Atomistry » Calcium » PDB 5wzv-5xiw » 5xen
Atomistry »
  Calcium »
    PDB 5wzv-5xiw »
      5xen »

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

Go back to Calcium Binding Sites List in 5xen
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

Go back to Calcium Binding Sites List in 5xen
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

Go back to Calcium Binding Sites List in 5xen
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

Go back to Calcium Binding Sites List in 5xen
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

Go back to Calcium Binding Sites List in 5xen
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

Go back to Calcium Binding Sites List in 5xen
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

Go back to Calcium Binding Sites List in 5xen
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: Mon Jul 15 14:55:12 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy