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Potassium in PDB 6s6y: X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran

Enzymatic activity of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran

All present enzymatic activity of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran:
2.3.1.101;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran, PDB code: 6s6y was solved by T.Wagner, J.L.Hemmann, S.Shima, J.Vorholt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.95 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.974, 130.322, 172.689, 84.97, 75.91, 82.09
R / Rfree (%) 22.1 / 25.1

Other elements in 6s6y:

The structure of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Calcium (Ca) 6 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran (pdb code 6s6y). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran, PDB code: 6s6y:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 6s6y

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Potassium binding site 1 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K609

b:70.1
occ:1.00
 OD1 A:ASP463 3.4 0.1 1.0
OD2 A:ASP463 3.7 0.9 1.0
CG A:ASP463 4.0 0.7 1.0
OG1 A:THR464 4.8 0.3 1.0

Potassium binding site 2 out of 9 in 6s6y

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Potassium binding site 2 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K610

b:70.1
occ:1.00
 OE1 A:GLU399 3.2 0.9 1.0
OD2 A:ASP465 3.8 0.7 1.0
CD A:GLU399 4.2 0.8 1.0
OE2 A:GLU399 4.7 0.3 1.0

Potassium binding site 3 out of 9 in 6s6y

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Potassium binding site 3 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K401

b:70.1
occ:1.00
 O D:ASP60 2.5 0.8 1.0
O D:LYS196 2.6 0.0 1.0
C D:LYS196 3.4 0.0 1.0
C D:ASP60 3.7 0.5 1.0
CB D:LYS196 3.9 0.4 1.0
CA D:LYS196 4.1 0.2 1.0
N D:ALA197 4.2 0.6 1.0
CA D:ALA197 4.3 0.5 1.0
O D:ILE59 4.5 0.2 1.0
CA D:ALA61 4.5 93.8 1.0
N D:ALA61 4.5 91.2 1.0
CA D:ASP60 4.6 0.6 1.0
OD1 D:ASP60 4.6 0.5 1.0
C D:ALA197 4.8 99.0 1.0
CB D:ALA61 4.8 95.3 1.0
CG D:LYS196 4.8 0.5 1.0

Potassium binding site 4 out of 9 in 6s6y

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Potassium binding site 4 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K402

b:80.1
occ:1.00
 O H:LYS196 2.4 0.8 1.0
O H:ASP60 2.4 97.8 1.0
C H:LYS196 3.2 0.8 1.0
C H:ASP60 3.6 99.3 1.0
CA H:ALA197 3.8 0.3 1.0
N H:ALA197 3.9 0.6 1.0
OD1 H:ASP60 4.1 0.0 1.0
C H:ALA197 4.1 0.8 1.0
CB H:LYS196 4.1 97.5 1.0
CA H:LYS196 4.1 0.9 1.0
O H:ALA197 4.2 0.7 1.0
CB H:ALA61 4.3 88.9 1.0
CA H:ALA61 4.4 88.7 1.0
N H:ALA61 4.4 87.6 1.0
CA H:ASP60 4.5 0.8 1.0
O H:ILE198 4.6 0.2 1.0
CG H:ASP60 4.8 0.2 1.0
N H:ILE198 4.8 0.7 1.0
O H:ILE59 5.0 98.0 1.0

Potassium binding site 5 out of 9 in 6s6y

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Potassium binding site 5 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K606

b:70.1
occ:1.00
 OE1 I:GLU423 3.2 76.4 1.0
OD1 I:ASP396 3.3 78.5 1.0
OE2 I:GLU423 3.5 75.7 1.0
CD I:GLU423 3.7 74.4 1.0
O I:MET395 4.4 72.1 1.0
CG I:ASP396 4.4 67.7 1.0
OE1 I:GLU398 4.6 0.2 1.0
CA I:ASP396 4.7 58.4 1.0
CB I:ASP396 5.0 61.2 1.0

