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Copper in PDB 5ytl: Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal

Enzymatic activity of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal

All present enzymatic activity of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal, PDB code: 5ytl 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) 26.32 / 1.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.314, 115.314, 84.534, 90.00, 90.00, 120.00
R / Rfree (%) 11.3 / 14

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal (pdb code 5ytl). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal, PDB code: 5ytl:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 5ytl

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Copper binding site 1 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:15.1
occ:1.00
 ND1 A:HIS95 2.0 13.7 1.0
ND1 A:HIS143 2.1 14.4 1.0
SG A:CYS135 2.3 13.4 1.0
SD A:MET148 2.6 16.1 1.0
CE1 A:HIS95 2.9 13.5 1.0
CE1 A:HIS143 3.0 15.4 1.0
CG A:HIS95 3.1 13.6 1.0
CG A:HIS143 3.1 14.0 1.0
CB A:CYS135 3.2 13.6 1.0
CB A:HIS95 3.5 12.6 1.0
CB A:HIS143 3.5 13.1 1.0
CE A:MET148 3.5 14.3 1.0
CA A:HIS95 3.8 13.0 1.0
O A:PRO94 4.0 14.6 1.0
NE2 A:HIS143 4.1 15.2 1.0
NE2 A:HIS95 4.1 13.5 1.0
CG A:MET148 4.1 13.8 1.0
CD2 A:HIS143 4.2 15.0 1.0
CD2 A:HIS95 4.2 15.1 1.0
CB A:THR137 4.3 16.2 1.0
OG1 A:THR137 4.4 17.0 1.0
N A:SER96 4.5 13.4 1.0
CA A:HIS143 4.6 13.1 1.0
CB A:MET148 4.6 13.2 1.0
CE3 A:TRP63 4.6 14.2 1.0
CA A:CYS135 4.6 12.9 1.0
C A:HIS95 4.7 14.2 1.0
N A:HIS95 4.8 13.9 1.0
C A:PRO94 4.8 14.2 1.0

Copper binding site 2 out of 5 in 5ytl

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Copper binding site 2 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:14.6
occ:0.94
 NE2 A:HIS134 2.0 12.3 1.0
NE2 A:HIS100 2.0 11.6 1.0
O A:HOH627 2.2 19.5 0.6
O A:HOH627 2.4 20.5 0.4
CD2 A:HIS134 2.9 11.9 1.0
CE1 A:HIS100 2.9 12.9 1.0
CE1 A:HIS134 3.1 12.1 1.0
CD2 A:HIS100 3.1 11.9 1.0
OD2 A:ASP98 3.9 19.6 1.0
ND1 A:HIS100 4.1 12.8 1.0
CG A:HIS134 4.1 11.4 1.0
ND1 A:HIS134 4.1 12.1 1.0
CG A:HIS100 4.2 11.4 1.0
CG A:ASP98 4.3 17.0 1.0
OD1 A:ASP98 4.5 17.9 1.0
O A:HOH754 4.6 42.0 1.0
O A:HOH643 4.7 17.1 1.0
SD A:MET132 5.0 12.2 1.0

Copper binding site 3 out of 5 in 5ytl

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Copper binding site 3 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:23.5
occ:0.52
 NE2 A:HIS42 2.0 21.5 1.0
ND1 A:HIS83 2.1 24.9 1.0
O A:HOH730 2.7 44.1 1.0
O A:HOH503 2.9 35.0 1.0
CE1 A:HIS83 2.9 25.1 1.0
CE1 A:HIS42 2.9 23.0 1.0
CD2 A:HIS42 2.9 20.7 1.0
CG A:HIS83 3.0 21.4 1.0
CB A:HIS83 3.4 17.6 1.0
NE2 A:HIS83 3.9 24.1 1.0
CD2 A:HIS83 3.9 23.5 1.0
ND1 A:HIS42 4.0 21.2 1.0
CG A:HIS42 4.0 18.2 1.0
O A:HOH752 4.3 32.4 1.0
O A:HOH747 4.5 40.0 1.0
CG2 A:VAL36 4.6 19.4 1.0
O A:HOH769 4.9 56.3 1.0
CA A:HIS83 5.0 15.1 1.0

Copper binding site 4 out of 5 in 5ytl

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Copper binding site 4 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:18.1
occ:0.20
 SD A:MET270 2.4 42.3 0.7
SD A:MET270 2.5 19.9 0.3
CE A:MET270 2.5 19.3 0.3
CE A:MET270 3.1 52.1 0.7
CG A:MET270 3.3 31.1 0.7
CG A:MET270 3.5 19.9 0.3
CB A:MET270 3.6 16.9 0.3
CB A:MET270 3.8 19.6 0.7
CA A:MET270 5.0 14.9 0.3

Copper binding site 5 out of 5 in 5ytl

Go back to Copper Binding Sites List in 5ytl
Copper binding site 5 out of 5 in the Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase Determined with An Anaerobically Manipulated Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:31.7
occ:0.41
 OD2 A:ASP167 2.0 21.9 1.0
O A:HOH508 2.3 43.5 1.0
O A:HOH504 2.6 53.6 1.0
CG A:ASP167 2.8 21.6 1.0
OD1 A:ASP167 3.0 25.0 1.0
O A:GLY225 4.0 21.7 1.0
N A:LYS227 4.0 16.5 1.0
O A:GLU165 4.1 23.2 1.0
CB A:ASP167 4.2 19.1 1.0
CA A:GLU226 4.4 17.6 1.0
C A:GLU226 4.7 16.7 1.0
CB A:LYS227 4.7 19.1 1.0
C A:GLY225 4.9 19.0 1.0
O A:HOH657 5.0 57.5 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 05:26:12 2024

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