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Copper in PDB 5f7b: Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K

Enzymatic activity of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K

All present enzymatic activity of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K:
1.7.2.1;

Protein crystallography data

The structure of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K, PDB code: 5f7b was solved by Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, T.Masuda, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, M.E.P.Murphy, T.Inoue, S.Iwata, E.Mizohata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.836, 103.511, 147.246, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.7

Copper Binding Sites:

The binding sites of Copper atom in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K (pdb code 5f7b). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K, PDB code: 5f7b:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 5f7b

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Copper binding site 1 out of 6 in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:21.8
occ:1.00
 ND1 A:HIS145 2.0 19.9 1.0
ND1 A:HIS95 2.1 19.6 1.0
SG A:CYS136 2.1 19.4 1.0
SD A:MET150 2.5 20.7 1.0
CE1 A:HIS145 2.9 22.3 1.0
CE1 A:HIS95 3.0 21.7 1.0
CG A:HIS145 3.1 19.3 1.0
CG A:HIS95 3.1 20.1 1.0
CB A:CYS136 3.2 21.0 1.0
CE A:MET150 3.3 21.9 1.0
CB A:HIS95 3.5 20.3 1.0
CB A:HIS145 3.5 19.8 1.0
CA A:HIS95 3.8 20.8 1.0
CG A:MET150 3.9 17.4 1.0
NE2 A:HIS145 4.0 21.4 1.0
NE2 A:HIS95 4.1 21.8 1.0
CD2 A:HIS145 4.2 21.3 1.0
CD2 A:HIS95 4.2 19.7 1.0
O A:MET94 4.2 22.3 0.7
O A:MET94 4.2 22.6 0.3
CG A:PRO138 4.2 26.2 1.0
CB A:MET150 4.4 19.1 1.0
SD A:MET62 4.4 24.1 1.0
CA A:CYS136 4.6 17.9 1.0
N A:ASN96 4.6 21.9 1.0
CD A:PRO138 4.6 21.8 1.0
CA A:HIS145 4.8 19.5 1.0
C A:HIS95 4.8 22.9 1.0
CB A:MET62 4.9 20.8 1.0
N A:HIS95 4.9 22.4 1.0
C A:MET94 4.9 21.7 0.7
C A:MET94 5.0 22.7 0.3

Copper binding site 2 out of 6 in 5f7b

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Copper binding site 2 out of 6 in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:18.6
occ:1.00
 NE2 A:HIS100 1.9 17.6 1.0
NE2 C:HIS306 2.0 15.2 1.0
NE2 A:HIS135 2.1 17.6 1.0
O C:HOH748 2.1 15.6 0.3
O C:HOH748 2.2 14.1 0.7
CE1 A:HIS100 2.9 18.0 1.0
CD2 A:HIS100 3.0 17.0 1.0
CE1 C:HIS306 3.0 14.8 1.0
CD2 A:HIS135 3.0 18.2 1.0
CD2 C:HIS306 3.1 17.4 1.0
CE1 A:HIS135 3.1 18.4 1.0
OD2 A:ASP98 3.9 27.9 1.0
NE2 C:HIS255 4.0 20.2 1.0
ND1 A:HIS100 4.0 18.0 1.0
CG A:HIS100 4.1 16.1 1.0
ND1 C:HIS306 4.1 16.1 1.0
CG C:HIS306 4.2 15.5 1.0
CG A:HIS135 4.2 18.4 1.0
CD2 C:HIS255 4.2 19.4 1.0
ND1 A:HIS135 4.2 17.8 1.0
CE1 C:HIS255 4.5 23.2 1.0
CG A:ASP98 4.6 23.0 1.0
CG C:HIS255 4.8 16.8 1.0
OD1 A:ASP98 4.9 23.8 1.0
ND1 C:HIS255 4.9 21.5 1.0
O C:HOH735 4.9 24.2 1.0
CD2 C:LEU308 5.0 20.4 1.0
CD1 C:LEU308 5.0 21.4 1.0

Copper binding site 3 out of 6 in 5f7b

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Copper binding site 3 out of 6 in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:22.7
occ:1.00
 ND1 B:HIS145 2.0 20.9 1.0
ND1 B:HIS95 2.0 20.9 1.0
SG B:CYS136 2.2 20.8 1.0
SD B:MET150 2.6 20.9 1.0
CE1 B:HIS145 2.9 24.3 1.0
CE1 B:HIS95 3.0 18.6 1.0
CG B:HIS145 3.1 20.1 1.0
CG B:HIS95 3.1 23.0 1.0
CB B:CYS136 3.2 19.4 1.0
CE B:MET150 3.4 24.8 1.0
CB B:HIS95 3.4 20.9 1.0
CB B:HIS145 3.5 19.0 1.0
CA B:HIS95 3.8 20.2 1.0
CG B:MET150 3.9 19.3 1.0
NE2 B:HIS145 4.1 22.8 1.0
NE2 B:HIS95 4.1 21.8 1.0
CD2 B:HIS145 4.2 23.6 1.0
CD2 B:HIS95 4.2 21.7 1.0
O B:MET94 4.2 24.8 0.6
CG B:PRO138 4.3 27.5 1.0
O B:MET94 4.3 25.6 0.4
SD B:MET62 4.4 23.5 1.0
CB B:MET150 4.5 18.1 1.0
CA B:CYS136 4.6 19.5 1.0
N B:ASN96 4.6 20.5 1.0
CA B:HIS145 4.7 16.7 1.0
CD B:PRO138 4.8 23.9 1.0
C B:HIS95 4.8 23.4 1.0
N B:HIS95 4.9 24.5 1.0
CB B:MET62 4.9 19.1 1.0
C B:MET94 5.0 23.5 0.6

