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Copper in PDB 1j9r: Crystal Structure of Nitrite Soaked Reduced D98N Afnir

Enzymatic activity of Crystal Structure of Nitrite Soaked Reduced D98N Afnir

All present enzymatic activity of Crystal Structure of Nitrite Soaked Reduced D98N Afnir:
1.7.99.3;

Protein crystallography data

The structure of Crystal Structure of Nitrite Soaked Reduced D98N Afnir, PDB code: 1j9r was solved by M.J.Boulanger, M.E.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.436, 102.319, 145.898, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.5

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir (pdb code 1j9r). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir, PDB code: 1j9r:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 1j9r

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Copper binding site 1 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


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 Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu600

b:36.0
occ:1.00
 ND1 A:HIS145 2.0 21.9 1.0
SG A:CYS136 2.1 22.3 1.0
CU A:CU601 2.3 32.9 1.0
CG A:PRO138 2.9 28.1 1.0
CG A:HIS145 2.9 21.9 1.0
CD A:PRO138 3.0 27.7 1.0
CE1 A:HIS145 3.1 21.9 1.0
CB A:HIS145 3.1 21.6 1.0
CB A:CYS136 3.2 22.1 1.0
ND1 A:HIS95 3.5 23.2 1.0
O A:MET94 3.8 25.0 1.0
CD2 A:HIS145 4.1 21.9 1.0
NE2 A:HIS145 4.1 22.0 1.0
CA A:HIS95 4.2 23.3 1.0
SD A:MET150 4.2 18.9 1.0
CB A:PRO138 4.3 28.1 1.0
CA A:CYS136 4.3 22.2 1.0
CE1 A:HIS95 4.4 23.1 1.0
C A:CYS136 4.4 23.0 1.0
CG A:HIS95 4.4 23.1 1.0
N A:ALA137 4.5 24.1 1.0
N A:PRO138 4.5 27.4 1.0
CB A:HIS95 4.5 23.0 1.0
CA A:HIS145 4.6 21.5 1.0
C A:MET94 4.8 25.2 1.0
OD1 A:ASN96 4.8 21.5 1.0
N A:ASN96 4.8 22.1 1.0
SD A:MET62 4.9 23.1 1.0
O A:CYS136 5.0 22.8 1.0

Copper binding site 2 out of 9 in 1j9r

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Copper binding site 2 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


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 Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:32.9
occ:1.00
 ND1 A:HIS95 2.1 23.2 1.0
SD A:MET150 2.2 18.9 1.0
CU A:CU600 2.3 36.0 1.0
SG A:CYS136 2.3 22.3 1.0
CE A:MET150 2.9 19.1 1.0
CG A:HIS95 3.0 23.1 1.0
CB A:CYS136 3.0 22.1 1.0
CE1 A:HIS95 3.1 23.1 1.0
CB A:HIS95 3.3 23.0 1.0
CG A:MET150 3.6 18.5 1.0
ND1 A:HIS145 3.6 21.9 1.0
CA A:HIS95 3.7 23.3 1.0
CD2 A:HIS95 4.1 23.1 1.0
NE2 A:HIS95 4.2 23.4 1.0
O A:MET94 4.3 25.0 1.0
CB A:MET150 4.3 18.1 1.0
CG A:HIS145 4.4 21.9 1.0
CB A:HIS145 4.4 21.6 1.0
N A:ASN96 4.4 22.1 1.0
CA A:CYS136 4.5 22.2 1.0
CE1 A:HIS145 4.5 21.9 1.0
C A:HIS95 4.7 22.6 1.0
O A:ASN96 4.7 21.3 1.0
CG A:PRO138 4.8 28.1 1.0
CB A:MET62 4.8 21.6 1.0
N A:HIS95 4.8 24.2 1.0
SD A:MET62 4.9 23.1 1.0
C A:MET94 4.9 25.2 1.0

Copper binding site 3 out of 9 in 1j9r

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Copper binding site 3 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


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 Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:20.9
occ:1.00
 NE2 A:HIS100 2.0 18.8 1.0
O2 A:NO2604 2.1 36.5 1.0
NE2 A:HIS135 2.2 19.5 1.0
NE2 B:HIS306 2.2 17.8 1.0
N A:NO2604 2.4 36.2 1.0
CE1 A:HIS100 2.9 18.6 1.0
CE1 B:HIS306 3.0 17.8 1.0
CD2 A:HIS135 3.1 19.3 1.0
CD2 A:HIS100 3.1 18.6 1.0
O1 A:NO2604 3.1 36.9 1.0
CE1 A:HIS135 3.2 19.3 1.0
CD2 B:HIS306 3.3 17.9 1.0
ND2 A:ASN98 3.9 22.4 1.0
ND1 A:HIS100 4.1 18.7 1.0
NE2 B:HIS255 4.2 21.0 1.0
ND1 B:HIS306 4.2 17.9 1.0
CG A:HIS100 4.2 18.7 1.0
CG A:HIS135 4.2 19.3 1.0
ND1 A:HIS135 4.3 19.1 1.0
CG B:HIS306 4.4 17.9 1.0
CE1 B:HIS255 4.4 21.1 1.0
CG A:ASN98 4.5 21.8 1.0
CD2 B:HIS255 4.5 20.8 1.0
OD1 A:ASN98 4.8 22.5 1.0
CD2 B:LEU308 4.9 17.8 1.0
ND1 B:HIS255 4.9 21.0 1.0
CG B:HIS255 5.0 20.9 1.0
O B:HOH6000 5.0 21.7 1.0

Copper binding site 4 out of 9 in 1j9r

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Copper binding site 4 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


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 Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu700

b:31.5
occ:1.00
 ND1 B:HIS145 1.8 29.9 1.0
SG B:CYS136 2.1 27.9 1.0
CG B:PRO138 2.2 36.0 1.0
CD B:PRO138 2.3 35.8 1.0
CU B:CU701 2.5 32.7 1.0
CG B:HIS145 2.7 29.8 1.0
CE1 B:HIS145 2.8 30.0 1.0
CB B:HIS145 3.1 29.4 1.0
CB B:CYS136 3.2 28.4 1.0
CB B:PRO138 3.6 36.3 1.0
N B:PRO138 3.7 35.5 1.0
CD2 B:HIS145 3.9 29.8 1.0
NE2 B:HIS145 3.9 30.1 1.0
N B:ALA137 3.9 31.2 1.0
C B:CYS136 4.0 29.6 1.0
ND1 B:HIS95 4.1 26.3 1.0
CA B:CYS136 4.2 28.6 1.0
CA B:PRO138 4.4 36.4 1.0
O B:MET94 4.5 28.1 1.0
CA B:ALA137 4.5 32.9 1.0
C B:ALA137 4.5 34.2 1.0
O B:CYS136 4.6 29.5 1.0
CA B:HIS145 4.6 29.1 1.0
SD B:MET150 4.6 21.5 1.0
CA B:HIS95 4.7 27.2 1.0
OD1 B:ASN96 4.7 26.8 1.0
O B:MET141 4.9 39.1 1.0
CE1 B:HIS95 4.9 26.1 1.0

Copper binding site 5 out of 9 in 1j9r

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Copper binding site 5 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


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 Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu701

