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Calcium in PDB 5xeo: Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum

Enzymatic activity of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum

All present enzymatic activity of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum:
2.5.1.47;

Protein crystallography data

The structure of Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum, PDB code: 5xeo 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 / 2.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.822, 116.822, 99.186, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 7 in 5xeo

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Calcium binding site 1 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:20.2
occ:1.00
 O A:GLY108 2.3 18.3 1.0
O A:HOH607 2.3 19.7 1.0
O A:HOH560 2.5 23.6 1.0
O A:ACT402 2.5 21.7 1.0
O A:HOH614 2.5 25.1 1.0
OXT A:ACT402 2.6 20.0 1.0
C A:ACT402 2.9 22.2 1.0
C A:GLY108 3.4 19.6 1.0
O A:HOH621 3.9 22.3 1.0
O A:HOH617 3.9 27.4 1.0
CA A:GLY108 4.1 19.4 1.0
CA A:CA409 4.3 25.1 1.0
CH3 A:ACT402 4.3 22.4 1.0
N A:THR109 4.4 20.2 1.0
N A:GLU110 4.4 22.6 1.0
CA A:THR109 4.5 20.6 1.0
C A:THR109 4.5 21.4 1.0
CG A:GLU110 4.6 24.9 0.5
O A:LEU88 4.7 16.3 1.0
OE2 A:GLU110 4.7 21.0 0.5
N A:LEU88 4.9 17.4 1.0
CG A:LYS87 5.0 28.0 1.0

Calcium binding site 2 out of 7 in 5xeo

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Calcium binding site 2 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:49.4
occ:1.00
 O A:HOH605 2.3 36.6 1.0
OD1 A:ASP283 4.2 44.1 1.0
OD1 A:ASP22 4.5 37.0 1.0
OD2 A:ASP283 4.6 45.9 1.0
CA A:PHE24 4.6 33.9 1.0
N A:GLY25 4.7 30.9 1.0
OD2 A:ASP22 4.8 40.2 1.0
C A:PHE24 4.8 32.1 1.0
CG A:ASP283 4.8 45.9 1.0

Calcium binding site 3 out of 7 in 5xeo

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Calcium binding site 3 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:57.4
occ:1.00
 OE1 A:GLU56 2.2 43.6 1.0
O A:HOH623 2.7 29.9 1.0
CD A:GLU56 3.5 35.9 1.0
OE2 A:GLU56 4.2 33.7 1.0
CG A:GLU56 4.5 31.0 1.0
CA A:GLU56 4.7 24.7 1.0
O A:LYS55 4.9 23.0 1.0

Calcium binding site 4 out of 7 in 5xeo

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Calcium binding site 4 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:25.1
occ:1.00
 O B:HOH515 2.3 18.8 1.0
O A:ACT402 2.4 21.7 1.0
O A:HOH617 2.4 27.4 1.0
O A:HOH517 2.4 22.7 1.0
O A:HOH628 2.8 35.0 1.0
C A:ACT402 3.3 22.2 1.0
O A:HOH536 3.4 32.7 1.0
CH3 A:ACT402 3.9 22.4 1.0
O A:HOH614 3.9 25.1 1.0
O B:PHE257 4.2 18.3 1.0
CA A:CA404 4.3 20.2 1.0
OXT A:ACT402 4.3 20.0 1.0
O A:TYR86 4.3 18.8 1.0
O A:TYR107 4.7 17.5 1.0
O A:CYS81 4.8 17.0 1.0
CA A:ALA82 4.9 17.9 1.0

Calcium binding site 5 out of 7 in 5xeo

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Calcium binding site 5 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:25.9
occ:1.00
 O B:HOH644 2.1 29.4 1.0
OE1 B:GLU244 2.3 18.0 1.0
OD2 B:ASP246 2.4 26.8 1.0
OD1 B:ASP246 2.4 21.9 1.0
CG B:ASP246 2.7 24.3 1.0
CD B:GLU244 3.6 21.4 1.0
O B:HOH642 4.0 31.2 1.0
O B:HOH564 4.0 24.8 1.0
CB B:GLU244 4.1 20.5 1.0
OD1 B:ASP247 4.2 21.9 1.0
CB B:ASP246 4.3 24.0 1.0
O B:HOH666 4.3 37.8 1.0
OE2 B:GLU244 4.4 20.7 1.0
CG B:GLU244 4.4 20.2 1.0
OD2 B:ASP247 4.5 21.7 1.0
CG B:ASP247 4.6 22.3 1.0
N B:ASP247 4.9 18.5 1.0

Calcium binding site 6 out of 7 in 5xeo

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Calcium binding site 6 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:41.6
occ:1.00
 O B:HOH662 2.3 38.1 1.0
O B:HOH638 2.3 39.3 1.0
O B:GLU190 2.4 22.2 1.0
C B:GLU190 3.5 22.9 1.0
CA B:GLU190 4.2 22.4 0.5
CA B:GLU190 4.2 21.3 0.5
N B:LYS191 4.6 22.8 1.0
CA B:LYS191 4.7 24.4 1.0
CB B:GLU190 4.7 22.4 0.5
CB B:GLU190 4.8 20.0 0.5
O B:LYS189 5.0 19.9 1.0

Calcium binding site 7 out of 7 in 5xeo

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Calcium binding site 7 out of 7 in the Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:70.3
occ:1.00
 OD1 B:ASP238 2.5 33.1 1.0
CG B:ASP238 3.6 25.1 1.0
NZ B:LYS189 4.1 19.0 1.0
OD2 B:ASP238 4.1 22.2 1.0
O B:HOH651 4.2 49.8 1.0
O B:HOH512 4.6 29.8 1.0
CB B:ASP238 4.8 23.3 1.0
CE B:LYS189 4.9 18.6 1.0

Reference:

Y.Kezuka, Y.Yoshida, T.Nonaka. Crystal Structure of A Hydrogen Sulfide-Producing Enzyme (FN1220) From Fusobacterium Nucleatum To Be Published.
Page generated: Mon Jul 15 14:55:17 2024

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