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Copper in PDB 6zat: Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx)

Enzymatic activity of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx)

All present enzymatic activity of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx):
1.7.2.1;

Protein crystallography data

The structure of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx), PDB code: 6zat was solved by S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.00
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.786, 106.786, 106.786, 90, 90, 90
R / Rfree (%) 12.6 / n/a

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx) (pdb code 6zat). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx), PDB code: 6zat:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 6zat

Go back to Copper Binding Sites List in 6zat
Copper binding site 1 out of 3 in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:7.5
occ:0.68
 CU A:CU501 0.0 7.5 0.7
CU A:CU501 0.4 8.9 0.3
ND1 A:HIS140 1.9 8.1 1.0
ND1 A:HIS89 2.0 7.8 1.0
SG A:CYS130 2.2 7.9 1.0
SD A:MET145 2.7 8.2 1.0
CE1 A:HIS140 2.8 8.3 1.0
CE1 A:HIS89 2.9 7.8 1.0
CG A:HIS140 3.0 8.1 1.0
CG A:HIS89 3.1 7.8 1.0
CB A:CYS130 3.3 7.1 1.0
CB A:HIS140 3.4 8.3 1.0
CE A:MET145 3.4 9.1 1.0
CB A:HIS89 3.5 7.5 1.0
CA A:HIS89 3.8 7.8 1.0
CG A:PRO132 3.9 7.5 0.4
O A:PRO88 3.9 9.1 1.0
NE2 A:HIS140 4.0 9.3 1.0
CD2 A:HIS140 4.1 10.4 1.0
NE2 A:HIS89 4.1 8.1 1.0
CG A:MET145 4.1 8.5 1.0
CG A:PRO132 4.2 8.6 0.6
CD2 A:HIS89 4.2 8.0 1.0
CD A:PRO132 4.4 7.1 0.4
CD A:PRO132 4.6 8.5 0.6
CB A:MET145 4.6 7.2 1.0
N A:ASN90 4.7 7.9 1.0
SD A:MET56 4.7 9.1 0.6
CA A:CYS130 4.7 6.8 1.0
CA A:HIS140 4.7 7.4 1.0
N A:HIS89 4.7 8.1 1.0
C A:PRO88 4.8 8.3 1.0
C A:HIS89 4.8 7.7 1.0

Copper binding site 2 out of 3 in 6zat

Go back to Copper Binding Sites List in 6zat
Copper binding site 2 out of 3 in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:8.9
occ:0.32
 CU A:CU501 0.0 8.9 0.3
CU A:CU501 0.4 7.5 0.7
ND1 A:HIS89 2.1 7.8 1.0
SG A:CYS130 2.1 7.9 1.0
ND1 A:HIS140 2.3 8.1 1.0
SD A:MET145 2.3 8.2 1.0
CE1 A:HIS89 3.0 7.8 1.0
CE A:MET145 3.1 9.1 1.0
CB A:CYS130 3.1 7.1 1.0
CG A:HIS89 3.1 7.8 1.0
CE1 A:HIS140 3.2 8.3 1.0
CG A:HIS140 3.3 8.1 1.0
CB A:HIS89 3.4 7.5 1.0
CB A:HIS140 3.5 8.3 1.0
CG A:MET145 3.8 8.5 1.0
CA A:HIS89 3.9 7.8 1.0
NE2 A:HIS89 4.2 8.1 1.0
CG A:PRO132 4.2 7.5 0.4
CD2 A:HIS89 4.2 8.0 1.0
O A:PRO88 4.2 9.1 1.0
CB A:MET145 4.3 7.2 1.0
NE2 A:HIS140 4.4 9.3 1.0
CD2 A:HIS140 4.4 10.4 1.0
CG A:PRO132 4.5 8.6 0.6
CA A:CYS130 4.5 6.8 1.0
N A:ASN90 4.6 7.9 1.0
CD A:PRO132 4.6 7.1 0.4
SD A:MET56 4.7 9.1 0.6
CA A:HIS140 4.8 7.4 1.0
C A:HIS89 4.8 7.7 1.0
CD A:PRO132 4.8 8.5 0.6
N A:HIS89 4.9 8.1 1.0
O A:ASN90 5.0 8.4 1.0
C A:PRO88 5.0 8.3 1.0

Copper binding site 3 out of 3 in 6zat

Go back to Copper Binding Sites List in 6zat
Copper binding site 3 out of 3 in the Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Nitrite-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) at 1.0 A Resolution (Unrestrained Full Matrix Refinement By Shelx) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:7.8
occ:0.95
 O2 A:NO2503 2.0 15.1 0.5
NE2 A:HIS94 2.0 6.9 1.0
NE2 A:HIS129 2.0 7.1 1.0
O2 A:NO2503 2.1 12.3 0.5
O1 A:NO2503 2.1 12.5 0.5
O1 A:NO2503 2.2 13.2 0.5
N A:NO2503 2.4 13.7 0.5
N A:NO2503 2.4 12.6 0.5
CE1 A:HIS94 3.0 6.4 1.0
CD2 A:HIS129 3.0 6.8 1.0
CE1 A:HIS129 3.0 7.2 1.0
CD2 A:HIS94 3.1 6.1 1.0
OD2 A:ASP92 3.5 18.4 0.6
ND1 A:HIS94 4.1 6.4 1.0
ND1 A:HIS129 4.2 6.9 1.0
CG A:HIS94 4.2 5.7 1.0
CG A:HIS129 4.2 6.8 1.0
CG A:ASP92 4.2 10.5 0.6
O A:HOH618 4.3 19.2 0.6
O A:HOH671 4.3 10.1 0.4
OD1 A:ASP92 4.6 9.0 0.6
OD2 A:ASP92 4.7 8.4 0.4
O A:HOH731 4.9 20.0 0.5
O A:HOH961 4.9 11.1 0.6

Reference:

S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain. An Unprecedented Insight Into the Catalytic Mechanism of Copper Nitrite Reductase From Atomic-Resolution and Damage-Free Structures Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABD8523
Page generated: Wed Jul 31 07:58:15 2024

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