 1.0
OE1 F:GLU210 4.5 82.7 1.0
O1P F:FMN501 4.5 59.6 1.0
CA F:GLN201 4.6 58.2 1.0
N F:GLN201 4.6 62.3 1.0
OD1 F:ASN147 4.7 90.5 1.0
CA F:SER200 4.7 55.3 1.0
O F:ALA199 4.8 58.8 1.0
CB F:SER149 4.8 63.8 1.0
O F:GLN201 4.9 57.7 1.0
CA F:SER149 4.9 62.6 1.0
CA F:ALA202 4.9 71.9 1.0
ND2 F:ASN147 4.9 71.3 1.0

Reference:

K.A.P.Payne, S.A.Marshall, K.Fisher, M.J.Cliff, D.M.Cannas, C.Yan, D.J.Heyes, D.A.Parker, I.Larrosa, D.Leys. Enzymatic Carboxylation of 2-Furoic Acid Yields 2,5-Furandicarboxylic Acid (Fdca). Acs Catalysis V. 9 2854 2019.
ISSN: ESSN 2155-5435
PubMed: 31057985
DOI: 10.1021/ACSCATAL.8B04862
Page generated: Mon Aug 12 16:20:33 2024

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