Atomistry » Copper » PDB 4rkn-4yss » 4ysd
Atomistry »
  Copper »
    PDB 4rkn-4yss »
      4ysd »

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

Go back to Copper Binding Sites List in 4ysd
Copper binding site 1 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 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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Go back to Copper Binding Sites List in 4ysd
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy