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Copper in PDB 1kbv: Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae

Protein crystallography data

The structure of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae, PDB code: 1kbv was solved by M.J.Boulanger, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.18 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.290, 98.095, 102.299, 83.89, 74.14, 73.32
R / Rfree (%) 19.5 / 22.3

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae (pdb code 1kbv). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae, PDB code: 1kbv:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 1kbv

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Copper binding site 1 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:20.2
occ:1.00
ND1 A:HIS94 2.0 15.3 1.0
ND1 A:HIS143 2.1 15.8 1.0
SG A:CYS135 2.2 17.6 1.0
SD A:MET148 2.7 26.5 1.0
CE1 A:HIS94 2.9 18.3 1.0
CE1 A:HIS143 3.0 17.4 1.0
CG A:HIS94 3.1 17.3 1.0
CG A:HIS143 3.1 15.8 1.0
CB A:CYS135 3.2 18.3 1.0
CE A:MET148 3.5 19.7 1.0
CB A:HIS143 3.5 16.2 1.0
CB A:HIS94 3.6 16.7 1.0
CA A:HIS94 3.7 17.9 1.0
O A:PRO93 3.8 16.4 1.0
NE2 A:HIS94 4.0 17.3 1.0
NE2 A:HIS143 4.1 15.4 1.0
CD2 A:HIS94 4.2 17.3 1.0
CD2 A:HIS143 4.2 16.8 1.0
CG A:MET148 4.3 21.2 1.0
CB A:VAL137 4.4 19.5 1.0
CG2 A:VAL137 4.5 20.7 1.0
N A:ASN95 4.5 18.2 1.0
CA A:HIS143 4.6 15.1 1.0
CE3 A:TRP61 4.6 13.6 1.0
CA A:CYS135 4.6 17.4 1.0
N A:HIS94 4.7 17.1 1.0
C A:PRO93 4.7 17.7 1.0
C A:HIS94 4.7 17.8 1.0
CB A:MET148 4.8 17.1 1.0

Copper binding site 2 out of 12 in 1kbv

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Copper binding site 2 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:21.3
occ:1.00
O2 A:NO22504 2.0 32.2 1.0
NE2 B:HIS289 2.1 14.7 1.0
NE2 A:HIS134 2.1 20.2 1.0
NE2 A:HIS99 2.2 12.5 1.0
N A:NO22504 2.4 35.6 1.0
O1 A:NO22504 2.4 33.4 1.0
CE1 B:HIS289 3.0 15.1 1.0
CD2 A:HIS134 3.1 17.2 1.0
CE1 A:HIS99 3.1 14.9 1.0
CE1 A:HIS134 3.1 18.4 1.0
CD2 B:HIS289 3.2 13.6 1.0
CD2 A:HIS99 3.2 15.8 1.0
OD1 A:ASP97 3.8 22.8 1.0
NE2 B:HIS240 3.9 15.8 1.0
ND1 B:HIS289 4.2 14.4 1.0
CD2 B:HIS240 4.2 14.2 1.0
O A:HOH2862 4.2 31.9 1.0
ND1 A:HIS134 4.2 17.9 1.0
ND1 A:HIS99 4.2 14.3 1.0
CG A:HIS134 4.2 17.9 1.0
CG B:HIS289 4.3 14.4 1.0
CG A:HIS99 4.3 15.5 1.0
CG A:ASP97 4.4 21.8 1.0
CE1 B:HIS240 4.7 14.9 1.0
O B:HOH553 4.8 19.2 1.0
OD2 A:ASP97 4.8 22.7 1.0

