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Calcium in PDB 5xen: Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base

Enzymatic activity of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base

All present enzymatic activity of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base:
2.5.1.47;

Protein crystallography data

The structure of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base, PDB code: 5xen was solved by Y.Kezuka, Y.Yoshida, T.Nonaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.50 / 1.94
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.869, 116.869, 99.393, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base (pdb code 5xen). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base, PDB code: 5xen:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5xen

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Calcium binding site 1 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:11.8
occ:1.00
 O A:GLY108 2.2 11.0 1.0
O A:HOH666 2.4 15.1 1.0
O A:HOH654 2.4 16.6 1.0
OXT A:ACT404 2.4 13.1 1.0
O A:HOH588 2.4 11.2 1.0
O A:ACT404 2.5 15.0 1.0
C A:ACT404 2.8 15.1 1.0
C A:GLY108 3.4 11.4 1.0
O A:HOH663 3.9 24.2 1.0
O A:HOH675 4.0 15.0 1.0
CA A:GLY108 4.1 11.2 1.0
CH3 A:ACT404 4.3 15.8 1.0
N A:THR109 4.3 11.2 1.0
CA A:CA410 4.4 16.5 1.0
CA A:THR109 4.5 12.1 1.0
O A:HOH537 4.6 18.0 1.0
N A:GLU110 4.6 13.5 1.0
O A:LEU88 4.6 8.5 1.0
C A:THR109 4.7 13.0 1.0
N A:LEU88 4.8 8.8 1.0
CG A:LYS87 4.9 12.8 1.0

Calcium binding site 2 out of 8 in 5xen

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Calcium binding site 2 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:66.6
occ:1.00
 O A:HOH598 2.3 38.5 1.0
OD1 A:ASP22 4.4 28.2 1.0
OD2 A:ASP22 4.5 32.7 1.0
OD1 A:ASP283 4.5 37.1 1.0
CA A:PHE24 4.8 25.1 1.0
N A:GLY25 4.9 23.1 1.0
O A:HOH585 4.9 32.2 1.0
CG A:ASP22 4.9 29.8 1.0

Calcium binding site 3 out of 8 in 5xen

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Calcium binding site 3 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:34.0
occ:1.00
 O A:HOH567 2.1 32.5 1.0
O A:HOH609 2.4 35.3 1.0
OE1 A:GLU56 2.4 28.7 1.0
O A:HOH670 2.6 26.1 1.0
CD A:GLU56 3.6 23.8 1.0
OE2 A:GLU56 4.3 23.9 1.0
CG A:GLU56 4.6 20.4 1.0
CA A:GLU56 4.7 16.4 1.0
O A:LYS55 4.7 14.9 1.0
O A:HOH522 4.8 25.8 1.0

Calcium binding site 4 out of 8 in 5xen

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Calcium binding site 4 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:49.2
occ:1.00
 OD2 A:ASP246 2.4 24.2 1.0
O A:HOH506 2.5 28.1 1.0
OD1 A:ASP246 2.5 18.7 1.0
CG A:ASP246 2.8 19.2 1.0
CB A:GLU244 4.1 15.2 1.0
OD1 A:ASP247 4.2 16.2 1.0
O A:HOH668 4.2 4.7 0.5
OD2 A:ASP247 4.3 18.1 1.0
CG A:GLU244 4.3 16.3 1.0
CB A:ASP246 4.3 16.3 1.0
CG A:ASP247 4.4 16.4 1.0
O A:HOH688 4.7 10.4 0.5
O A:HOH692 4.8 34.2 1.0
CD A:GLU244 4.9 18.9 1.0

Calcium binding site 5 out of 8 in 5xen

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Calcium binding site 5 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:16.5
occ:1.00
 O A:HOH536 2.3 14.8 1.0
O A:HOH663 2.3 24.2 1.0
O A:ACT404 2.4 15.0 1.0
O B:HOH516 2.4 9.7 1.0
O A:HOH682 2.6 28.1 1.0
O A:HOH610 3.0 25.2 1.0
C A:ACT404 3.4 15.1 1.0
O A:HOH654 3.9 16.6 1.0
CH3 A:ACT404 3.9 15.8 1.0
O B:PHE257 4.3 9.8 1.0
OXT A:ACT404 4.3 13.1 1.0
CA A:CA405 4.4 11.8 1.0
O A:TYR86 4.4 9.1 1.0
O A:HOH642 4.4 22.6 1.0
O A:TYR107 4.8 10.1 1.0
O A:CYS81 4.8 9.4 1.0
CA A:ALA82 4.9 9.6 1.0
CA A:ASN85 5.0 13.6 1.0

Calcium binding site 6 out of 8 in 5xen

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Calcium binding site 6 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:22.3
occ:1.00
 O B:HOH669 2.0 25.2 1.0
OE1 B:GLU244 2.3 12.1 1.0
OD2 B:ASP246 2.4 20.9 1.0
OD1 B:ASP246 2.4 17.5 1.0
O B:HOH530 2.5 24.1 1.0
CG B:ASP246 2.7 17.5 1.0
CD B:GLU244 3.6 14.1 1.0
O B:HOH679 3.9 25.7 1.0
CB B:GLU244 4.1 12.8 1.0
CB B:ASP246 4.2 16.9 1.0
OD1 B:ASP247 4.3 17.1 1.0
CG B:GLU244 4.4 13.4 1.0
OE2 B:GLU244 4.5 14.7 1.0
OD2 B:ASP247 4.6 16.2 1.0
CG B:ASP247 4.6 15.6 1.0
N B:ASP247 4.9 12.5 1.0

Calcium binding site 7 out of 8 in 5xen

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Calcium binding site 7 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:27.9
occ:1.00
 O B:HOH699 2.3 31.5 1.0
O B:GLU190 2.3 15.2 1.0
C B:GLU190 3.5 15.2 1.0
CA B:GLU190 4.1 14.7 0.6
CA B:GLU190 4.2 14.6 0.5
N B:LYS191 4.6 15.3 1.0
CB B:GLU190 4.7 14.8 0.6
O B:LYS189 4.8 13.4 1.0
CA B:LYS191 4.8 16.1 1.0
CB B:GLU190 4.9 14.7 0.5

Calcium binding site 8 out of 8 in 5xen

Go back to Calcium Binding Sites List in 5xen
Calcium binding site 8 out of 8 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca407

b:63.6
occ:1.00
 OD1 B:ASP238 2.4 20.6 1.0
O B:HOH695 3.0 39.1 1.0
O B:HOH582 3.2 45.7 1.0
CG B:ASP238 3.5 18.1 1.0
NZ B:LYS189 4.0 12.7 1.0
OD2 B:ASP238 4.1 16.6 1.0
O B:HOH532 4.4 24.9 1.0
CB B:ASP238 4.7 16.6 1.0
CE B:LYS189 4.8 12.0 1.0

Reference:

Y.Kezuka, Y.Yoshida, T.Nonaka. Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Serine-Plp Schiff Base To Be Published.
Page generated: Wed Jul 9 11:39:14 2025

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