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Copper in PDB 6kng: Cryoem Map and Model of Nitrite Reductase at pH 8.1

Enzymatic activity of Cryoem Map and Model of Nitrite Reductase at pH 8.1

All present enzymatic activity of Cryoem Map and Model of Nitrite Reductase at pH 8.1:
1.7.2.1;

Copper Binding Sites:

The binding sites of Copper atom in the Cryoem Map and Model of Nitrite Reductase at pH 8.1 (pdb code 6kng). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Cryoem Map and Model of Nitrite Reductase at pH 8.1, PDB code: 6kng:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 6kng

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Copper binding site 1 out of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:74.0
occ:1.00
ND1 A:HIS95 2.2 57.6 1.0
ND1 A:HIS145 2.2 55.3 1.0
SG A:CYS136 2.3 56.0 1.0
SD A:MET150 2.4 53.4 1.0
CE1 A:HIS95 3.0 57.6 1.0
CE1 A:HIS145 3.0 55.3 1.0
CB A:CYS136 3.2 56.0 1.0
CG A:HIS145 3.3 55.3 1.0
CG A:HIS95 3.3 57.6 1.0
CE A:MET150 3.3 53.4 1.0
CB A:HIS145 3.7 55.3 1.0
CB A:HIS95 3.7 57.6 1.0
CG A:MET150 4.0 53.4 1.0
CA A:HIS95 4.1 57.6 1.0
NE2 A:HIS95 4.1 57.6 1.0
NE2 A:HIS145 4.2 55.3 1.0
CD2 A:HIS145 4.3 55.3 1.0
CD2 A:HIS95 4.3 57.6 1.0
CG A:PRO138 4.3 59.2 1.0
O A:LEU94 4.5 58.9 1.0
CB A:MET150 4.5 53.4 1.0
SD A:MET62 4.5 60.9 1.0
CA A:CYS136 4.7 56.0 1.0
CD A:PRO138 4.7 59.2 1.0
CA A:HIS145 4.8 55.3 1.0
N A:ASN96 4.9 56.9 1.0

Copper binding site 2 out of 6 in 6kng

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Copper binding site 2 out of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:74.2
occ:1.00
NE2 C:HIS306 2.1 53.6 1.0
NE2 A:HIS100 2.1 53.6 1.0
NE2 A:HIS135 2.2 52.0 1.0
CE1 A:HIS100 2.7 53.6 1.0
CE1 C:HIS306 3.0 53.6 1.0
CD2 A:HIS135 3.1 52.0 1.0
CE1 A:HIS135 3.2 52.0 1.0
CD2 C:HIS306 3.2 53.6 1.0
CD2 A:HIS100 3.4 53.6 1.0
ND1 A:HIS100 4.0 53.6 1.0
NE2 C:HIS255 4.1 52.6 1.0
ND1 C:HIS306 4.1 53.6 1.0
CD2 C:HIS255 4.2 52.6 1.0
CG C:HIS306 4.3 53.6 1.0
ND1 A:HIS135 4.3 52.0 1.0
CG A:HIS135 4.3 52.0 1.0
CG A:HIS100 4.3 53.6 1.0
OD2 A:ASP98 4.8 57.2 1.0
CE1 C:HIS255 5.0 52.6 1.0

Copper binding site 3 out of 6 in 6kng

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Copper binding site 3 out of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:74.7
occ:1.00
ND1 B:HIS95 2.2 58.1 1.0
ND1 B:HIS145 2.2 56.2 1.0
SG B:CYS136 2.3 56.2 1.0
SD B:MET150 2.4 54.2 1.0
CE1 B:HIS95 3.0 58.1 1.0
CE1 B:HIS145 3.0 56.2 1.0
CB B:CYS136 3.2 56.2 1.0
CG B:HIS145 3.3 56.2 1.0
CG B:HIS95 3.3 58.1 1.0
CE B:MET150 3.3 54.2 1.0
CB B:HIS145 3.7 56.2 1.0
CB B:HIS95 3.7 58.1 1.0
CG B:MET150 4.0 54.2 1.0
CA B:HIS95 4.1 58.1 1.0
NE2 B:HIS95 4.1 58.1 1.0
NE2 B:HIS145 4.2 56.2 1.0
CD2 B:HIS145 4.3 56.2 1.0
CD2 B:HIS95 4.3 58.1 1.0
CG B:PRO138 4.3 59.0 1.0
O B:LEU94 4.5 59.6 1.0
CB B:MET150 4.5 54.2 1.0
SD B:MET62 4.5 60.4 1.0
CA B:CYS136 4.7 56.2 1.0
CD B:PRO138 4.7 59.0 1.0
CA B:HIS145 4.8 56.2 1.0
N B:ASN96 4.9 57.0 1.0

