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Copper in PDB 4ysd: Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans

Protein crystallography data

The structure of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 4ysd was solved by Y.Fukuda, K.M.Tse, M.Suzuki, K.Diederichs, K.Hirata, T.Nakane, M.Sugahara, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, H.Matsumura, T.Inoue, S.Iwata, E.Mizohata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.53 / 1.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 116.197, 116.197, 85.553, 90.00, 90.00, 120.00
R / Rfree (%) 9.7 / 12.1

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Copper atom in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 4ysd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 13 binding sites of Copper where determined in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 4ysd:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 13 in 4ysd

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Copper binding site 1 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


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Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:11.6
occ:0.90
 ND1 A:HIS143 1.9 12.9 1.0
ND1 A:HIS95 2.0 12.4 1.0
SG A:CYS135 2.2 12.8 1.0
SD A:MET148 2.6 12.4 0.8
CE1 A:HIS143 2.9 13.6 1.0
CE1 A:HIS95 2.9 13.1 1.0
CG A:HIS143 3.1 13.2 1.0
CG A:HIS95 3.1 12.1 1.0
CB A:CYS135 3.2 11.5 1.0
CB A:HIS143 3.4 12.9 1.0
CB A:HIS95 3.5 13.4 1.0
CE A:MET148 3.5 12.2 0.8
CE A:MET148 3.6 18.3 0.2
CA A:HIS95 3.8 11.8 1.0
CG A:MET148 3.9 17.6 0.2
O A:PRO94 4.0 14.2 1.0
NE2 A:HIS143 4.0 14.0 1.0
NE2 A:HIS95 4.1 13.2 1.0
CG A:MET148 4.1 12.8 0.8
CD2 A:HIS143 4.1 13.9 1.0
CD2 A:HIS95 4.2 13.5 1.0
CB A:THR137 4.4 12.5 1.0
OG1 A:THR137 4.4 14.4 1.0
SD A:MET148 4.5 30.6 0.2
CA A:HIS143 4.5 12.1 1.0
CB A:MET148 4.5 12.7 0.2
N A:SER96 4.5 12.7 1.0
CA A:CYS135 4.6 10.8 1.0
CE3 A:TRP63 4.6 13.3 1.0
CB A:MET148 4.6 11.7 0.8
C A:HIS95 4.7 12.2 1.0
N A:HIS95 4.8 13.1 1.0
C A:PRO94 4.8 13.2 1.0

Copper binding site 2 out of 13 in 4ysd

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Copper binding site 2 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:10.4
occ:0.90
 NE2 A:HIS100 2.0 10.5 1.0
NE2 A:HIS134 2.1 11.0 1.0
O A:HOH681 2.2 11.4 1.0
O A:HOH504 2.4 14.3 0.5
CE1 A:HIS100 3.0 10.3 1.0
CD2 A:HIS100 3.0 9.9 1.0
CD2 A:HIS134 3.1 10.8 1.0
CE1 A:HIS134 3.1 11.1 1.0
CU A:CU411 3.7 24.7 0.2
OD2 A:ASP98 4.0 18.3 1.0
ND1 A:HIS100 4.1 10.4 1.0
CG A:HIS100 4.2 9.1 1.0
ND1 A:HIS134 4.2 11.2 1.0
CG A:HIS134 4.2 10.0 1.0
CG A:ASP98 4.5 14.1 1.0
OD1 A:ASP98 4.6 14.9 1.0
O A:HOH698 4.8 30.1 1.0
O A:HOH616 4.8 14.1 0.8

Copper binding site 3 out of 13 in 4ysd

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Copper binding site 3 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:47.0
occ:0.40
 OD1 A:ASP55 2.1 17.6 1.0
O A:HOH521 2.3 34.7 0.5
O A:HOH546 2.5 28.6 0.3
CG A:ASP55 2.9 15.0 1.0
OD2 A:ASP55 3.0 18.8 1.0
OG1 A:THR212 4.0 13.5 1.0
O A:HOH623 4.0 39.7 1.0
O A:HOH686 4.2 47.8 1.0
CB A:ASP55 4.4 13.9 1.0
N A:LYS56 4.4 15.1 1.0
CB A:THR212 4.7 12.4 1.0
CA A:ASP55 4.9 11.9 1.0
CB A:LYS56 5.0 21.3 1.0