Copper binding site 3 out of 12 in 1kbv

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Copper binding site 3 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:22.3
occ:1.00
ND1 B:HIS94 2.0 16.9 1.0
ND1 B:HIS143 2.1 20.6 1.0
SG B:CYS135 2.2 20.2 1.0
SD B:MET148 2.5 21.9 1.0
CE1 B:HIS94 2.9 18.6 1.0
CE1 B:HIS143 3.0 21.8 1.0
CG B:HIS94 3.1 18.6 1.0
CB B:CYS135 3.1 19.9 1.0
CG B:HIS143 3.2 20.5 1.0
CE B:MET148 3.5 20.2 1.0
CB B:HIS94 3.5 18.6 1.0
CB B:HIS143 3.6 19.7 1.0
CA B:HIS94 3.8 21.4 1.0
NE2 B:HIS94 4.0 19.1 1.0
O B:PRO93 4.1 21.8 1.0
NE2 B:HIS143 4.1 22.4 1.0
CD2 B:HIS94 4.2 18.2 1.0
CG B:MET148 4.2 19.7 1.0
CD2 B:HIS143 4.2 21.1 1.0
CB B:VAL137 4.4 18.5 1.0
CG2 B:VAL137 4.5 21.6 1.0
N B:ASN95 4.5 20.9 1.0
CE3 B:TRP61 4.6 17.4 1.0
CA B:CYS135 4.6 19.7 1.0
CA B:HIS143 4.6 18.4 1.0
CB B:MET148 4.7 16.7 1.0
C B:HIS94 4.7 21.7 1.0
N B:HIS94 4.8 20.6 1.0
C B:PRO93 4.9 22.9 1.0

Copper binding site 4 out of 12 in 1kbv

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Copper binding site 4 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:24.3
occ:1.00
O2 C:NO22505 2.0 32.3 1.0
NE2 B:HIS99 2.1 16.5 1.0
NE2 B:HIS134 2.1 18.4 1.0
NE2 C:HIS289 2.2 17.8 1.0
N C:NO22505 2.3 35.9 1.0
O1 C:NO22505 2.7 35.8 1.0
CE1 B:HIS99 3.0 14.8 1.0
CE1 B:HIS134 3.1 18.7 1.0
CE1 C:HIS289 3.1 17.3 1.0
CD2 B:HIS134 3.1 18.5 1.0
CD2 B:HIS99 3.1 17.3 1.0
CD2 C:HIS289 3.3 18.1 1.0
OD1 B:ASP97 3.9 27.1 1.0
NE2 C:HIS240 3.9 16.6 1.0
ND1 B:HIS99 4.1 15.2 1.0
CD2 C:HIS240 4.2 16.3 1.0
ND1 B:HIS134 4.2 17.3 1.0
CG B:HIS134 4.2 17.9 1.0
CG B:HIS99 4.2 15.7 1.0
ND1 C:HIS289 4.2 15.5 1.0
CG C:HIS289 4.4 17.1 1.0
O C:HOH2745 4.4 32.8 1.0
CG B:ASP97 4.5 25.1 1.0
O B:HOH623 4.7 30.3 1.0
CE1 C:HIS240 4.7 17.5 1.0
OD2 B:ASP97 4.9 23.7 1.0

Copper binding site 5 out of 12 in 1kbv

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Copper binding site 5 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:21.5
occ:1.00
ND1 C:HIS94 2.0 17.2 1.0
ND1 C:HIS143 2.1 15.1 1.0
SG C:CYS135 2.2 17.2 1.0
SD C:MET148 2.5 27.3 1.0
CE1 C:HIS94 2.9 17.4 1.0
CE1 C:HIS143 2.9 16.7 1.0
CG C:HIS143 3.1 16.2 1.0
CG C:HIS94 3.2 18.6 1.0
CB C:CYS135 3.2 17.2 1.0
CE C:MET148 3.5 20.9 1.0
CB C:HIS143 3.6 15.8 1.0
CB C:HIS94 3.6 19.7 1.0
CA C:HIS94 3.7 21.3 1.0
O C:PRO93 3.8 22.0 1.0
NE2 C:HIS143 4.1 16.4 1.0
NE2 C:HIS94 4.1 16.0 1.0
CG C:MET148 4.2 19.9 1.0
CD2 C:HIS143 4.2 15.9 1.0
CD2 C:HIS94 4.2 17.1 1.0
CB C:VAL137 4.4 20.9 1.0
CG2 C:VAL137 4.4 20.7 1.0
CE3 C:TRP61 4.5 18.2 1.0
N C:ASN95 4.5 19.2 1.0
CA C:HIS143 4.5 15.7 1.0
CA C:CYS135 4.6 19.2 1.0
C C:PRO93 4.7 21.7 1.0
N C:HIS94 4.7 20.4 1.0
C C:HIS94 4.7 21.1 1.0
CB C:MET148 4.7 16.7 1.0
CZ3 C:TRP61 5.0 18.8 1.0

