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Magnesium in PDB 2a3t: Cu-Containing Nitrite Reductase

Enzymatic activity of Cu-Containing Nitrite Reductase

All present enzymatic activity of Cu-Containing Nitrite Reductase:
1.7.2.1;

Protein crystallography data

The structure of Cu-Containing Nitrite Reductase, PDB code: 2a3t was solved by F.Jacobson, H.Guo, K.Olesen, M.Okvist, R.Neutze, L.Sjolin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.50 / 1.85
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 72.436, 72.436, 148.089, 90.00, 90.00, 120.00
R / Rfree (%) 14.9 / 17.6

Other elements in 2a3t:

The structure of Cu-Containing Nitrite Reductase also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cu-Containing Nitrite Reductase (pdb code 2a3t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cu-Containing Nitrite Reductase, PDB code: 2a3t:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2a3t

Go back to Magnesium Binding Sites List in 2a3t
Magnesium binding site 1 out of 3 in the Cu-Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cu-Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:20.8
occ:1.00
O A:HOH557 2.0 20.7 1.0
OD1 A:ASP220 2.1 23.2 1.0
O A:HOH559 2.1 25.6 1.0
OG1 A:THR224 2.2 20.1 1.0
CB A:THR224 3.2 23.1 1.0
CG A:ASP220 3.2 23.3 1.0
CB A:ASP220 3.8 25.5 1.0
OD1 A:ASP222 4.0 30.5 1.0
CG2 A:THR224 4.1 23.6 1.0
OD2 A:ASP222 4.2 29.9 1.0
OD2 A:ASP220 4.3 22.0 1.0
CA A:THR224 4.4 22.7 1.0
C A:THR224 4.4 22.7 1.0
O A:THR224 4.5 23.1 1.0
CG A:ASP222 4.6 31.0 1.0
O A:TYR225 4.6 20.9 1.0
N A:TYR225 5.0 22.3 1.0
N A:THR224 5.0 23.8 1.0

Magnesium binding site 2 out of 3 in 2a3t

Go back to Magnesium Binding Sites List in 2a3t
Magnesium binding site 2 out of 3 in the Cu-Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cu-Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:33.5
occ:1.00
O A:HOH728 2.1 32.7 1.0
O A:HOH726 2.1 38.3 1.0
OE1 A:GLU233 4.0 37.6 1.0
OE2 A:GLU233 4.3 35.0 1.0
O A:ARG227 4.5 26.6 1.0
CD A:GLU233 4.6 34.5 1.0
O A:HOH660 5.0 34.8 1.0

Magnesium binding site 3 out of 3 in 2a3t

Go back to Magnesium Binding Sites List in 2a3t
Magnesium binding site 3 out of 3 in the Cu-Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cu-Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:41.4
occ:1.00
O A:HOH727 2.0 36.1 1.0
O A:HOH732 2.0 39.1 1.0
O A:HOH705 2.3 30.8 1.0
O A:HOH562 2.3 20.6 1.0
O A:HOH531 3.9 25.2 1.0
O A:HOH715 4.0 33.5 1.0
OD2 A:ASP96 4.2 22.9 1.0
OD1 A:ASP96 4.2 23.8 1.0
O A:GLU74 4.4 19.5 1.0
CG A:ASP96 4.6 23.1 1.0
OE1 A:GLU74 4.7 30.6 1.0
O A:HOH717 4.9 45.9 1.0

Reference:

F.Jacobson, H.Guo, K.Olesen, M.Okvist, R.Neutze, L.Sjolin. Structures of the Oxidized and Reduced Forms of Nitrite Reductase From Rhodobacter Sphaeroides 2.4.3 at High pH: Changes in the Interactions of the Type 2 Copper. Acta Crystallogr.,Sect.D V. 61 1190 2005.
ISSN: ISSN 0907-4449
PubMed: 16131751
DOI: 10.1107/S0907444905017488
Page generated: Mon Dec 14 07:13:06 2020

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