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

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

All present enzymatic activity of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base, PDB code: 5xem 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) 38.12 / 1.84
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.749, 116.749, 99.343, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.4

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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-Lanthionine-Plp Schiff Base (pdb code 5xem). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-Plp Schiff Base, PDB code: 5xem:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 5xem

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Calcium binding site 1 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:15.7
occ:1.00
 O A:GLY108 2.3 15.0 1.0
O A:HOH763 2.4 18.8 1.0
O A:HOH757 2.4 20.2 1.0
OXT A:ACT503 2.5 15.8 1.0
O A:HOH649 2.5 17.7 1.0
O A:ACT503 2.6 18.9 1.0
C A:ACT503 2.9 18.5 1.0
C A:GLY108 3.4 15.2 1.0
O A:HOH776 4.1 16.6 1.0
CA A:GLY108 4.1 14.9 1.0
O A:HOH773 4.1 23.4 1.0
N A:THR109 4.4 15.2 1.0
CH3 A:ACT503 4.4 18.4 1.0
CA A:CA513 4.4 17.0 1.0
CA A:THR109 4.6 16.4 1.0
O A:HOH640 4.6 21.6 1.0
O A:LEU88 4.6 10.5 1.0
N A:GLU110 4.7 17.5 1.0
C A:THR109 4.7 17.5 1.0
N A:LEU88 4.8 11.3 1.0
CG A:LYS87 4.9 15.1 1.0

Calcium binding site 2 out of 12 in 5xem

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Calcium binding site 2 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:63.7
occ:1.00
 O A:HOH735 2.3 42.8 1.0
O A:HOH748 2.6 44.0 1.0
OD1 A:ASP283 4.2 40.0 1.0
OD1 A:ASP22 4.6 31.2 1.0
N A:GLY25 4.7 26.0 1.0
OD2 A:ASP283 4.9 40.7 1.0
OD2 A:ASP22 4.9 34.4 1.0
CA A:PHE24 4.9 27.0 1.0
C A:PHE24 5.0 27.0 1.0
CG A:ASP283 5.0 39.7 1.0

Calcium binding site 3 out of 12 in 5xem

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Calcium binding site 3 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:36.6
occ:1.00
 O A:HOH722 2.2 30.3 1.0
OE1 A:GLU56 2.4 28.2 1.0
O A:HOH765 2.5 23.3 1.0
O A:HOH675 2.6 24.6 1.0
CD A:GLU56 3.5 24.0 1.0
OE2 A:GLU56 4.3 22.4 1.0
CA A:GLU56 4.5 17.1 1.0
CG A:GLU56 4.5 20.9 1.0
O A:LYS55 4.5 15.8 1.0
O A:HOH632 4.7 25.8 1.0
N A:GLU56 4.9 15.2 1.0
C A:LYS55 5.0 17.2 1.0
CB A:GLU56 5.0 18.2 1.0

Calcium binding site 4 out of 12 in 5xem

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Calcium binding site 4 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:47.1
occ:1.00
 O A:HOH616 2.3 31.9 1.0
OD1 A:ASP246 2.6 21.7 1.0
OD2 A:ASP246 2.6 24.1 1.0
O A:HOH658 2.8 35.8 1.0
CG A:ASP246 2.9 21.9 1.0
CB A:GLU244 4.1 15.9 1.0
OD2 A:ASP247 4.2 18.3 1.0
OD1 A:ASP247 4.2 17.8 1.0
CG A:GLU244 4.2 16.7 1.0
O A:HOH755 4.4 22.9 1.0
CG A:ASP247 4.4 17.9 1.0
CB A:ASP246 4.5 18.8 1.0
O A:HOH798 4.7 27.9 1.0
CD A:GLU244 4.9 19.8 1.0

Calcium binding site 5 out of 12 in 5xem

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Calcium binding site 5 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:54.5
occ:1.00
 O A:HOH687 2.3 30.3 1.0
O A:ASP8 4.5 16.2 1.0
CA A:ASP8 4.5 16.4 1.0
OD1 A:ASP8 4.6 23.6 1.0
O A:ILE7 4.6 12.2 1.0
O A:ILE10 4.6 15.0 1.0
O A:HOH762 4.7 29.6 1.0
C A:ASP8 4.8 15.5 1.0

