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Calcium in PDB 5ssx: Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant

Enzymatic activity of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant

All present enzymatic activity of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant:
1.8.3.7;

Protein crystallography data

The structure of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant, PDB code: 5ssx was solved by K.Radhakrishnan, L.Schlotawa, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.95 / 1.02
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.494, 61.64, 109.579, 90, 90, 90
R / Rfree (%) 12.3 / 13.8

Other elements in 5ssx:

The structure of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant also contains other interesting chemical elements:

Copper (Cu) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant (pdb code 5ssx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant, PDB code: 5ssx:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5ssx

Go back to Calcium Binding Sites List in 5ssx
Calcium binding site 1 out of 3 in the Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:11.2
occ:0.70
 CA A:CA402 0.0 11.2 0.7
O A:HOH592 1.4 7.7 0.3
CA A:CA402 1.8 12.2 0.3
O A:HOH592 2.0 18.0 0.7
O A:HOH509 2.7 14.2 1.0
O A:ASN293 2.7 6.8 1.0
O A:GLY296 2.7 6.6 1.0
O A:ALA298 2.7 6.2 1.0
OE2 A:GLU300 2.8 7.6 1.0
O A:ILE294 2.9 9.6 1.0
HG3 A:GLU300 3.2 8.4 1.0
H A:ALA298 3.4 7.7 1.0
C A:ILE294 3.4 6.8 1.0
CD A:GLU300 3.5 6.8 1.0
HA A:VAL295 3.5 7.3 1.0
HA A:ILE294 3.7 8.2 1.0
HA3 A:GLY331 3.7 8.9 1.0
C A:ASN293 3.8 6.2 1.0
CG A:GLU300 3.8 7.0 1.0
C A:ALA298 3.8 6.0 1.0
C A:GLY296 3.9 6.5 1.0
C A:VAL295 4.0 6.0 1.0
N A:VAL295 4.0 6.4 1.0
N A:GLY296 4.0 6.4 1.0
CA A:ILE294 4.0 6.8 1.0
CA A:VAL295 4.0 6.1 1.0
O A:GLY332 4.0 7.3 1.0
HH21 A:ARG364 4.1 7.8 1.0
HZ2 A:TRP231 4.1 8.7 1.0
N A:ALA298 4.1 6.4 1.0
H A:GLY296 4.1 7.7 1.0
HG2 A:GLU300 4.3 8.4 1.0
HB3 A:ASN297 4.3 7.5 1.0
OD2 A:ASP130 4.4 22.9 1.0
HB3 A:ASN293 4.4 7.4 1.0
N A:ILE294 4.4 6.3 1.0
O A:VAL295 4.4 6.2 1.0
O A:GLY331 4.4 8.3 1.0
HA A:TRP299 4.4 6.9 1.0
OE1 A:GLU300 4.4 7.1 1.0
CA A:GLY296 4.6 6.5 1.0
CA A:GLY331 4.6 7.4 1.0
C A:GLY331 4.6 6.8 1.0
CA A:ALA298 4.6 6.5 1.0
H A:VAL295 4.7 7.7 1.0
HD11 A:ILE294 4.8 11.1 1.0
O A:LYS330 4.8 6.3 1.0
N A:TRP299 4.8 5.5 1.0
NH2 A:ARG364 4.8 6.5 1.0
HB3 A:ALA298 4.9 9.9 1.0
HB2 A:GLU300 4.9 7.2 1.0
N A:ASN297 4.9 5.9 1.0
CA A:TRP299 4.9 5.7 1.0
CA A:ASN293 4.9 6.2 1.0
C A:TRP299 5.0 5.5 1.0
CB A:ASN297 5.0 6.3 1.0
CB A:GLU300 5.0 6.0 1.0

