Calcium in PDB 6hbe: Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01

Protein crystallography data

The structure of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01, PDB code: 6hbe was solved by D.J.Opperman, F.M.Ferroni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.51 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.692, 110.553, 88.810, 90.00, 107.51, 90.00
R / Rfree (%) 16.1 / 19

Other elements in 6hbe:

The structure of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 also contains other interesting chemical elements:

Copper (Cu) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 (pdb code 6hbe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01, PDB code: 6hbe:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6hbe

Go back to Calcium Binding Sites List in 6hbe
Calcium binding site 1 out of 3 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:23.4
occ:1.00
O A:HOH763 2.3 38.5 1.0
OE1 A:GLN37 2.4 25.1 1.0
O A:HOH646 2.4 27.2 1.0
OD1 A:ASP36 2.5 24.1 1.0
O A:HOH688 2.5 24.6 1.0
O B:HOH639 2.5 28.2 1.0
O A:HOH675 2.6 24.7 1.0
CG A:ASP36 3.5 25.6 1.0
CD A:GLN37 3.5 26.0 1.0
OD2 A:ASP36 3.9 24.2 1.0
O A:HOH736 4.0 36.0 1.0
NE2 A:GLN37 4.1 26.9 1.0
OD1 B:ASP380 4.2 28.7 1.0
O A:HOH713 4.4 27.7 1.0
OD2 A:ASP189 4.5 24.5 1.0
N A:GLN37 4.6 23.5 1.0
O B:VAL378 4.7 24.2 1.0
OD1 A:ASP189 4.8 27.1 1.0
CG A:GLN37 4.8 25.6 1.0
CB A:ASP36 4.8 23.9 1.0
O A:ASN184 4.9 20.5 1.0
CG B:ASP380 4.9 25.4 1.0
OD2 B:ASP380 4.9 25.6 1.0
CB A:GLN37 4.9 25.0 1.0

Calcium binding site 2 out of 3 in 6hbe

Go back to Calcium Binding Sites List in 6hbe
Calcium binding site 2 out of 3 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:24.8
occ:1.00
O B:HOH816 2.3 34.4 1.0
OE1 B:GLN37 2.4 24.0 1.0
O B:HOH694 2.4 21.2 1.0
O B:HOH628 2.5 26.9 1.0
O C:HOH615 2.5 29.0 1.0
OD1 B:ASP36 2.5 24.6 1.0
O B:HOH727 2.6 26.6 1.0
CD B:GLN37 3.5 25.5 1.0
CG B:ASP36 3.6 26.5 1.0
OD2 B:ASP36 3.9 24.8 1.0
NE2 B:GLN37 4.0 25.3 1.0
OD1 C:ASP380 4.3 27.8 1.0
O B:HOH661 4.4 28.6 1.0
OD2 B:ASP189 4.4 25.4 1.0
N B:GLN37 4.6 23.8 1.0
O B:HOH876 4.7 40.3 1.0
CG B:GLN37 4.8 25.6 1.0
O B:HOH866 4.8 33.4 1.0
O C:VAL378 4.8 24.3 1.0
OD1 B:ASP189 4.9 27.3 1.0
O B:ASN184 4.9 20.3 1.0
CB B:ASP36 4.9 23.3 1.0
CB B:GLN37 4.9 24.0 1.0

Calcium binding site 3 out of 3 in 6hbe

Go back to Calcium Binding Sites List in 6hbe
Calcium binding site 3 out of 3 in the Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cu-Containing Nitrite Reductase (Nirk) From Thermus Scotoductus Sa-01 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:22.4
occ:1.00
O C:HOH759 2.1 31.3 1.0
O C:HOH765 2.2 21.7 1.0
O C:HOH659 2.4 27.8 1.0
OE1 C:GLN37 2.4 24.4 1.0
OD1 C:ASP36 2.4 24.9 1.0
O A:HOH632 2.5 29.1 1.0
O C:HOH723 2.6 25.0 1.0
CG C:ASP36 3.5 25.8 1.0
CD C:GLN37 3.5 24.9 1.0
OD2 C:ASP36 3.8 25.0 1.0
NE2 C:GLN37 4.0 26.1 1.0
OD1 A:ASP380 4.1 30.8 1.0
O C:HOH685 4.4 30.1 1.0
OD2 C:ASP189 4.5 26.1 1.0
N C:GLN37 4.6 24.6 1.0
O A:VAL378 4.7 23.3 1.0
CG C:GLN37 4.8 24.7 1.0
OD1 C:ASP189 4.8 25.1 1.0
CB C:ASP36 4.8 24.9 1.0
CG A:ASP380 4.9 30.9 1.0
OD2 A:ASP380 4.9 31.5 1.0
CB C:GLN37 5.0 26.0 1.0
O C:ASN184 5.0 21.6 1.0

Reference:

D.J.Opperman, D.H.Murgida, S.D.Dalosto, C.D.Brondino, F.M.Ferroni. A Three-Domain Copper-Nitrite Reductase with A Unique Sensing Loop. Iucrj V. 6 248 2019.
ISSN: ESSN 2052-2525
PubMed: 30867922
DOI: 10.1107/S2052252519000241
Page generated: Sat Dec 12 06:09:32 2020

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