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Copper in PDB 1ibz: Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea

Protein crystallography data

The structure of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea, PDB code: 1ibz was solved by R.L.Lieberman, D.M.Arciero, A.B.Hooper, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.97 / 2.30
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 97.585, 97.585, 283.010, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 22.8

Copper Binding Sites:

The binding sites of Copper atom in the Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea (pdb code 1ibz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea, PDB code: 1ibz:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1ibz

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Copper binding site 1 out of 4 in the Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:12.8
occ:1.00
ND1 A:HIS103 2.0 20.1 1.0
OE1 A:GLU60 2.0 18.8 1.0
SG A:CYS95 2.2 16.2 1.0
ND1 A:HIS98 2.4 40.6 1.0
CE1 A:HIS103 2.9 18.8 1.0
CG A:HIS103 3.0 19.1 1.0
CE1 A:HIS98 3.1 42.6 1.0
CD A:GLU60 3.2 19.0 1.0
CB A:CYS95 3.2 14.7 1.0
CG A:HIS98 3.3 36.7 1.0
CB A:HIS103 3.4 14.3 1.0
CB A:HIS98 3.8 28.9 1.0
OE2 A:GLU60 3.8 19.9 1.0
NE2 A:HIS103 4.0 20.4 1.0
N A:GLY61 4.1 17.7 1.0
CD2 A:HIS103 4.1 20.1 1.0
NE2 A:HIS98 4.1 41.5 1.0
CD2 A:HIS98 4.2 39.8 1.0
CA A:GLU60 4.3 18.9 1.0
CG A:GLU60 4.4 19.1 1.0
CB A:GLU60 4.4 19.4 1.0
N A:HIS98 4.4 22.1 1.0
CG1 A:VAL33 4.5 17.7 1.0
CA A:CYS95 4.6 16.1 1.0
CB A:VAL33 4.7 17.3 1.0
CA A:HIS98 4.7 24.5 1.0
C A:GLU60 4.8 18.6 1.0
O A:GLY61 4.9 18.3 1.0
CA A:HIS103 4.9 15.1 1.0
CB A:LEU97 4.9 13.7 1.0
CG2 A:VAL33 4.9 16.9 1.0

Copper binding site 2 out of 4 in 1ibz

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Copper binding site 2 out of 4 in the Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:25.0
occ:1.00
ND1 B:HIS103 2.0 21.0 1.0
OE1 B:GLU60 2.0 31.6 1.0
SG B:CYS95 2.3 19.2 1.0
ND1 B:HIS98 2.4 35.8 1.0
CE1 B:HIS103 3.0 20.9 1.0
CG B:HIS103 3.0 19.1 1.0
CB B:CYS95 3.1 20.0 1.0
CE1 B:HIS98 3.1 36.5 1.0
CD B:GLU60 3.2 29.4 1.0
CB B:HIS103 3.4 14.9 1.0
CG B:HIS98 3.5 35.1 1.0
OE2 B:GLU60 3.8 30.2 1.0
CB B:HIS98 3.9 28.4 1.0
NE2 B:HIS103 4.1 19.3 1.0
N B:GLY61 4.1 18.5 1.0
CD2 B:HIS103 4.1 18.5 1.0
CA B:GLU60 4.3 21.4 1.0
NE2 B:HIS98 4.3 36.6 1.0
CB B:GLU60 4.3 24.0 1.0
CG B:GLU60 4.3 26.9 1.0
N B:HIS98 4.4 24.9 1.0
CD2 B:HIS98 4.5 35.2 1.0
CA B:CYS95 4.6 20.6 1.0
CG1 B:VAL33 4.6 17.6 1.0
C B:GLU60 4.8 20.6 1.0
CA B:HIS98 4.8 25.2 1.0
CB B:VAL33 4.8 18.4 1.0
CB B:LEU97 4.8 23.2 1.0
O B:GLY61 4.9 19.2 1.0
CA B:HIS103 4.9 12.6 1.0

