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Copper in PDB 5ytn: C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide

Enzymatic activity of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide

All present enzymatic activity of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide:
1.7.2.1;

Protein crystallography data

The structure of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide, PDB code: 5ytn was solved by Y.Fukuda, T.Matsusaki, K.M.Tse, E.Mizohata, M.E.P.Murphy, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.50 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.566, 115.566, 84.013, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 22.7

Copper Binding Sites:

The binding sites of Copper atom in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide (pdb code 5ytn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide, PDB code: 5ytn:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5ytn

Go back to Copper Binding Sites List in 5ytn
Copper binding site 1 out of 3 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:6.5
occ:0.10
 ND1 A:HIS95 2.1 12.8 1.0
ND1 A:HIS143 2.1 10.2 1.0
SD A:MET148 2.2 18.2 1.0
CE1 A:HIS95 2.9 8.4 1.0
CG A:HIS95 3.0 13.1 1.0
CE1 A:HIS143 3.1 10.0 1.0
CG A:HIS143 3.1 9.7 1.0
CB A:ALA135 3.3 11.3 1.0
CB A:HIS143 3.4 7.7 1.0
CB A:HIS95 3.5 10.6 1.0
CE A:MET148 3.5 14.8 1.0
CG A:MET148 3.6 10.9 1.0
NE2 A:HIS95 4.0 9.2 1.0
CD2 A:HIS95 4.0 10.8 1.0
CA A:HIS95 4.1 9.0 1.0
CE3 A:TRP63 4.1 8.9 1.0
NE2 A:HIS143 4.2 13.1 1.0
CB A:MET148 4.2 10.0 1.0
CD2 A:HIS143 4.2 8.6 1.0
CA A:HIS143 4.3 9.9 1.0
O A:PRO94 4.5 12.9 1.0
CZ3 A:TRP63 4.6 13.8 1.0
CA A:ALA135 4.8 13.0 1.0
N A:SER96 4.9 14.2 1.0
O A:HIS143 5.0 10.0 1.0
OG1 A:THR137 5.0 11.4 1.0

Copper binding site 2 out of 3 in 5ytn

Go back to Copper Binding Sites List in 5ytn
Copper binding site 2 out of 3 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:10.8
occ:1.00
 NE2 A:HIS100 2.0 8.2 1.0
NE2 A:HIS134 2.0 9.3 1.0
O2 A:PEO405 2.1 9.6 0.2
O1 A:PEO405 2.2 9.8 0.8
O2 A:PEO405 2.7 16.7 0.8
CE1 A:HIS100 2.9 10.1 1.0
CD2 A:HIS134 2.9 12.3 1.0
CE1 A:HIS134 3.1 15.1 1.0
CD2 A:HIS100 3.1 11.9 1.0
O1 A:PEO405 3.5 10.9 0.2
ND1 A:HIS100 4.1 13.1 1.0
OD2 A:ASP98 4.1 13.9 1.0
CG A:HIS134 4.1 6.7 1.0
ND1 A:HIS134 4.1 7.1 1.0
CG A:HIS100 4.2 9.0 1.0
CG A:ASP98 4.5 10.6 1.0
O A:HOH501 4.6 13.3 0.8
OD1 A:ASP98 4.7 11.6 1.0
O A:HOH674 4.7 11.9 1.0

Copper binding site 3 out of 3 in 5ytn

Go back to Copper Binding Sites List in 5ytn
Copper binding site 3 out of 3 in the C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of C135A Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Peroxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:16.0
occ:0.80
 ND1 A:HIS83 2.0 15.2 1.0
NE2 A:HIS42 2.1 13.7 1.0
CE1 A:HIS83 2.9 22.1 1.0
CD2 A:HIS42 2.9 12.2 1.0
CG A:HIS83 3.1 13.0 1.0
CE1 A:HIS42 3.1 17.5 1.0
CB A:HIS83 3.5 10.9 1.0
NE2 A:HIS83 4.0 14.9 1.0
CG A:HIS42 4.1 10.5 1.0
CD2 A:HIS83 4.1 15.8 1.0
ND1 A:HIS42 4.1 13.9 1.0
O A:HOH625 4.3 22.2 1.0
O A:HOH782 4.3 12.6 1.0
CG2 A:VAL36 4.6 10.2 1.0

Reference:

Y.Fukuda, T.Matsusaki, K.M.Tse, E.Mizohata, M.E.P.Murphy, T.Inoue. Crystallographic Study of Dioxygen Chemistry in A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans. Acta Crystallogr D Struct V. 74 769 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30082512
DOI: 10.1107/S2059798318010082
Page generated: Wed Jul 31 05:26:13 2024

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