Copper binding site 4 out of 13 in 4ysd

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Copper binding site 4 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:51.9
occ:0.60
 O A:HOH677 2.0 51.6 0.8
NE2 A:HIS39 2.1 33.1 1.0
CE1 A:HIS39 3.1 31.3 1.0
CD2 A:HIS39 3.1 27.6 1.0
ND1 A:HIS39 4.2 25.3 1.0
CG A:HIS39 4.2 22.3 1.0
CB A:PRO38 4.8 23.2 1.0

Copper binding site 5 out of 13 in 4ysd

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Copper binding site 5 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:26.5
occ:0.40
 O A:HOH503 1.9 30.0 0.3
O A:HOH501 2.0 34.3 0.7
OD2 A:ASP167 2.1 20.6 1.0
OXT A:ACY413 2.1 26.0 0.3
O A:HOH511 2.1 51.5 1.0
O A:ACY413 2.3 33.1 0.3
O A:HOH528 2.4 44.0 1.0
C A:ACY413 2.5 25.1 0.3
CG A:ASP167 2.8 22.8 1.0
OD1 A:ASP167 2.9 27.9 1.0
O A:GLU165 4.0 24.2 1.0
CH3 A:ACY413 4.0 29.6 0.3
O A:GLY225 4.2 22.5 1.0
N A:LYS227 4.2 15.5 1.0
CB A:ASP167 4.2 18.6 1.0
CA A:GLU226 4.5 17.0 1.0
CB A:LYS227 4.9 17.7 1.0
C A:GLU226 4.9 14.6 1.0

Copper binding site 6 out of 13 in 4ysd

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Copper binding site 6 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:11.7
occ:0.85
 ND1 A:HIS83 2.0 12.9 1.0
O A:HOH605 2.0 24.9 1.0
NE2 A:HIS42 2.0 13.5 1.0
O A:HOH680 2.4 19.6 1.0
CE1 A:HIS83 2.9 14.8 1.0
CE1 A:HIS42 2.9 14.2 1.0
CD2 A:HIS42 3.1 13.6 1.0
CG A:HIS83 3.1 12.8 1.0
CB A:HIS83 3.6 14.0 1.0
NE2 A:HIS83 4.1 14.9 1.0
ND1 A:HIS42 4.1 14.7 1.0
O A:HOH642 4.1 31.0 1.0
CG A:HIS42 4.2 13.4 1.0
CD2 A:HIS83 4.2 15.7 1.0
O A:HOH703 4.2 33.3 1.0
O A:HOH696 4.4 23.4 1.0
O A:HOH704 4.4 37.8 1.0
O A:HOH701 4.6 22.2 1.0
CG2 A:VAL36 4.7 18.2 1.0

Copper binding site 7 out of 13 in 4ysd

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Copper binding site 7 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:12.5
occ:0.28
 SD A:MET270 2.1 11.5 0.3
SD A:MET270 2.3 13.2 0.3
SD A:MET270 2.5 16.0 0.4
CE A:MET270 2.9 20.1 0.3
CG A:MET270 3.2 7.3 0.3
CE A:MET270 3.2 9.9 0.3
CG A:MET270 3.2 14.6 0.3
CE A:MET270 3.4 15.1 0.4
CG A:MET270 3.5 14.3 0.4
CB A:MET270 3.6 12.7 0.3
CB A:MET270 3.7 8.4 0.3
CB A:MET270 3.7 15.1 0.4
CA A:MET270 5.0 10.9 0.3

Copper binding site 8 out of 13 in 4ysd

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Copper binding site 8 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:18.3
occ:0.30
 ND1 A:HIS21 1.9 21.6 1.0
O A:HOH683 1.9 22.8 0.8
CE1 A:HIS21 2.7 20.4 1.0
O A:HOH683 2.8 11.5 0.2
CG A:HIS21 2.8 18.2 1.0
NE1 A:TRP63 3.3 16.1 1.0
CB A:HIS21 3.3 20.5 1.0
CD1 A:ILE18 3.4 46.7 1.0
OH A:TYR180 3.5 22.5 0.3
CB A:ILE18 3.5 41.4 1.0
CG1 A:ILE18 3.7 45.8 1.0
NE2 A:HIS21 3.8 18.9 1.0
CD2 A:HIS21 3.9 19.5 1.0
OH A:TYR180 3.9 19.3 0.7
CE2 A:TRP63 3.9 14.2 1.0
N A:ILE18 3.9 39.8 1.0
CZ2 A:TRP63 3.9 16.4 1.0
CA A:ILE18 4.4 40.6 1.0
CD1 A:TRP63 4.4 15.1 1.0
CG2 A:VAL17 4.5 40.2 1.0
CG2 A:ILE18 4.6 49.3 1.0
CZ A:TYR180 4.7 20.6 0.3
O A:ILE18 4.8 35.9 1.0
CA A:HIS21 4.8 21.2 1.0
C A:VAL17 4.9 52.0 1.0
CA A:VAL17 4.9 62.1 1.0
CZ A:TYR180 4.9 15.5 0.7

