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Calcium in PDB 4x8b: Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form

Protein crystallography data

The structure of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form, PDB code: 4x8b was solved by A.Vit, K.V.Goncharenko, W.Blankenfeldt, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 134.780, 134.780, 141.204, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 15.7

Other elements in 4x8b:

The structure of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form (pdb code 4x8b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form, PDB code: 4x8b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4x8b

Go back to Calcium Binding Sites List in 4x8b
Calcium binding site 1 out of 2 in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:16.6
occ:1.00
O A:VAL358 2.6 12.8 1.0
O A:GLY356 2.6 13.7 1.0
O A:MET354 2.7 12.8 1.0
O A:GLY399 2.9 18.1 1.0
O A:HOH707 3.0 14.8 1.0
HA3 A:GLY398 3.2 15.0 1.0
OE2 A:GLU360 3.2 13.7 1.0
HG3 A:GLU360 3.4 14.3 1.0
H A:VAL358 3.4 15.8 1.0
O A:GLN353 3.5 11.6 1.0
O A:GLY398 3.5 14.9 1.0
C A:MET354 3.5 12.7 1.0
C A:GLY398 3.6 14.4 1.0
C A:VAL358 3.6 11.2 1.0
H A:GLY356 3.7 14.4 1.0
C A:GLY356 3.7 13.4 1.0
N A:GLY356 3.8 12.1 1.0
HA A:LEU355 3.8 14.2 1.0
CD A:GLU360 3.9 13.3 1.0
CA A:GLY398 3.9 12.5 1.0
HA A:MET354 3.9 14.2 0.5
N A:VAL358 4.0 13.2 1.0
HA A:MET354 4.0 14.8 0.6
C A:GLY399 4.1 14.5 1.0
O A:ARG397 4.1 13.9 1.0
CG A:GLU360 4.1 11.9 1.0
C A:LEU355 4.1 13.8 1.0
HZ2 A:TRP299 4.1 15.3 1.0
HA A:TRP359 4.2 12.9 1.0
N A:GLY399 4.2 14.2 1.0
N A:LEU355 4.3 12.5 1.0
CA A:LEU355 4.3 11.8 1.0
CA A:MET354 4.3 11.8 0.5
CA A:GLY356 4.3 11.8 1.0
CA A:MET354 4.3 12.3 0.6
HB2 A:ASP357 4.3 18.1 1.0
CA A:VAL358 4.4 11.7 1.0
HH21 A:ARG428 4.4 14.3 1.0
HA2 A:GLY398 4.4 15.0 1.0
HG23 A:VAL358 4.5 17.5 1.0
N A:TRP359 4.5 11.5 1.0
C A:GLN353 4.5 11.8 1.0
HA A:SER400 4.6 14.6 1.0
H A:GLY399 4.7 17.0 1.0
HG2 A:GLU360 4.7 14.3 1.0
HA2 A:GLY356 4.7 14.2 1.0
CA A:GLY399 4.7 12.8 1.0
CA A:TRP359 4.8 10.8 1.0
N A:ASP357 4.8 14.0 1.0
OE1 A:GLU360 4.8 13.2 1.0
H A:GLU360 4.8 13.7 1.0
O A:LEU355 4.8 14.3 1.0
HG22 A:VAL358 4.8 17.5 1.0
N A:GLY398 4.9 13.1 1.0
C A:ARG397 4.9 13.4 1.0
C A:ASP357 4.9 13.4 1.0
N A:MET354 4.9 13.3 1.0
HB2 A:GLU360 4.9 13.9 1.0
N A:GLU360 5.0 11.4 1.0

Calcium binding site 2 out of 2 in 4x8b

Go back to Calcium Binding Sites List in 4x8b
Calcium binding site 2 out of 2 in the Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ergothioneine-Biosynthetic Sulfoxide Synthase Egtb, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca509

b:23.1
occ:1.00
O B:GLY356 2.6 19.6 1.0
O B:VAL358 2.6 18.3 1.0
O B:MET354 2.6 20.2 1.0
O B:GLY399 2.9 24.7 1.0
O B:HOH642 2.9 20.6 1.0
HA3 B:GLY398 3.1 21.4 1.0
OE2 B:GLU360 3.3 21.2 1.0
H B:VAL358 3.4 22.7 1.0
C B:MET354 3.5 18.7 1.0
O B:GLN353 3.5 21.7 1.0
HG3 B:GLU360 3.5 22.5 1.0
O B:GLY398 3.5 21.8 1.0
C B:GLY398 3.6 21.3 1.0
H B:GLY356 3.6 24.8 1.0
C B:GLY356 3.7 18.9 1.0
C B:VAL358 3.7 17.6 1.0
N B:GLY356 3.7 20.7 1.0
HA B:LEU355 3.8 23.6 1.0
CA B:GLY398 3.8 17.8 1.0
CD B:GLU360 3.9 22.1 1.0
HA B:MET354 3.9 23.4 0.7
HA B:MET354 4.0 23.5 0.3
N B:VAL358 4.0 18.9 1.0
O B:ARG397 4.0 19.9 1.0
C B:GLY399 4.0 21.9 1.0
C B:LEU355 4.1 21.7 1.0
HZ2 B:TRP299 4.1 25.2 1.0
HA B:TRP359 4.2 21.9 1.0
CG B:GLU360 4.2 18.7 1.0
N B:LEU355 4.2 19.9 1.0
N B:GLY399 4.2 18.8 1.0
CA B:LEU355 4.2 19.6 1.0
CA B:MET354 4.3 19.5 0.7
CA B:GLY356 4.3 19.7 1.0
CA B:MET354 4.3 19.6 0.3
HB2 B:ASP357 4.3 23.4 1.0
HA2 B:GLY398 4.4 21.4 1.0
HH21 B:ARG428 4.5 26.5 1.0
CA B:VAL358 4.5 17.6 1.0
HG23 B:VAL358 4.5 26.7 1.0
C B:GLN353 4.5 20.4 1.0
N B:TRP359 4.6 18.8 1.0
HA B:SER400 4.6 21.1 1.0
H B:GLY399 4.7 22.6 1.0
HA2 B:GLY356 4.7 23.7 1.0
H B:GLU360 4.7 23.0 1.0
CA B:GLY399 4.7 19.6 1.0
O B:LEU355 4.7 24.0 1.0
OE1 B:GLU360 4.8 21.2 1.0
HG22 B:VAL358 4.8 26.7 1.0
N B:ASP357 4.8 20.9 1.0
CA B:TRP359 4.8 18.3 1.0
HG2 B:GLU360 4.8 22.5 1.0
N B:GLY398 4.8 19.0 1.0
C B:ARG397 4.9 17.4 1.0
N B:MET354 4.9 20.4 1.0
C B:ASP357 4.9 19.7 1.0
HB2 B:GLU360 4.9 22.3 1.0
N B:GLU360 4.9 19.1 1.0
H B:LEU355 5.0 23.9 1.0

Reference:

K.V.Goncharenko, A.Vit, W.Blankenfeldt, F.P.Seebeck. Structure of the Sulfoxide Synthase Egtb From the Ergothioneine Biosynthetic Pathway. Angew.Chem.Int.Ed.Engl. 2015.
ISSN: ESSN 1521-3773
PubMed: 25597398
DOI: 10.1002/ANIE.201410045
Page generated: Sat Dec 12 05:11:44 2020

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