Copper binding site 4 out of 6 in 6kng

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Copper binding site 4 out of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:78.0
occ:1.00
NE2 B:HIS100 2.1 54.0 1.0
NE2 A:HIS306 2.1 54.7 1.0
NE2 B:HIS135 2.2 52.3 1.0
CE1 B:HIS100 2.7 54.0 1.0
CE1 A:HIS306 3.0 54.7 1.0
CD2 B:HIS135 3.1 52.3 1.0
CE1 B:HIS135 3.2 52.3 1.0
CD2 A:HIS306 3.2 54.7 1.0
CD2 B:HIS100 3.4 54.0 1.0
ND1 B:HIS100 4.0 54.0 1.0
NE2 A:HIS255 4.1 52.7 1.0
ND1 A:HIS306 4.1 54.7 1.0
CD2 A:HIS255 4.2 52.7 1.0
ND1 B:HIS135 4.3 52.3 1.0
CG A:HIS306 4.3 54.7 1.0
CG B:HIS100 4.3 54.0 1.0
CG B:HIS135 4.3 52.3 1.0
OD2 B:ASP98 4.8 57.6 1.0
CE1 A:HIS255 5.0 52.7 1.0

Copper binding site 5 out of 6 in 6kng

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Copper binding site 5 out of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu500

b:74.0
occ:1.00
ND1 C:HIS95 2.2 58.7 1.0
ND1 C:HIS145 2.2 55.7 1.0
SG C:CYS136 2.3 56.8 1.0
SD C:MET150 2.4 54.2 1.0
CE1 C:HIS95 3.0 58.7 1.0
CE1 C:HIS145 3.0 55.7 1.0
CB C:CYS136 3.2 56.8 1.0
CG C:HIS145 3.3 55.7 1.0
CG C:HIS95 3.3 58.7 1.0
CE C:MET150 3.3 54.2 1.0
CB C:HIS145 3.7 55.7 1.0
CB C:HIS95 3.7 58.7 1.0
CG C:MET150 4.0 54.2 1.0
CA C:HIS95 4.1 58.7 1.0
NE2 C:HIS95 4.1 58.7 1.0
NE2 C:HIS145 4.2 55.7 1.0
CD2 C:HIS145 4.3 55.7 1.0
CD2 C:HIS95 4.3 58.7 1.0
CG C:PRO138 4.3 59.9 1.0
O C:LEU94 4.5 61.9 1.0
CB C:MET150 4.5 54.2 1.0
SD C:MET62 4.5 59.9 1.0
CA C:CYS136 4.7 56.8 1.0
CD C:PRO138 4.7 59.9 1.0
CA C:HIS145 4.8 55.7 1.0
N C:ASN96 4.9 57.8 1.0

Copper binding site 6 out of 6 in 6kng

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Copper binding site 6 out of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:77.6
occ:1.00
NE2 C:HIS100 2.1 54.7 1.0
NE2 B:HIS306 2.1 53.7 1.0
NE2 C:HIS135 2.2 53.0 1.0
CE1 C:HIS100 2.7 54.7 1.0
CE1 B:HIS306 3.0 53.7 1.0
CD2 C:HIS135 3.1 53.0 1.0
CE1 C:HIS135 3.2 53.0 1.0
CD2 B:HIS306 3.2 53.7 1.0
CD2 C:HIS100 3.4 54.7 1.0
ND1 C:HIS100 4.0 54.7 1.0
NE2 B:HIS255 4.0 53.0 1.0
ND1 B:HIS306 4.1 53.7 1.0
CD2 B:HIS255 4.2 53.0 1.0
ND1 C:HIS135 4.3 53.0 1.0
CG B:HIS306 4.3 53.7 1.0
CG C:HIS135 4.3 53.0 1.0
CG C:HIS100 4.3 54.7 1.0
OD2 C:ASP98 4.8 58.4 1.0
CE1 B:HIS255 4.9 53.0 1.0

Reference:

N.Adachi, T.Yamaguchi, T.Moriya, M.Kawasaki, K.Koiwai, A.Shinoda, Y.Yamada, F.Yumoto, T.Kohzuma, T.Senda. Cryoem Map and Model of Nitrite Reductase at pH 8.1 To Be Published.
Page generated: Sun Dec 13 11:23:36 2020

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