Calcium binding site 2 out of 3 in 5ssx

Go back to Calcium Binding Sites List in 5ssx
Calcium binding site 2 out of 3 in the Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:12.2
occ:0.30
 CA A:CA402 0.0 12.2 0.3
O A:HOH592 1.3 18.0 0.7
CA A:CA402 1.8 11.2 0.7
O A:HOH592 2.3 7.7 0.3
O A:GLY332 2.3 7.3 1.0
O A:ALA298 2.4 6.2 1.0
O A:GLY296 2.4 6.6 1.0
H A:GLY296 3.1 7.7 1.0
O A:GLY331 3.1 8.3 1.0
HA3 A:GLY331 3.2 8.9 1.0
C A:ALA298 3.2 6.0 1.0
C A:GLY296 3.2 6.5 1.0
C A:GLY331 3.3 6.8 1.0
N A:GLY296 3.3 6.4 1.0
C A:GLY332 3.3 6.2 1.0
H A:ALA298 3.3 7.7 1.0
HA A:VAL295 3.4 7.3 1.0
HA A:TRP299 3.4 6.9 1.0
CA A:GLY296 3.7 6.5 1.0
O A:ILE294 3.7 9.6 1.0
N A:GLY332 3.7 6.3 1.0
CA A:GLY331 3.7 7.4 1.0
HA A:SER333 3.7 7.4 1.0
N A:ALA298 3.7 6.4 1.0
C A:VAL295 3.8 6.0 1.0
HG3 A:GLU300 3.8 8.4 1.0
O A:HOH509 3.8 14.2 1.0
N A:TRP299 3.8 5.5 1.0
HA2 A:GLY296 3.9 7.8 1.0
CA A:TRP299 4.0 5.7 1.0
CA A:VAL295 4.0 6.1 1.0
CA A:GLY332 4.1 6.5 1.0
CA A:ALA298 4.1 6.5 1.0
H A:GLY332 4.2 7.5 1.0
O A:LYS330 4.2 6.3 1.0
N A:SER333 4.2 6.2 1.0
O A:ASN293 4.2 6.8 1.0
N A:ASN297 4.3 5.9 1.0
HA2 A:GLY331 4.3 8.9 1.0
C A:ILE294 4.4 6.8 1.0
OE2 A:GLU300 4.4 7.6 1.0
CA A:SER333 4.5 6.2 1.0
HA3 A:GLY332 4.5 7.8 1.0
H A:TRP299 4.5 6.6 1.0
O A:VAL295 4.5 6.2 1.0
C A:TRP299 4.6 5.5 1.0
HA3 A:GLY296 4.6 7.8 1.0
C A:ASN297 4.6 6.2 1.0
N A:VAL295 4.6 6.4 1.0
HA A:ALA298 4.6 7.8 1.0
CG A:GLU300 4.7 7.0 1.0
HB3 A:ASN297 4.7 7.5 1.0
HZ2 A:TRP231 4.7 8.7 1.0
N A:GLY331 4.8 6.1 1.0
CD A:GLU300 4.8 6.8 1.0
H A:GLU300 4.8 6.7 1.0
HA2 A:GLY332 4.8 7.8 1.0
CA A:ASN297 4.9 6.0 1.0
N A:GLU300 4.9 5.5 1.0
C A:LYS330 4.9 6.1 1.0
H A:SER333 5.0 7.4 1.0
H A:ASN297 5.0 7.1 1.0

Calcium binding site 3 out of 3 in 5ssx

Go back to Calcium Binding Sites List in 5ssx
Calcium binding site 3 out of 3 in the Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Human Formylglycine Generating Enzyme E130D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:5.8
occ:1.00
 OD1 A:ASN259 2.3 6.4 1.0
O A:PHE275 2.3 6.8 1.0
O A:ILE260 2.3 6.6 1.0
O A:HOH559 2.3 6.8 1.0
O A:HOH609 2.4 6.8 1.0
OD1 A:ASP273 2.4 6.8 1.0
OD2 A:ASP273 2.5 6.7 1.0
CG A:ASP273 2.8 6.7 1.0
C A:ILE260 3.5 6.0 1.0
C A:PHE275 3.5 6.3 1.0
CG A:ASN259 3.5 6.0 1.0
H A:ILE260 3.6 7.1 1.0
HB2 A:PHE275 3.7 7.8 1.0
H A:PHE275 3.7 7.3 1.0
HA A:ASN259 3.7 7.0 1.0
N A:ILE260 3.8 5.9 1.0
HA A:GLN276 4.0 8.6 0.7
HA A:TRP261 4.0 7.6 1.0
OE1 A:GLN262 4.1 7.1 1.0
HB2 A:TYR334 4.1 7.6 1.0
C A:ASN259 4.2 5.9 1.0
HA2 A:GLY271 4.2 9.9 1.0
CA A:ILE260 4.3 6.1 1.0
CA A:ASN259 4.3 5.8 1.0
CB A:ASP273 4.3 6.8 1.0
CA A:PHE275 4.3 6.2 1.0
N A:PHE275 4.3 6.1 1.0
HA A:GLN276 4.4 7.5 0.3
H A:ASP273 4.4 8.2 1.0
ND2 A:ASN259 4.4 6.2 1.0
CB A:PHE275 4.4 6.5 1.0
NE2 A:GLN262 4.4 7.2 1.0
CB A:ASN259 4.5 6.0 1.0
N A:TRP261 4.5 6.0 1.0
O A:TYR334 4.5 6.8 1.0
N A:GLN276 4.5 6.6 1.0
O A:GLN276 4.6 8.4 1.0
HA A:TYR334 4.6 7.3 1.0
ND2 A:ASN269 4.6 9.0 1.0
HA A:ILE260 4.6 7.3 1.0
OD1 A:ASN269 4.6 9.6 1.0
HB3 A:ASP273 4.6 8.2 1.0
CA A:GLN276 4.6 7.2 0.7
CD A:GLN262 4.6 7.3 1.0
CA A:TRP261 4.7 6.3 1.0
HB2 A:ASP273 4.8 8.2 1.0
HB3 A:PHE275 4.8 7.8 1.0
CA A:GLN276 4.8 6.2 0.3
H A:GLN262 4.8 8.2 1.0
C A:GLN276 4.9 6.8 1.0
HB2 A:ASN259 4.9 7.2 1.0
O A:ASN259 4.9 6.1 1.0
O A:GLY277 5.0 7.0 1.0
CB A:TYR334 5.0 6.3 1.0

Reference:

J.Kowal, L.Schlotawa, H.Niemann, M.G.Rudolph. Crystal Structure of Human Formylglycine Generating Enzyme E130D Mutant To Be Published.
Page generated: Thu Dec 28 01:24:39 2023

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