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Calcium 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:

Potassium (K) 9 atoms
Zinc (Zn) 8 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6s6y

Go back to Calcium Binding Sites List in 6s6y
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca606

b:90.1
occ:1.00
 OE2 A:GLU218 2.3 0.6 1.0
OE1 A:GLU218 2.4 0.2 1.0
CD A:GLU218 2.6 0.8 1.0
CG A:GLU218 4.1 0.6 1.0
O A:GLU218 4.6 0.0 1.0
C A:GLU218 5.0 0.0 1.0

Calcium binding site 2 out of 6 in 6s6y

Go back to Calcium Binding Sites List in 6s6y
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca607

b:70.1
occ:1.00
 OE2 A:GLU423 2.7 0.3 1.0
OE1 A:GLU398 2.9 0.3 1.0
CD A:GLU423 3.7 0.7 1.0
OE1 A:GLU423 4.0 0.7 1.0
CD A:GLU398 4.2 0.2 1.0
OD1 A:ASP396 4.5 0.4 1.0

Calcium binding site 3 out of 6 in 6s6y

Go back to Calcium Binding Sites List in 6s6y
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca608

b:70.1
occ:1.00
 OD2 A:ASP334 3.2 93.5 1.0
OG A:SER117 3.4 84.0 1.0
CG A:ASP334 4.1 92.6 1.0
CB A:SER117 4.1 80.9 1.0
CB A:ASP334 4.2 88.7 1.0
O A:GLY333 4.3 99.5 1.0
C A:GLY333 4.7 93.6 1.0
CG1 B:VAL325 4.8 70.3 1.0
CB A:ASN118 4.9 84.4 1.0

Calcium binding site 4 out of 6 in 6s6y

Go back to Calcium Binding Sites List in 6s6y
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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
B:Ca401

b:70.1
occ:1.00
 OE2 B:GLU66 3.4 92.8 1.0
OD2 B:ASP217 3.4 61.1 1.0
CD B:ARG222 3.4 94.1 1.0
CG B:ARG222 4.0 83.9 1.0
CA B:VAL63 4.0 51.1 1.0
NH1 B:ARG222 4.1 96.3 1.0
NE B:ARG222 4.1 97.5 1.0
CG2 B:VAL63 4.1 51.2 1.0
CB B:ARG222 4.3 79.0 1.0
CZ B:ARG222 4.4 95.2 1.0
O B:SER62 4.4 53.3 1.0
CG B:ASP217 4.5 60.6 1.0
N B:ASP217 4.5 62.9 1.0
CA B:ARG222 4.5 76.2 1.0
N B:VAL63 4.6 52.5 1.0
CD B:GLU66 4.6 89.5 1.0
CB B:VAL63 4.6 50.6 1.0
C B:SER62 4.7 54.6 1.0
N B:ARG222 4.8 73.9 1.0
O B:LEU215 4.8 85.2 1.0
O B:VAL63 4.8 49.9 1.0
CA B:ALA216 4.9 91.6 1.0
CB B:ASP217 4.9 61.8 1.0
CB B:GLU66 4.9 76.4 1.0
C B:VAL63 5.0 50.4 1.0

Calcium binding site 5 out of 6 in 6s6y

Go back to Calcium Binding Sites List in 6s6y
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca 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
L:Ca401

b:65.1
occ:1.00
 O L:LYS196 2.2 0.4 1.0
O L:ASP60 2.2 79.6 1.0
C L:LYS196 3.3 0.6 1.0
C L:ASP60 3.4 70.9 1.0
OD1 L:ASP60 3.6 79.7 1.0
CA L:LYS196 4.1 0.2 1.0
CA L:ASP60 4.1 70.7 1.0
O L:ALA201 4.2 87.4 1.0
CB L:LYS196 4.2 0.7 1.0
N L:ALA197 4.2 67.8 1.0
O L:ILE198 4.4 0.7 1.0
CA L:ALA197 4.4 69.6 1.0
O L:ILE59 4.4 48.2 1.0
N L:ALA61 4.4 51.2 1.0
CG L:ASP60 4.5 75.4 1.0
C L:ALA197 4.5 70.5 1.0
CA L:ALA61 4.7 53.2 1.0
O L:ALA197 4.7 76.1 1.0
CB L:ALA61 4.8 55.4 1.0
CB L:ASP60 4.9 69.4 1.0
N L:ILE198 5.0 91.9 1.0

Calcium binding site 6 out of 6 in 6s6y

Go back to Calcium Binding Sites List in 6s6y
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca 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
L:Ca402

b:70.1
occ:1.00
 OE1 L:GLU189 3.1 83.1 1.0
OE2 L:GLU189 3.2 78.0 1.0
CD L:GLU189 3.6 79.0 1.0
NZ P:LYS34 4.0 95.8 1.0
NE1 P:TRP35 4.0 84.7 1.0
CD P:LYS34 4.0 89.3 1.0
CD1 P:TRP35 4.3 81.6 1.0
CE P:LYS34 4.6 91.4 1.0
OG1 P:THR32 4.8 84.8 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: Wed Jul 9 17:40:30 2025

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