Copper binding site 6 out of 12 in 1kbv

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Copper binding site 6 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:23.3
occ:1.00
NE2 C:HIS134 2.0 15.1 1.0
NE2 C:HIS99 2.1 18.6 1.0
O2 A:NO22506 2.1 27.8 1.0
NE2 A:HIS289 2.2 14.4 1.0
N A:NO22506 2.2 33.0 1.0
O1 A:NO22506 2.5 32.1 1.0
CE1 C:HIS134 2.9 15.3 1.0
CE1 C:HIS99 3.0 16.8 1.0
CD2 C:HIS134 3.1 14.9 1.0
CD2 C:HIS99 3.1 17.9 1.0
CD2 A:HIS289 3.2 17.1 1.0
CE1 A:HIS289 3.2 15.3 1.0
OD1 C:ASP97 4.0 24.9 1.0
NE2 A:HIS240 4.0 18.1 1.0
ND1 C:HIS134 4.0 14.7 1.0
ND1 C:HIS99 4.1 15.7 1.0
CG C:HIS134 4.2 15.2 1.0
CG C:HIS99 4.2 18.4 1.0
CD2 A:HIS240 4.3 17.6 1.0
ND1 A:HIS289 4.3 15.0 1.0
CG A:HIS289 4.3 16.0 1.0
O A:HOH2864 4.4 54.4 1.0
CG C:ASP97 4.5 23.7 1.0
CE1 A:HIS240 4.6 19.3 1.0
O C:HOH2605 4.8 25.6 1.0
OD2 C:ASP97 4.9 24.4 1.0

Copper binding site 7 out of 12 in 1kbv

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Copper binding site 7 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu501

b:20.8
occ:1.00
ND1 D:HIS143 2.1 16.4 1.0
ND1 D:HIS94 2.1 15.9 1.0
SG D:CYS135 2.2 22.1 1.0
SD D:MET148 2.7 19.5 1.0
CE1 D:HIS143 2.9 17.0 1.0
CE1 D:HIS94 3.0 18.7 1.0
CG D:HIS143 3.1 16.6 1.0
CB D:CYS135 3.1 21.3 1.0
CG D:HIS94 3.2 17.2 1.0
CB D:HIS143 3.5 17.9 1.0
CE D:MET148 3.6 17.9 1.0
CB D:HIS94 3.6 15.8 1.0
CA D:HIS94 3.9 17.5 1.0
NE2 D:HIS143 4.1 15.4 1.0
CG D:MET148 4.1 16.6 1.0
NE2 D:HIS94 4.1 17.6 1.0
CD2 D:HIS143 4.1 16.4 1.0
CD2 D:HIS94 4.3 16.5 1.0
O D:PRO93 4.3 15.3 1.0
CA D:HIS143 4.5 16.6 1.0
CB D:VAL137 4.5 19.6 1.0
CE3 D:TRP61 4.5 13.9 1.0
CA D:CYS135 4.5 20.2 1.0
CG2 D:VAL137 4.6 20.1 1.0
N D:ASN95 4.6 18.6 1.0
CB D:MET148 4.6 16.0 1.0
C D:HIS94 4.8 17.5 1.0
N D:HIS94 4.9 16.6 1.0

Copper binding site 8 out of 12 in 1kbv

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Copper binding site 8 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:23.2
occ:1.00
O2 E:NO22507 2.0 30.4 1.0
NE2 E:HIS289 2.1 14.2 1.0
NE2 D:HIS134 2.1 20.5 1.0
NE2 D:HIS99 2.2 14.4 1.0
N E:NO22507 2.3 35.5 1.0
O1 E:NO22507 2.5 33.3 1.0
CE1 E:HIS289 3.0 13.7 1.0
CE1 D:HIS99 3.1 16.0 1.0
CD2 D:HIS134 3.1 19.2 1.0
CE1 D:HIS134 3.1 17.9 1.0
CD2 E:HIS289 3.2 13.7 1.0
CD2 D:HIS99 3.2 16.6 1.0
OD1 D:ASP97 3.9 22.8 1.0
NE2 E:HIS240 3.9 17.0 1.0
ND1 E:HIS289 4.1 13.0 1.0
CD2 E:HIS240 4.2 16.6 1.0
ND1 D:HIS99 4.2 16.0 1.0
O D:HOH2770 4.2 29.1 1.0
ND1 D:HIS134 4.2 19.1 1.0
CG E:HIS289 4.2 13.5 1.0
CG D:HIS134 4.3 19.4 1.0
CG D:HIS99 4.3 17.2 1.0
CG D:ASP97 4.5 21.2 1.0
CE1 E:HIS240 4.6 17.4 1.0
O E:HOH2526 4.7 21.5 1.0
OD2 D:ASP97 4.9 21.2 1.0