Calcium binding site 6 out of 12 in 5xem

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Calcium binding site 6 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca510

b:66.9
occ:1.00
 O A:LEU300 2.4 26.3 1.0
O A:SER301 3.1 35.4 1.0
C A:SER301 3.2 36.3 1.0
C A:LEU300 3.4 25.2 1.0
OE1 B:GLN102 3.6 20.4 0.5
CA A:SER301 3.6 33.6 1.0
N A:ASN302 3.8 39.6 1.0
CD B:GLN102 3.9 19.1 0.5
N A:SER301 4.0 28.9 1.0
CG B:GLN102 4.1 18.5 0.5
CA A:ASN302 4.1 44.3 1.0
CG B:GLN102 4.4 17.2 0.5
CA A:LEU300 4.6 22.7 1.0
NE2 B:GLN102 4.7 20.3 0.5
CB B:GLN102 4.7 17.9 0.5
CD B:GLN102 4.7 17.7 0.5
NE2 B:GLN102 5.0 18.6 0.5

Calcium binding site 7 out of 12 in 5xem

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Calcium binding site 7 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca513

b:17.0
occ:1.00
 O A:HOH773 2.3 23.4 1.0
O A:HOH639 2.3 16.2 1.0
O B:HOH520 2.4 14.5 1.0
O A:ACT503 2.4 18.9 1.0
O A:HOH778 2.5 25.6 1.0
O A:HOH699 2.9 25.3 1.0
C A:ACT503 3.4 18.5 1.0
O A:HOH757 4.0 20.2 1.0
CH3 A:ACT503 4.0 18.4 1.0
O B:PHE257 4.3 11.5 1.0
OXT A:ACT503 4.4 15.8 1.0
O A:HOH729 4.4 29.3 1.0
O A:TYR86 4.4 12.6 1.0
CA A:CA505 4.4 15.7 1.0
O A:CYS81 4.8 11.2 1.0
CA A:ALA82 4.8 11.5 1.0
O A:TYR107 4.8 14.1 1.0
CA A:ASN85 4.9 15.1 1.0

Calcium binding site 8 out of 12 in 5xem

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Calcium binding site 8 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-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-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:21.9
occ:1.00
 O B:HOH669 2.2 31.1 1.0
OE1 B:GLU244 2.3 12.8 1.0
OD2 B:ASP246 2.4 19.2 1.0
OD1 B:ASP246 2.4 16.9 1.0
O B:HOH530 2.5 22.8 1.0
CG B:ASP246 2.7 16.9 1.0
CD B:GLU244 3.5 15.7 1.0
O B:HOH646 4.1 25.9 1.0
CB B:GLU244 4.2 14.8 1.0
CB B:ASP246 4.2 17.0 1.0
OD1 B:ASP247 4.3 19.8 1.0
OE2 B:GLU244 4.4 16.1 1.0
CG B:GLU244 4.4 14.9 1.0
OD2 B:ASP247 4.7 18.2 1.0
CG B:ASP247 4.7 17.9 1.0
N B:ASP247 4.9 14.1 1.0

Calcium binding site 9 out of 12 in 5xem

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Calcium binding site 9 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:27.5
occ:1.00
 O B:HOH702 2.2 28.5 1.0
O B:HOH687 2.2 38.4 1.0
O B:GLU190 2.3 16.4 1.0
C B:GLU190 3.5 16.7 1.0
CA B:GLU190 4.1 16.3 0.6
CA B:GLU190 4.1 16.6 0.5
N B:LYS191 4.5 16.6 1.0
CG B:GLU190 4.6 17.4 0.5
O B:LYS189 4.8 13.8 1.0
CA B:LYS191 4.8 18.1 1.0
CB B:GLU190 4.8 16.4 0.6
CB B:GLU190 4.9 17.0 0.5

Calcium binding site 10 out of 12 in 5xem

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Calcium binding site 10 out of 12 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-Plp Schiff Base


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum in Complex with L-Lanthionine-Plp Schiff Base within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca407

b:68.4
occ:1.00
 OD1 B:ASP238 2.6 24.6 1.0
O B:HOH574 3.6 35.4 1.0
CG B:ASP238 3.7 20.2 1.0
NZ B:LYS189 4.1 14.4 1.0
OD2 B:ASP238 4.2 17.6 1.0
O B:HOH512 4.4 24.0 1.0
CE B:LYS189 4.9 14.5 1.0
CB B:ASP238 4.9 17.9 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-Lanthionine-Plp Schiff Base To Be Published.
Page generated: Wed Jul 9 11:39:14 2025

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