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Copper in PDB 2pp7: Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)

Enzymatic activity of Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)

All present enzymatic activity of Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound):
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound), PDB code: 2pp7 was solved by E.I.Tocheva, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.111, 101.833, 145.508, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) (pdb code 2pp7). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound), PDB code: 2pp7:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2pp7

Go back to Copper Binding Sites List in 2pp7
Copper binding site 1 out of 6 in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)


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 Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:13.7
occ:1.00
 ND1 A:HIS145 2.0 11.7 1.0
ND1 A:HIS95 2.1 11.8 1.0
SG A:CYS136 2.2 13.0 1.0
SD A:MET150 2.4 13.2 1.0
CE1 A:HIS145 2.9 13.4 1.0
CE1 A:HIS95 3.0 13.8 1.0
CG A:HIS145 3.1 11.8 1.0
CG A:HIS95 3.1 14.2 1.0
CB A:CYS136 3.2 13.3 1.0
CE A:MET150 3.2 12.3 1.0
CB A:HIS95 3.5 12.9 1.0
CB A:HIS145 3.6 11.8 1.0
CG A:MET150 3.8 11.9 1.0
CA A:HIS95 3.9 13.1 1.0
NE2 A:HIS145 4.0 13.3 1.0
NE2 A:HIS95 4.1 13.7 1.0
CD2 A:HIS145 4.2 12.2 1.0
CD2 A:HIS95 4.2 12.6 1.0
CB A:MET150 4.3 11.2 1.0
CG A:PRO138 4.3 13.6 1.0
O A:MET94 4.3 14.1 1.0
SD A:MET62 4.4 16.6 1.0
CA A:CYS136 4.6 12.1 1.0
CD A:PRO138 4.6 14.7 1.0
N A:ASN96 4.6 12.6 1.0
CB A:MET62 4.7 14.8 1.0
CA A:HIS145 4.7 12.0 1.0
C A:HIS95 4.8 12.8 1.0
N A:HIS95 4.9 13.3 1.0

Copper binding site 2 out of 6 in 2pp7

Go back to Copper Binding Sites List in 2pp7
Copper binding site 2 out of 6 in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)


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 Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:13.4
occ:1.00
 NE2 A:HIS100 2.0 10.9 1.0
NE2 B:HIS306 2.0 11.9 1.0
NE2 A:HIS135 2.1 11.4 1.0
OXT A:ACT503 2.2 34.8 1.0
O A:ACT503 2.4 34.2 1.0
C A:ACT503 2.5 34.8 1.0
CE1 A:HIS100 2.9 10.2 1.0
CE1 B:HIS306 2.9 10.0 1.0
CD2 A:HIS135 3.0 12.1 1.0
CD2 A:HIS100 3.1 12.0 1.0
CE1 A:HIS135 3.1 12.6 1.0
CD2 B:HIS306 3.1 12.6 1.0
CH3 A:ACT503 3.8 34.7 1.0
ND1 A:HIS100 4.1 10.6 1.0
ND1 B:HIS306 4.1 10.8 1.0
NE2 B:HIS255 4.1 15.2 1.0
O A:HOH2377 4.2 41.0 1.0
CG A:HIS135 4.2 12.2 1.0
CG A:HIS100 4.2 10.0 1.0
ND1 A:HIS135 4.2 11.1 1.0
CG B:HIS306 4.2 11.4 1.0
CE1 B:HIS255 4.3 15.6 1.0
CD2 B:HIS255 4.5 15.1 1.0
ND1 B:HIS255 4.8 14.3 1.0
CD2 B:LEU308 4.8 12.6 1.0
CG B:HIS255 4.9 12.9 1.0

Copper binding site 3 out of 6 in 2pp7

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Copper binding site 3 out of 6 in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)


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 Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:15.8
occ:1.00
 ND1 B:HIS95 2.1 15.3 1.0
ND1 B:HIS145 2.1 13.7 1.0
SG B:CYS136 2.2 15.3 1.0
SD B:MET150 2.5 14.5 1.0
CE1 B:HIS145 3.0 17.1 1.0
CE1 B:HIS95 3.0 14.3 1.0
CG B:HIS95 3.1 15.8 1.0
CB B:CYS136 3.1 13.5 1.0
CG B:HIS145 3.2 15.0 1.0
CE B:MET150 3.3 15.5 1.0
CB B:HIS95 3.5 15.2 1.0
CB B:HIS145 3.6 13.9 1.0
CA B:HIS95 3.8 15.5 1.0
CG B:MET150 3.9 14.1 1.0
NE2 B:HIS145 4.1 15.8 1.0
NE2 B:HIS95 4.1 13.4 1.0
CG B:PRO138 4.2 16.8 1.0
CD2 B:HIS95 4.2 15.9 1.0
CD2 B:HIS145 4.2 16.2 1.0
O B:MET94 4.3 16.9 1.0
SD B:MET62 4.4 16.5 1.0
CB B:MET150 4.4 13.3 1.0
CA B:CYS136 4.6 13.6 1.0
CD B:PRO138 4.6 15.3 1.0
N B:ASN96 4.6 15.2 1.0
CA B:HIS145 4.8 14.2 1.0
C B:HIS95 4.8 15.5 1.0
CB B:MET62 4.8 15.0 1.0
N B:HIS95 4.9 15.9 1.0
C B:MET94 5.0 16.4 1.0

Copper binding site 4 out of 6 in 2pp7

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Copper binding site 4 out of 6 in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)