Copper binding site 9 out of 12 in 1kbv

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Copper binding site 9 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:25.3
occ:1.00
ND1 E:HIS94 2.0 22.0 1.0
ND1 E:HIS143 2.2 23.0 1.0
SG E:CYS135 2.2 20.6 1.0
SD E:MET148 2.6 22.8 1.0
CE1 E:HIS94 2.9 21.7 1.0
CE1 E:HIS143 3.1 23.8 1.0
CG E:HIS94 3.1 22.6 1.0
CB E:CYS135 3.1 21.0 1.0
CG E:HIS143 3.2 23.5 1.0
CB E:HIS94 3.5 22.2 1.0
CE E:MET148 3.5 20.3 1.0
CB E:HIS143 3.6 22.4 1.0
CA E:HIS94 3.8 23.5 1.0
NE2 E:HIS94 4.1 23.2 1.0
O E:PRO93 4.1 25.3 1.0
CG E:MET148 4.2 20.8 1.0
CD2 E:HIS94 4.2 22.9 1.0
NE2 E:HIS143 4.2 23.6 1.0
CD2 E:HIS143 4.3 23.3 1.0
CB E:VAL137 4.4 23.3 1.0
CG2 E:VAL137 4.5 23.6 1.0
CE3 E:TRP61 4.5 21.2 1.0
N E:ASN95 4.6 22.6 1.0
CA E:HIS143 4.6 21.4 1.0
CA E:CYS135 4.6 20.6 1.0
CB E:MET148 4.7 18.2 1.0
C E:HIS94 4.7 23.8 1.0
N E:HIS94 4.8 23.8 1.0
C E:PRO93 4.9 25.7 1.0
CZ3 E:TRP61 5.0 21.4 1.0

Copper binding site 10 out of 12 in 1kbv

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Copper binding site 10 out of 12 in the Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Nitrite-Soaked Crystal Structure of the Soluble Domain of Ania From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:25.0
occ:1.00
O2 F:NO22508 1.9 31.2 1.0
NE2 E:HIS99 2.1 21.5 1.0
NE2 E:HIS134 2.1 19.5 1.0
NE2 F:HIS289 2.2 17.0 1.0
N F:NO22508 2.4 35.0 1.0
O1 F:NO22508 2.7 34.4 1.0
CE1 E:HIS99 3.0 20.0 1.0
CE1 E:HIS134 3.1 18.8 1.0
CD2 E:HIS134 3.1 21.1 1.0
CE1 F:HIS289 3.2 17.6 1.0
CD2 F:HIS289 3.2 17.6 1.0
CD2 E:HIS99 3.2 21.9 1.0
OD1 E:ASP97 3.9 30.4 1.0
NE2 F:HIS240 4.0 17.5 1.0
ND1 E:HIS99 4.1 21.4 1.0
ND1 E:HIS134 4.2 18.3 1.0
CD2 F:HIS240 4.2 18.2 1.0
CG E:HIS134 4.2 19.4 1.0
CG E:HIS99 4.2 20.0 1.0
ND1 F:HIS289 4.3 16.6 1.0
CG F:HIS289 4.3 17.2 1.0
O F:HOH2803 4.4 39.7 1.0
CG E:ASP97 4.5 28.3 1.0
CE1 F:HIS240 4.7 19.8 1.0
O E:HOH2621 4.9 29.2 1.0
OD2 E:ASP97 5.0 26.8 1.0

Reference:

M.J.Boulanger, M.E.Murphy. Crystal Structure of the Soluble Domain of the Major Anaerobically Induced Outer Membrane Protein (Ania) From Pathogenic Neisseria: A New Class of Copper-Containing Nitrite Reductases. J.Mol.Biol. V. 315 1111 2002.
ISSN: ISSN 0022-2836
PubMed: 11827480
DOI: 10.1006/JMBI.2001.5251
Page generated: Sun Dec 13 10:59:57 2020

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