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Yttrium in PDB 6the: Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

Enzymatic activity of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375

All present enzymatic activity of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375, PDB code: 6the was solved by D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.57 / 2.87
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 125.141, 125.141, 125.141, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 23.4

Other elements in 6the:

The structure of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 also contains other interesting chemical elements:

Ytterbium (Yb) 3 atoms
Erbium (Er) 4 atoms
Terbium (Tb) 1 atom
Chlorine (Cl) 1 atom
Copper (Cu) 2 atoms

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (pdb code 6the). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 2 binding sites of Yttrium where determined in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375, PDB code: 6the:
Jump to Yttrium binding site number: 1; 2;

Yttrium binding site 1 out of 2 in 6the

Go back to Yttrium Binding Sites List in 6the
Yttrium binding site 1 out of 2 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y511

b:39.1
occ:0.50
TB A:TB510 3.1 38.6 0.6
ER A:ER3507 3.8 34.0 0.2
OD2 A:ASP154 3.9 24.8 1.0
CG A:ASP154 4.8 24.7 1.0
OD1 A:ASP154 4.9 24.8 1.0

Yttrium binding site 2 out of 2 in 6the

Go back to Yttrium Binding Sites List in 6the
Yttrium binding site 2 out of 2 in the Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Crystal Structure of Core Domain of Four-Domain Heme-Cupredoxin-Cu Nitrite Reductase From Bradyrhizobium Sp. Ors 375 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y512

b:12.0
occ:0.20
O A:VAL17 3.7 25.9 1.0
OD1 A:ASP16 3.9 25.6 1.0
CA A:PRO18 3.9 26.1 1.0
C A:VAL17 4.0 25.8 1.0
N A:PRO18 4.0 25.9 1.0
N A:VAL17 4.7 25.4 1.0
CB A:PRO18 4.7 26.0 1.0
CD A:PRO19 4.7 26.6 1.0
CG A:PRO18 4.8 25.9 1.0
CD A:PRO18 4.8 25.9 1.0
CA A:VAL17 4.9 25.6 1.0

Reference:

D.Sasaki, T.F.Watanabe, R.R.Eady, R.C.Garratt, S.V.Antonyuk, S.S.Hasnain. Reverse Protein Engineering of A Novel 4-Domain Copper Nitrite Reductase Reveals Functional Regulation By Protein-Protein Interaction. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32255260
DOI: 10.1111/FEBS.15324
Page generated: Wed Dec 16 02:41:19 2020

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