b:32.7
occ:1.00
 ND1 B:HIS95 2.0 26.3 1.0
SG B:CYS136 2.2 27.9 1.0
SD B:MET150 2.5 21.5 1.0
CU B:CU700 2.5 31.5 1.0
CE B:MET150 3.0 21.3 1.0
CE1 B:HIS95 3.0 26.1 1.0
CG B:HIS95 3.0 26.5 1.0
CB B:CYS136 3.0 28.4 1.0
ND1 B:HIS145 3.3 29.9 1.0
CB B:HIS95 3.4 26.8 1.0
CA B:HIS95 3.7 27.2 1.0
CG B:MET150 4.0 21.2 1.0
CE1 B:HIS145 4.1 30.0 1.0
NE2 B:HIS95 4.1 26.2 1.0
CG B:HIS145 4.1 29.8 1.0
O B:MET94 4.1 28.1 1.0
CD2 B:HIS95 4.1 26.2 1.0
CG B:PRO138 4.2 36.0 1.0
CB B:HIS145 4.3 29.4 1.0
N B:ASN96 4.4 26.7 1.0
CA B:CYS136 4.5 28.6 1.0
C B:HIS95 4.6 27.0 1.0
CB B:MET150 4.6 21.0 1.0
CD B:PRO138 4.7 35.8 1.0
SD B:MET62 4.7 26.1 1.0
O B:ASN96 4.7 26.2 1.0
N B:HIS95 4.8 27.7 1.0
C B:MET94 4.9 28.1 1.0

Copper binding site 6 out of 9 in 1j9r

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Copper binding site 6 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


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 Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu702

b:23.9
occ:1.00
 NE2 B:HIS100 2.0 23.3 1.0
NE2 B:HIS135 2.1 24.7 1.0
O2 B:NO2704 2.1 37.6 1.0
NE2 C:HIS306 2.1 21.5 1.0
N B:NO2704 2.4 37.2 1.0
O1 B:NO2704 2.6 37.3 1.0
CE1 B:HIS100 2.8 23.5 1.0
CD2 B:HIS135 3.0 24.7 1.0
CE1 C:HIS306 3.0 21.4 1.0
CD2 B:HIS100 3.1 23.5 1.0
CE1 B:HIS135 3.2 24.5 1.0
CD2 C:HIS306 3.2 21.4 1.0
ND1 B:HIS100 4.0 23.4 1.0
ND2 B:ASN98 4.1 26.8 1.0
CG B:HIS100 4.1 23.7 1.0
NE2 C:HIS255 4.1 23.1 1.0
ND1 C:HIS306 4.2 21.4 1.0
CG B:HIS135 4.2 24.7 1.0
ND1 B:HIS135 4.3 24.6 1.0
CG C:HIS306 4.3 21.4 1.0
CE1 C:HIS255 4.4 23.1 1.0
CD2 C:HIS255 4.5 23.1 1.0
CG B:ASN98 4.7 26.6 1.0
ND1 C:HIS255 4.8 23.2 1.0
O C:HOH7000 4.9 35.9 1.0
CG C:HIS255 5.0 23.0 1.0
CD2 C:LEU308 5.0 22.2 1.0
OD1 B:ASN98 5.0 27.0 1.0

Copper binding site 7 out of 9 in 1j9r

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Copper binding site 7 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu800

b:36.9
occ:1.00
 CG C:PRO138 2.0 39.3 1.0
SG C:CYS136 2.1 30.8 1.0
CD C:PRO138 2.1 38.8 1.0
ND1 C:HIS145 2.3 37.4 1.0
CG C:HIS145 2.7 37.2 1.0
CU C:CU801 2.7 35.2 1.0
CB C:HIS145 3.0 36.6 1.0
CE1 C:HIS145 3.1 37.6 1.0
CB C:CYS136 3.2 30.9 1.0
CB C:PRO138 3.4 39.4 1.0
N C:PRO138 3.5 38.5 1.0
CD2 C:HIS145 3.6 37.4 1.0
NE2 C:HIS145 3.8 37.5 1.0
N C:ALA137 3.8 34.0 1.0
C C:CYS136 3.9 32.4 1.0
CA C:PRO138 4.1 39.6 1.0
CA C:CYS136 4.1 31.1 1.0
C C:ALA137 4.3 37.1 1.0
CA C:ALA137 4.3 35.7 1.0
O C:CYS136 4.4 32.3 1.0
ND1 C:HIS95 4.5 32.9 1.0
O C:MET94 4.5 34.8 1.0
CA C:HIS145 4.5 35.9 1.0
OD1 C:ASN96 4.6 30.3 1.0
SD C:MET150 4.7 27.3 1.0
CA C:HIS95 4.9 32.9 1.0