Copper binding site 4 out of 6 in 5f7b

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Copper binding site 4 out of 6 in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:19.6
occ:1.00
 O A:HOH712 2.0 25.7 0.3
NE2 A:HIS306 2.0 16.6 1.0
NE2 B:HIS100 2.0 17.0 1.0
NE2 B:HIS135 2.1 19.8 1.0
O A:HOH712 2.2 16.4 0.7
CE1 B:HIS100 2.9 16.4 1.0
CE1 A:HIS306 3.0 18.1 1.0
CD2 B:HIS135 3.0 17.2 1.0
CD2 A:HIS306 3.0 16.9 1.0
CE1 B:HIS135 3.1 17.8 1.0
CD2 B:HIS100 3.1 18.1 1.0
OD2 B:ASP98 3.9 29.5 1.0
NE2 A:HIS255 4.0 22.1 1.0
ND1 B:HIS100 4.1 17.8 1.0
ND1 A:HIS306 4.1 15.4 1.0
CD2 A:HIS255 4.1 22.8 1.0
ND1 B:HIS135 4.2 18.8 1.0
CG A:HIS306 4.2 15.8 1.0
CG B:HIS135 4.2 16.8 1.0
CG B:HIS100 4.2 17.3 1.0
CE1 A:HIS255 4.5 24.2 1.0
CG B:ASP98 4.5 23.9 1.0
OD1 B:ASP98 4.8 22.4 1.0
CG A:HIS255 4.8 20.4 1.0
CD2 A:LEU308 4.9 21.9 1.0
O A:HOH684 4.9 25.1 1.0
ND1 A:HIS255 4.9 24.0 1.0

Copper binding site 5 out of 6 in 5f7b

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Copper binding site 5 out of 6 in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:16.2
occ:1.00
 ND1 C:HIS95 2.0 14.5 1.0
ND1 C:HIS145 2.0 14.2 1.0
SG C:CYS136 2.1 16.0 1.0
SD C:MET150 2.5 16.4 1.0
CE1 C:HIS145 2.9 15.6 1.0
CE1 C:HIS95 2.9 16.6 1.0
CG C:HIS95 3.0 13.9 1.0
CG C:HIS145 3.1 16.1 1.0
CB C:CYS136 3.3 14.0 1.0
CE C:MET150 3.4 17.8 1.0
CB C:HIS95 3.4 15.3 1.0
CB C:HIS145 3.4 14.8 1.0
CA C:HIS95 3.9 15.5 1.0
CG C:MET150 4.0 15.1 1.0
NE2 C:HIS95 4.0 15.6 1.0
NE2 C:HIS145 4.1 15.2 1.0
CD2 C:HIS95 4.1 16.4 1.0
CD2 C:HIS145 4.2 15.7 1.0
CG C:PRO138 4.3 20.7 1.0
O C:MET94 4.3 18.1 1.0
CB C:MET150 4.4 13.9 1.0
SD C:MET62 4.4 19.2 1.0
N C:ASN96 4.6 14.8 1.0
CA C:CYS136 4.7 12.2 1.0
CD C:PRO138 4.7 17.1 1.0
CA C:HIS145 4.8 13.8 1.0
C C:HIS95 4.8 15.8 1.0
N C:HIS95 4.9 15.3 1.0
CB C:MET62 4.9 15.6 1.0

Copper binding site 6 out of 6 in 5f7b

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Copper binding site 6 out of 6 in the Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Resting State Structure of Cunir Form Alcaligenes Faecalis Determined at 293 K within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:15.3
occ:1.00
 O B:HOH740 2.0 14.1 0.3
NE2 C:HIS135 2.0 13.2 1.0
NE2 B:HIS306 2.0 13.8 1.0
NE2 C:HIS100 2.0 12.5 1.0
O B:HOH740 2.3 13.1 0.7
CE1 C:HIS100 2.9 12.5 1.0
CD2 C:HIS135 3.0 13.5 1.0
CE1 B:HIS306 3.0 12.6 1.0
CE1 C:HIS135 3.0 15.4 1.0
CD2 B:HIS306 3.0 15.1 1.0
CD2 C:HIS100 3.1 13.5 1.0
OD2 C:ASP98 3.9 24.2 1.0
NE2 B:HIS255 4.0 18.4 1.0
ND1 C:HIS100 4.1 13.9 1.0
ND1 C:HIS135 4.1 13.8 1.0
ND1 B:HIS306 4.1 12.5 1.0
CG C:HIS135 4.2 12.8 1.0
CG B:HIS306 4.2 13.3 1.0
CG C:HIS100 4.2 13.0 1.0
CD2 B:HIS255 4.4 19.0 1.0
CE1 B:HIS255 4.5 21.6 1.0
CG C:ASP98 4.6 19.6 1.0
OD1 C:ASP98 4.8 17.7 1.0
O B:HOH721 4.8 19.5 1.0
CG B:HIS255 4.9 16.1 1.0
ND1 B:HIS255 4.9 20.3 1.0
CD2 B:LEU308 4.9 18.7 1.0

Reference:

Y.Fukuda, K.M.Tse, T.Nakane, T.Nakatsu, M.Suzuki, M.Sugahara, S.Inoue, T.Masuda, F.Yumoto, N.Matsugaki, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, M.E.P.Murphy, T.Inoue, S.Iwata, E.Mizohata. Redox-Coupled Proton Transfer Mechanism in Nitrite Reductase Revealed By Femtosecond Crystallography Proc.Natl.Acad.Sci.Usa V. 113 2928 2016.
ISSN: ESSN 1091-6490
PubMed: 26929369
DOI: 10.1073/PNAS.1517770113
Page generated: Sun Dec 13 11:17:32 2020

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