Copper binding site 9 out of 13 in 4ysd

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Copper binding site 9 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu409

b:19.0
occ:0.20
 CU A:CU409 0.0 19.0 0.2
O A:HOH671 1.2 24.5 0.8
CU A:CU409 2.1 21.9 0.3
NE2 A:HIS298 2.2 11.8 1.0
OE1 A:GLU239 2.4 14.4 0.1
OE2 A:GLU239 2.6 29.9 0.9
CD A:GLU239 3.0 18.9 0.9
O A:HOH599 3.1 23.8 1.0
OE1 A:GLU239 3.2 20.0 0.9
CE1 A:HIS298 3.2 13.2 1.0
CD2 A:HIS298 3.2 10.5 1.0
CD A:GLU239 3.3 11.8 0.1
O A:HOH691 3.3 35.1 0.7
CD A:PRO191 3.6 13.1 1.0
CG A:PRO191 3.9 17.5 1.0
CG A:GLU239 3.9 12.2 0.1
CU A:CU412 4.0 23.1 0.2
CG A:GLU239 4.0 14.2 0.9
OE2 A:GLU239 4.1 14.2 0.1
O A:HOH682 4.3 35.4 1.0
ND1 A:HIS298 4.3 11.0 1.0
CG A:HIS298 4.4 8.9 1.0
ND2 A:ASN297 4.4 15.1 1.0
OD1 A:ASN297 4.9 11.2 1.0
CG A:ASN297 4.9 10.0 1.0
N A:PRO191 4.9 11.1 1.0

Copper binding site 10 out of 13 in 4ysd

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Copper binding site 10 out of 13 in the Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Room Temperature Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu409

b:21.9
occ:0.30
 CU A:CU409 0.0 21.9 0.3
O A:HOH691 1.7 35.1 0.7
CU A:CU409 2.1 19.0 0.2
O A:HOH671 2.2 24.5 0.8
OE1 A:GLU239 2.2 14.4 0.1
OE2 A:GLU239 2.3 29.9 0.9
CU A:CU412 2.4 23.1 0.2
OE1 A:GLU239 3.0 20.0 0.9
CD A:GLU239 3.0 18.9 0.9
CD A:GLU239 3.0 11.8 0.1
OE2 A:GLU239 3.2 14.2 0.1
O A:HOH649 3.9 25.0 1.0
CD A:PRO191 4.1 13.1 1.0
O A:HOH637 4.2 37.1 1.0
NE2 A:HIS298 4.2 11.8 1.0
O A:HOH688 4.2 50.8 1.0
CG A:GLU239 4.3 12.2 0.1
CG A:GLU239 4.4 14.2 0.9
O A:HOH599 4.6 23.8 1.0
CG1 A:VAL190 4.6 19.8 1.0
O A:HOH682 4.7 35.4 1.0
CE1 A:HIS298 4.8 13.2 1.0
CG A:PRO191 4.9 17.5 1.0
CA A:VAL190 4.9 13.2 1.0
CB A:VAL190 4.9 16.0 1.0

Reference:

Y.Fukuda, K.M.Tse, M.Suzuki, K.Diederichs, K.Hirata, T.Nakane, M.Sugahara, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, H.Matsumura, T.Inoue, S.Iwata, E.Mizohata. Redox-Coupled Structural Changes in Nitrite Reductase Revealed By Serial Femtosecond and Microfocus Crystallography J.Biochem. V. 159 527 2016.
ISSN: ISSN 0021-924X
PubMed: 26769972
DOI: 10.1093/JB/MVV133
Page generated: Sun Dec 13 11:16:20 2020

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