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Copper in PDB 2afn: Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc

Enzymatic activity of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc

All present enzymatic activity of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc:
1.7.99.3;

Protein crystallography data

The structure of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc, PDB code: 2afn was solved by M.E.P.Murphy, E.T.Adman, S.Turley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.035, 103.610, 146.900, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 22.3

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc (pdb code 2afn). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc, PDB code: 2afn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2afn

Go back to Copper Binding Sites List in 2afn
Copper binding site 1 out of 6 in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:18.1
occ:1.00
 ND1 A:HIS145 2.1 14.0 1.0
SG A:CYS136 2.1 13.2 1.0
ND1 A:HIS95 2.2 17.6 1.0
SD A:MET150 2.6 15.2 1.0
CE1 A:HIS145 3.0 13.6 1.0
CG A:HIS145 3.1 14.5 1.0
CB A:CYS136 3.1 10.6 1.0
CE1 A:HIS95 3.2 10.9 1.0
CG A:HIS95 3.2 14.0 1.0
CE A:MET150 3.4 10.3 1.0
CB A:HIS145 3.4 10.6 1.0
CB A:HIS95 3.5 13.5 1.0
CA A:HIS95 3.9 13.9 1.0
CG A:MET150 4.0 6.4 1.0
CG A:PRO138 4.1 15.6 1.0
NE2 A:HIS145 4.2 14.9 1.0
CD2 A:HIS145 4.2 14.1 1.0
O A:MET94 4.3 16.7 1.0
NE2 A:HIS95 4.3 14.7 1.0
CD2 A:HIS95 4.4 13.2 1.0
SD A:MET62 4.5 12.8 1.0
CB A:MET150 4.5 3.9 1.0
CD A:PRO138 4.5 13.3 1.0
CA A:CYS136 4.6 11.3 1.0
CA A:HIS145 4.7 12.9 1.0
N A:ASN96 4.7 13.8 1.0
C A:HIS95 4.9 13.7 1.0
N A:HIS95 4.9 16.7 1.0
CB A:MET62 4.9 11.1 1.0

Copper binding site 2 out of 6 in 2afn

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Copper binding site 2 out of 6 in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:20.7
occ:1.00
 NE2 A:HIS100 2.0 12.6 1.0
NE2 A:HIS135 2.1 15.8 1.0
O A:HOH503 2.1 22.8 1.0
NE2 B:HIS306 2.1 17.2 1.0
CE1 A:HIS100 2.9 10.5 1.0
CE1 B:HIS306 3.0 11.9 1.0
CE1 A:HIS135 3.0 15.9 1.0
CD2 A:HIS100 3.2 11.2 1.0
CD2 A:HIS135 3.2 15.7 1.0
CD2 B:HIS306 3.2 14.6 1.0
OD2 A:ASP98 3.4 29.1 1.0
ND1 A:HIS100 4.1 12.7 1.0
NE2 B:HIS255 4.1 18.7 1.0
ND1 A:HIS135 4.2 16.1 1.0
ND1 B:HIS306 4.2 16.2 1.0
CG A:HIS100 4.2 11.2 1.0
CD2 B:HIS255 4.3 20.3 1.0
CG A:HIS135 4.3 15.4 1.0
CG B:HIS306 4.3 15.3 1.0
CG A:ASP98 4.4 23.3 1.0
CE1 B:HIS255 4.6 20.2 1.0
O B:HOH536 4.8 12.9 1.0
OD1 A:ASP98 4.8 25.8 1.0
CG1 B:ILE257 4.9 17.4 1.0
CG B:HIS255 4.9 17.6 1.0
CD2 B:LEU308 5.0 15.1 1.0

Copper binding site 3 out of 6 in 2afn

Go back to Copper Binding Sites List in 2afn
Copper binding site 3 out of 6 in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:24.2
occ:1.00
 ND1 B:HIS145 1.9 18.9 1.0
SG B:CYS136 2.0 17.6 1.0
ND1 B:HIS95 2.0 17.2 1.0
SD B:MET150 2.7 19.7 1.0
CE1 B:HIS145 2.7 22.3 1.0
CG B:HIS95 3.0 18.1 1.0
CG B:HIS145 3.1 19.0 1.0
CE1 B:HIS95 3.1 15.7 1.0
CB B:CYS136 3.2 19.5 1.0
CB B:HIS95 3.3 21.2 1.0
CE B:MET150 3.5 16.9 1.0
CB B:HIS145 3.6 14.5 1.0
CA B:HIS95 3.7 23.4 1.0
NE2 B:HIS145 3.9 20.8 1.0
CG B:PRO138 4.0 24.5 1.0
CG B:MET150 4.0 20.8 1.0
CD2 B:HIS145 4.1 17.7 1.0
O B:MET94 4.1 23.7 1.0
CD2 B:HIS95 4.2 18.7 1.0
NE2 B:HIS95 4.2 18.5 1.0
SD B:MET62 4.4 18.0 1.0
CD B:PRO138 4.5 22.6 1.0
CB B:MET150 4.5 18.3 1.0
N B:ASN96 4.6 22.4 1.0
CA B:CYS136 4.6 20.1 1.0
C B:HIS95 4.8 23.6 1.0
N B:HIS95 4.8 24.3 1.0
CA B:HIS145 4.8 17.1 1.0
C B:MET94 4.8 25.1 1.0
CB B:MET62 4.9 15.7 1.0

Copper binding site 4 out of 6 in 2afn

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Copper binding site 4 out of 6 in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:26.0
occ:1.00
 NE2 B:HIS135 2.0 20.9 1.0
NE2 B:HIS100 2.1 18.2 1.0
O B:HOH503 2.1 25.2 1.0
NE2 C:HIS306 2.2 19.6 1.0
CE1 B:HIS100 2.9 17.2 1.0
CE1 B:HIS135 2.9 17.9 1.0
CE1 C:HIS306 3.1 17.1 1.0
CD2 B:HIS135 3.2 21.2 1.0
CD2 B:HIS100 3.2 15.1 1.0
CD2 C:HIS306 3.3 16.5 1.0
OD2 B:ASP98 3.3 29.5 1.0
NE2 C:HIS255 3.7 26.1 1.0
CD2 C:HIS255 4.0 23.6 1.0
ND1 B:HIS100 4.1 17.1 1.0
ND1 B:HIS135 4.1 18.2 1.0
CG B:HIS135 4.3 17.4 1.0
CG B:HIS100 4.3 16.2 1.0
ND1 C:HIS306 4.3 18.1 1.0
CG B:ASP98 4.3 25.8 1.0
CG C:HIS306 4.4 14.7 1.0
CE1 C:HIS255 4.4 22.9 1.0
O B:HOH659 4.7 21.6 1.0
CG C:HIS255 4.8 22.0 1.0
OD1 B:ASP98 4.9 30.2 1.0

Copper binding site 5 out of 6 in 2afn

Go back to Copper Binding Sites List in 2afn
Copper binding site 5 out of 6 in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:24.7
occ:1.00
 ND1 C:HIS145 1.9 20.1 1.0
ND1 C:HIS95 2.1 22.4 1.0
SG C:CYS136 2.2 21.4 1.0
SD C:MET150 2.6 20.4 1.0
CE1 C:HIS145 2.9 17.8 1.0
CG C:HIS145 3.0 16.6 1.0
CE1 C:HIS95 3.0 16.3 1.0
CG C:HIS95 3.1 20.7 1.0
CB C:CYS136 3.2 19.7 1.0
CE C:MET150 3.4 11.3 1.0
CB C:HIS145 3.5 16.4 1.0
CB C:HIS95 3.5 19.1 1.0
CA C:HIS95 3.8 18.8 1.0
CG C:MET150 4.0 14.7 1.0
NE2 C:HIS145 4.1 17.3 1.0
CG C:PRO138 4.1 28.5 1.0
CD2 C:HIS145 4.1 15.4 1.0
O C:MET94 4.2 18.5 1.0
NE2 C:HIS95 4.2 19.1 1.0
CD2 C:HIS95 4.2 16.6 1.0
SD C:MET62 4.5 23.1 1.0
CB C:MET150 4.5 13.6 1.0
N C:ASN96 4.6 20.6 1.0
CA C:CYS136 4.6 18.9 1.0
CA C:HIS145 4.7 18.0 1.0
CD C:PRO138 4.8 24.3 1.0
C C:HIS95 4.8 18.7 1.0
N C:HIS95 4.9 19.7 1.0
CB C:MET62 4.9 21.3 1.0
C C:MET94 5.0 20.6 1.0

Copper binding site 6 out of 6 in 2afn

Go back to Copper Binding Sites List in 2afn
Copper binding site 6 out of 6 in the Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:23.6
occ:1.00
 NE2 C:HIS100 2.0 13.2 1.0
NE2 A:HIS306 2.1 17.9 1.0
NE2 C:HIS135 2.3 20.8 1.0
O A:HOH504 2.3 24.0 1.0
CE1 C:HIS100 2.8 11.6 1.0
CE1 A:HIS306 3.0 17.2 1.0
CE1 C:HIS135 3.1 17.4 1.0
CD2 C:HIS100 3.1 11.8 1.0
CD2 A:HIS306 3.3 15.2 1.0
CD2 C:HIS135 3.4 19.1 1.0
OD2 C:ASP98 3.6 31.7 1.0
NE2 A:HIS255 3.9 12.7 1.0
ND1 C:HIS100 4.0 10.6 1.0
CD2 A:HIS255 4.1 13.6 1.0
ND1 A:HIS306 4.2 18.7 1.0
CG C:HIS100 4.2 12.2 1.0
ND1 C:HIS135 4.3 21.0 1.0
CG A:HIS306 4.4 17.2 1.0
CG C:ASP98 4.4 26.3 1.0
CE1 A:HIS255 4.4 13.4 1.0
CG C:HIS135 4.5 20.2 1.0
CG A:HIS255 4.8 15.0 1.0
OD1 C:ASP98 4.8 27.8 1.0
O C:HOH503 4.8 24.0 1.0
ND1 A:HIS255 4.9 12.2 1.0
CG1 A:ILE257 5.0 16.9 1.0

Reference:

M.E.Murphy, S.Turley, M.Kukimoto, M.Nishiyama, S.Horinouchi, H.Sasaki, M.Tanokura, E.T.Adman. Structure of Alcaligenes Faecalis Nitrite Reductase and A Copper Site Mutant, M150E, That Contains Zinc. Biochemistry V. 34 12107 1995.
ISSN: ISSN 0006-2960
PubMed: 7547950
DOI: 10.1021/BI00038A003
Page generated: Tue Jul 30 23:07:36 2024

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