Potassium binding site 6 out of 9 in 6s6y

Go back to Potassium Binding Sites List in 6s6y
Potassium binding site 6 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K403

b:70.1
occ:1.00
 OE2 J:GLU191 3.1 0.9 1.0
OE1 J:GLU191 3.5 0.1 1.0
CD J:GLU191 3.7 99.9 1.0
NH2 K:ARG176 3.9 74.5 1.0
O K:ALA132 4.1 75.9 1.0
O K:VAL133 4.3 49.9 1.0
C K:VAL133 4.5 53.3 1.0
CA K:TYR134 4.6 55.6 1.0
OD2 K:ASP157 4.7 70.8 1.0
N K:TYR134 4.7 56.0 1.0
OH K:TYR109 4.7 57.1 1.0
CZ K:ARG176 4.9 72.3 1.0

Potassium binding site 7 out of 9 in 6s6y

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Potassium binding site 7 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K403

b:70.1
occ:1.00
 OE2 L:GLU155 3.1 71.8 1.0
O L:PHE130 3.7 84.7 1.0
CB P:THR234 4.1 64.5 1.0
OG1 P:THR234 4.1 65.7 1.0
CD L:GLU155 4.2 71.6 1.0
NH2 K:ARG248 4.3 65.1 1.0
CB L:PRO150 4.3 49.3 1.0
CG2 L:VAL132 4.4 73.7 1.0
CG L:PRO150 4.4 49.1 1.0
CG2 P:THR234 4.5 62.5 1.0
CD L:PRO150 4.6 53.4 1.0
O L:ARG148 4.6 60.0 1.0
CG L:GLU155 4.7 65.2 1.0
C L:PHE130 4.9 77.3 1.0

Potassium binding site 8 out of 9 in 6s6y

Go back to Potassium Binding Sites List in 6s6y
Potassium binding site 8 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
P:K401

b:70.1
occ:1.00
 O P:ASP60 2.4 85.6 1.0
O P:LYS196 2.6 88.3 1.0
C P:LYS196 3.6 86.7 1.0
C P:ASP60 3.6 84.0 1.0
CB P:LYS196 4.2 88.3 1.0
CA P:LYS196 4.3 84.8 1.0
CA P:ALA61 4.3 80.8 1.0
N P:ALA197 4.4 69.2 1.0
N P:ALA61 4.4 77.8 1.0
OD1 P:ASP60 4.4 83.2 1.0
CA P:ALA197 4.5 76.4 1.0
CB P:ALA61 4.6 87.3 1.0
CA P:ASP60 4.6 73.9 1.0
O P:ILE59 4.6 70.1 1.0
C P:ALA197 4.8 72.0 1.0

Potassium binding site 9 out of 9 in 6s6y

Go back to Potassium Binding Sites List in 6s6y
Potassium binding site 9 out of 9 in the X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of X-Ray Crystal Structure of the Formyltransferase/Hydrolase Complex (Fhcabcd) From Methylorubrum Extorquens in Complex with Methylofuran within 5.0Å range:
probe atom residue distance (Å) B Occ
P:K402

b:70.1
occ:1.00
 OE2 P:GLU189 3.3 66.0 1.0
OE1 P:GLU189 3.4 69.3 1.0
NZ L:LYS34 3.7 86.0 1.0
CD P:GLU189 3.8 63.9 1.0
CD L:LYS34 3.9 73.2 1.0
NE1 L:TRP35 4.3 65.7 1.0
CE L:LYS34 4.4 79.6 1.0
CD1 L:TRP35 4.6 62.7 1.0

Reference:

J.L.Hemmann, T.Wagner, S.Shima, J.Vorholt. Methylofuran Is A Prosthetic Group of the Formyltransferase/Hydrolase Complex and Shuttles One-Carbon Units Between Two Active Sites To Be Published.
Page generated: Mon Aug 12 17:34:18 2024

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