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 Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:15.5
occ:1.00
 NE2 B:HIS100 2.0 11.4 1.0
NE2 B:HIS135 2.1 15.8 1.0
NE2 C:HIS306 2.1 11.9 1.0
OXT B:ACT503 2.1 34.2 1.0
O B:ACT503 2.4 33.2 1.0
C B:ACT503 2.5 33.2 1.0
CE1 B:HIS100 2.9 13.1 1.0
CD2 B:HIS135 3.0 13.7 1.0
CE1 C:HIS306 3.0 13.7 1.0
CD2 B:HIS100 3.1 13.5 1.0
CE1 B:HIS135 3.1 14.1 1.0
CD2 C:HIS306 3.1 13.4 1.0
CH3 B:ACT503 3.8 32.7 1.0
ND1 B:HIS100 4.0 13.7 1.0
CG B:HIS100 4.2 13.0 1.0
ND1 C:HIS306 4.2 12.3 1.0
ND1 B:HIS135 4.2 13.0 1.0
CG B:HIS135 4.2 13.9 1.0
CG C:HIS306 4.2 12.7 1.0
NE2 C:HIS255 4.2 17.9 1.0
O B:HOH2370 4.3 41.6 1.0
CE1 C:HIS255 4.4 18.1 1.0
CD2 C:HIS255 4.6 17.1 1.0
ND1 C:HIS255 4.8 16.9 1.0
CD2 C:LEU308 4.9 14.7 1.0
O C:HOH2206 5.0 18.4 1.0
CG C:HIS255 5.0 16.0 1.0

Copper binding site 5 out of 6 in 2pp7

Go back to Copper Binding Sites List in 2pp7
Copper binding site 5 out of 6 in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)


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 Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:18.4
occ:1.00
 ND1 C:HIS145 2.1 18.9 1.0
ND1 C:HIS95 2.1 15.7 1.0
SG C:CYS136 2.2 15.9 1.0
SD C:MET150 2.5 16.7 1.0
CE1 C:HIS145 3.0 17.4 1.0
CE1 C:HIS95 3.1 18.6 1.0
CG C:HIS145 3.1 17.3 1.0
CB C:CYS136 3.1 15.7 1.0
CG C:HIS95 3.1 18.4 1.0
CE C:MET150 3.3 17.4 1.0
CB C:HIS95 3.5 18.6 1.0
CB C:HIS145 3.5 15.9 1.0
CA C:HIS95 3.8 18.2 1.0
CG C:MET150 3.8 15.2 1.0
NE2 C:HIS145 4.1 17.0 1.0
CG C:PRO138 4.2 16.5 1.0
CD2 C:HIS145 4.2 17.5 1.0
NE2 C:HIS95 4.2 17.1 1.0
CD2 C:HIS95 4.3 17.9 1.0
O C:MET94 4.3 19.5 1.0
CB C:MET150 4.4 15.1 1.0
SD C:MET62 4.4 18.0 1.0
CA C:CYS136 4.6 14.9 1.0
CD C:PRO138 4.6 17.1 1.0
N C:ASN96 4.6 17.3 1.0
CA C:HIS145 4.7 15.7 1.0
CB C:MET62 4.8 17.6 1.0
C C:HIS95 4.8 18.1 1.0
N C:HIS95 4.8 18.6 1.0
C C:MET94 5.0 19.3 1.0

Copper binding site 6 out of 6 in 2pp7

Go back to Copper Binding Sites List in 2pp7
Copper binding site 6 out of 6 in the Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Anaerobically Manipulated Wild Type Oxidized Afnir (Acetate Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:16.4
occ:1.00
 NE2 C:HIS100 2.0 13.4 1.0
NE2 A:HIS306 2.1 12.4 1.0
NE2 C:HIS135 2.1 14.1 1.0
O C:ACT503 2.1 34.7 1.0
OXT C:ACT503 2.4 33.8 1.0
C C:ACT503 2.5 34.3 1.0
CE1 C:HIS100 2.9 13.9 1.0
CE1 A:HIS306 3.0 12.7 1.0
CD2 C:HIS135 3.0 12.6 1.0
CD2 C:HIS100 3.1 16.6 1.0
CE1 C:HIS135 3.1 16.1 1.0
CD2 A:HIS306 3.1 13.4 1.0
CH3 C:ACT503 3.8 34.1 1.0
ND1 C:HIS100 4.1 14.5 1.0
ND1 A:HIS306 4.1 12.6 1.0
CG C:HIS135 4.2 14.2 1.0
CG C:HIS100 4.2 14.7 1.0
ND1 C:HIS135 4.2 15.4 1.0
NE2 A:HIS255 4.2 17.1 1.0
CG A:HIS306 4.2 12.7 1.0
CE1 A:HIS255 4.4 16.2 1.0
O C:HOH2310 4.4 35.4 1.0
CD2 A:HIS255 4.6 16.7 1.0
ND1 A:HIS255 4.8 16.1 1.0
CG A:HIS255 4.9 14.9 1.0
CD1 A:LEU308 5.0 14.5 1.0
CD2 A:LEU308 5.0 15.7 1.0
CG1 A:ILE257 5.0 17.8 1.0

Reference:

E.I.Tocheva, L.D.Eltis, M.E.Murphy. Conserved Active Site Residues Limit Inhibition of A Copper-Containing Nitrite Reductase By Small Molecules. Biochemistry V. 47 4452 2008.
ISSN: ISSN 0006-2960
PubMed: 18358002
DOI: 10.1021/BI7020537
Page generated: Tue Jul 30 23:53:08 2024

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