Atomistry » Copper » PDB 5wbd-5z85 » 5ytl
Atomistry »
  Copper »
    PDB 5wbd-5z85 »
      5ytl »

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

Go back to Copper Binding Sites List in 5ytl
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

Go back to Copper Binding Sites List in 5ytl
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

Go back to Copper Binding Sites List in 5ytl
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

Go back to Copper Binding Sites List in 5ytl
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: Mon Jul 14 05:36:18 2025

Last articles

Hg in 1MMS
Hg in 1MIU
Hg in 1MUA
Hg in 1MOO
Hg in 1LZI
Hg in 1LZJ
Hg in 1KWP
Hg in 1M3W
Hg in 1LZ7
Hg in 1LZ0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy