Calcium in PDB 6gyi: Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide

Protein crystallography data

The structure of Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide, PDB code: 6gyi was solved by G.J.Palm, D.Kohlhause, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.83 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.736, 59.781, 79.727, 90.00, 90.38, 90.00
R / Rfree (%) 19.2 / 24.3

Other elements in 6gyi:

The structure of Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide (pdb code 6gyi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide, PDB code: 6gyi:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6gyi

Go back to Calcium Binding Sites List in 6gyi
Calcium binding site 1 out of 4 in the Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:30.1
occ:1.00
O A:HOH396 2.2 39.3 1.0
O A:HOH325 2.3 26.5 1.0
O A:HOH385 2.4 27.8 1.0
O A:HOH301 2.4 35.4 1.0
O A:SER94 2.5 23.0 1.0
C A:SER94 3.7 21.9 1.0
OD1 A:ASP93 3.8 35.0 1.0
OD2 A:ASP93 4.2 24.0 1.0
NZ A:LYS85 4.3 37.2 1.0
N A:SER94 4.3 21.1 1.0
CG A:ASP93 4.4 25.0 1.0
CA A:SER94 4.5 22.1 1.0
CA A:VAL95 4.5 22.3 1.0
O A:HOH392 4.6 22.9 1.0
N A:VAL95 4.6 21.7 1.0
O A:HOH321 4.6 29.5 1.0
O A:HOH334 4.7 27.5 1.0
O A:HOH341 4.9 47.1 1.0
CB A:SER94 4.9 23.6 1.0
O A:HOH393 4.9 47.2 1.0

Calcium binding site 2 out of 4 in 6gyi

Go back to Calcium Binding Sites List in 6gyi
Calcium binding site 2 out of 4 in the Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:58.5
occ:1.00
O B:HOH308 2.4 25.8 1.0
OD2 B:ASP93 2.6 31.0 1.0
O B:HOH303 2.7 37.9 1.0
O B:SER94 2.8 24.1 1.0
OD1 B:ASP93 2.9 36.7 1.0
CG B:ASP93 3.1 33.1 1.0
C B:SER94 3.9 24.4 1.0
N B:LYS85 4.3 24.6 1.0
NZ B:LYS85 4.3 49.6 1.0
CA B:THR84 4.4 21.1 1.0
N B:SER94 4.5 26.7 1.0
CE B:LYS85 4.6 46.7 1.0
CB B:ASP93 4.6 29.5 1.0
O B:HIS83 4.6 19.1 1.0
O B:HOH368 4.7 47.1 1.0
CA B:VAL95 4.7 20.7 1.0
C B:THR84 4.7 22.1 1.0
N B:VAL95 4.8 21.4 1.0
CB B:VAL95 4.8 20.2 1.0
CA B:SER94 4.8 27.0 0.7
CA B:SER94 4.9 25.1 0.3

Calcium binding site 3 out of 4 in 6gyi

Go back to Calcium Binding Sites List in 6gyi
Calcium binding site 3 out of 4 in the Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca202

b:61.3
occ:1.00
O C:HOH307 2.3 27.6 1.0
O B:HOH332 2.3 43.2 1.0
OD2 C:ASP93 2.6 30.1 1.0
O C:SER94 2.7 24.8 1.0
OD1 C:ASP93 2.8 35.9 1.0
O B:HOH307 3.0 50.9 1.0
CG C:ASP93 3.0 32.1 1.0
O C:HOH308 3.2 46.4 1.0
C C:SER94 3.9 24.6 1.0
O C:HOH341 4.3 38.5 1.0
N C:SER94 4.4 27.3 1.0
CB C:ASP93 4.5 31.2 1.0
O B:HOH386 4.5 42.9 1.0
N C:LYS85 4.5 28.0 1.0
CA C:VAL95 4.6 21.3 1.0
CA C:THR84 4.6 24.6 1.0
N C:VAL95 4.7 21.9 1.0
O B:GLY105 4.7 52.5 1.0
CB C:VAL95 4.7 20.9 1.0
O C:HIS83 4.7 23.1 1.0
CD C:LYS85 4.8 40.1 1.0
CA C:SER94 4.8 25.7 0.3
CA C:SER94 4.8 25.4 0.7
OE1 B:GLN107 4.9 33.0 1.0
C C:THR84 5.0 26.5 1.0

Calcium binding site 4 out of 4 in 6gyi

Go back to Calcium Binding Sites List in 6gyi
Calcium binding site 4 out of 4 in the Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Azurin Fom Pseudomonas Aeruginosa Treated with Hydrosulfide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:30.6
occ:1.00
O A:HOH387 2.2 30.5 1.0
O D:HOH404 2.3 35.7 1.0
O A:HOH347 2.3 33.5 1.0
O D:HOH387 2.4 31.0 1.0
O D:SER94 2.5 27.0 1.0
O D:HOH312 2.5 27.0 1.0
O D:HOH347 2.5 34.8 1.0
C D:SER94 3.7 24.1 1.0
OD2 D:ASP93 4.2 26.5 1.0
N D:SER94 4.2 26.4 1.0
O A:GLY105 4.3 48.5 1.0
CB A:GLN107 4.4 35.8 1.0
OD1 D:ASP93 4.4 36.0 1.0
CA D:SER94 4.5 25.5 1.0
CG D:ASP93 4.5 31.5 1.0
NZ D:LYS85 4.5 36.0 1.0
O D:HOH392 4.6 22.7 1.0
N D:VAL95 4.6 22.9 1.0
CA D:VAL95 4.7 22.3 1.0
O D:HOH350 4.7 24.2 1.0
O D:HOH324 4.7 28.4 1.0
N A:GLN107 4.8 39.0 1.0
OE1 A:GLU106 4.9 41.0 1.0
CB D:SER94 4.9 27.7 1.0

Reference:

M.Strianese, G.J.Palm, D.Kohlhause, L.A.Ndamba, L.C.Tabares, C.Pellecchia. Azurin and Hs-: Towards Implementation of A Sensor For Hs-Detection. Eur J Inorg Chem 2019.
ISSN: ESSN 1099-0682
DOI: 10.1002/EJIC.201801399
Page generated: Sat Dec 12 06:08:46 2020

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