Copper binding site 8 out of 9 in 1j9r

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Copper binding site 8 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu801

b:35.2
occ:1.00
 ND1 C:HIS95 2.1 32.9 1.0
SG C:CYS136 2.3 30.8 1.0
SD C:MET150 2.4 27.3 1.0
ND1 C:HIS145 2.6 37.4 1.0
CU C:CU800 2.7 36.9 1.0
CE1 C:HIS95 3.0 32.9 1.0
CB C:CYS136 3.1 30.9 1.0
CE C:MET150 3.2 26.9 1.0
CG C:HIS95 3.2 33.0 1.0
CE1 C:HIS145 3.4 37.6 1.0
CB C:HIS95 3.6 32.9 1.0
CG C:HIS145 3.6 37.2 1.0
CG C:MET150 3.8 27.0 1.0
CA C:HIS95 3.8 32.9 1.0
CB C:HIS145 3.9 36.6 1.0
O C:MET94 4.1 34.8 1.0
NE2 C:HIS95 4.2 33.0 1.0
CG C:PRO138 4.2 39.3 1.0
CD2 C:HIS95 4.3 33.0 1.0
SD C:MET62 4.4 34.2 1.0
CB C:MET150 4.5 26.8 1.0
N C:ASN96 4.5 31.4 1.0
NE2 C:HIS145 4.6 37.5 1.0
CA C:CYS136 4.6 31.1 1.0
CB C:MET62 4.7 32.4 1.0
CD2 C:HIS145 4.7 37.4 1.0
CD C:PRO138 4.8 38.8 1.0
C C:HIS95 4.8 32.2 1.0
N C:HIS95 4.8 33.8 1.0
O C:ASN96 4.9 29.8 1.0
C C:MET94 4.9 34.8 1.0
CG C:MET62 5.0 33.1 1.0

Copper binding site 9 out of 9 in 1j9r

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Copper binding site 9 out of 9 in the Crystal Structure of Nitrite Soaked Reduced D98N Afnir


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Nitrite Soaked Reduced D98N Afnir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu802

b:25.3
occ:1.00
 NE2 C:HIS100 2.0 24.5 1.0
NE2 C:HIS135 2.1 26.4 1.0
NE2 A:HIS306 2.2 19.9 1.0
N C:NO2804 2.3 39.6 1.0
O1 C:NO2804 2.3 39.5 1.0
O2 C:NO2804 2.4 40.0 1.0
CE1 C:HIS100 2.9 24.6 1.0
CE1 A:HIS306 3.0 19.7 1.0
CD2 C:HIS135 3.0 26.7 1.0
CD2 C:HIS100 3.1 24.6 1.0
CE1 C:HIS135 3.2 26.6 1.0
CD2 A:HIS306 3.2 19.6 1.0
ND1 C:HIS100 4.0 24.6 1.0
NE2 A:HIS255 4.1 21.5 1.0
CG C:HIS100 4.1 24.7 1.0
ND1 A:HIS306 4.2 19.7 1.0
CG C:HIS135 4.2 26.9 1.0
ND1 C:HIS135 4.3 26.6 1.0
CG A:HIS306 4.3 19.7 1.0
CD2 A:HIS255 4.4 21.1 1.0
CE1 A:HIS255 4.4 21.2 1.0
ND2 C:ASN98 4.6 29.8 1.0
CG C:ASN98 4.8 29.3 1.0
OD1 C:ASN98 4.8 29.9 1.0
ND1 A:HIS255 5.0 21.1 1.0
CG A:HIS255 5.0 20.9 1.0

Reference:

M.J.Boulanger, M.E.Murphy. Alternate Substrate Binding Modes to Two Mutant (D98N and H255N) Forms of Nitrite Reductase From Alcaligenes Faecalis S-6: Structural Model of A Transient Catalytic Intermediate Biochemistry V. 40 9132 2001.
ISSN: ISSN 0006-2960
PubMed: 11478880
DOI: 10.1021/BI0107400
Page generated: Tue Jul 30 22:01:50 2024

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