Copper binding site 3 out of 4 in 1ibz

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Copper binding site 3 out of 4 in the Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu404

b:39.2
occ:1.00
OE1 C:GLU60 1.9 22.5 1.0
ND1 C:HIS103 2.0 27.0 1.0
SG C:CYS95 2.2 28.2 1.0
ND1 C:HIS98 2.6 45.2 1.0
CE1 C:HIS103 3.0 26.2 1.0
CG C:HIS103 3.0 24.2 1.0
CB C:CYS95 3.1 21.8 1.0
CD C:GLU60 3.2 26.1 1.0
CE1 C:HIS98 3.3 46.0 1.0
CB C:HIS103 3.4 21.3 1.0
CG C:HIS98 3.5 40.0 1.0
CB C:HIS98 3.9 31.6 1.0
OE2 C:GLU60 3.9 24.8 1.0
N C:GLY61 4.1 24.3 1.0
NE2 C:HIS103 4.1 25.7 1.0
CB C:GLU60 4.1 28.9 1.0
CD2 C:HIS103 4.2 24.8 1.0
CG C:GLU60 4.2 24.8 1.0
NE2 C:HIS98 4.2 47.4 1.0
CA C:GLU60 4.3 27.8 1.0
CD2 C:HIS98 4.4 44.3 1.0
N C:HIS98 4.4 23.3 1.0
CG1 C:VAL33 4.4 10.7 1.0
CA C:CYS95 4.6 22.6 1.0
CB C:VAL33 4.7 12.1 1.0
C C:GLU60 4.7 27.8 1.0
O C:GLY61 4.8 22.4 1.0
CA C:HIS98 4.8 25.5 1.0
CA C:HIS103 4.9 18.6 1.0
O C:HOH481 4.9 47.9 1.0
CB C:LEU97 4.9 17.8 1.0

Copper binding site 4 out of 4 in 1ibz

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Copper binding site 4 out of 4 in the Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Red Copper Protein Nitrosocyanin From Nitrosomonas Europaea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:13.4
occ:1.00
ND1 D:HIS103 2.1 12.5 1.0
OE1 D:GLU60 2.1 20.7 1.0
ND1 D:HIS98 2.1 17.3 1.0
SG D:CYS95 2.3 13.9 1.0
CE1 D:HIS98 2.8 18.4 1.0
CG D:HIS103 3.1 11.8 1.0
CE1 D:HIS103 3.1 12.5 1.0
CD D:GLU60 3.3 18.9 1.0
CB D:CYS95 3.3 14.2 1.0
CG D:HIS98 3.3 17.0 1.0
CB D:HIS103 3.3 9.2 1.0
OE2 D:GLU60 3.8 16.1 1.0
CB D:HIS98 3.8 14.7 1.0
NE2 D:HIS98 4.0 19.0 1.0
N D:GLY61 4.1 12.3 1.0
NE2 D:HIS103 4.2 13.2 1.0
CD2 D:HIS103 4.2 10.7 1.0
CD2 D:HIS98 4.2 17.9 1.0
N D:HIS98 4.4 15.4 1.0
CA D:GLU60 4.4 15.5 1.0
CG D:GLU60 4.5 17.5 1.0
CB D:GLU60 4.6 18.3 1.0
CG1 D:VAL33 4.7 7.1 1.0
CA D:CYS95 4.7 15.4 1.0
CA D:HIS98 4.8 14.4 1.0
CB D:VAL33 4.8 10.3 1.0
C D:GLU60 4.8 14.3 1.0
CA D:HIS103 4.8 11.6 1.0
CB D:LEU97 4.9 10.2 1.0
O D:GLY61 4.9 13.4 1.0
CG2 D:VAL33 5.0 4.5 1.0

Reference:

R.L.Lieberman, D.M.Arciero, A.B.Hooper, A.C.Rosenzweig. Crystal Structure of A Novel Red Copper Protein From Nitrosomonas Europaea. Biochemistry V. 40 5674 2001.
ISSN: ISSN 0006-2960
PubMed: 11341832
DOI: 10.1021/BI0102611
Page generated: Thu Sep 3 15:59:31 2020
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