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Ytterbium 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:

Yttrium (Y) 2 atoms
Erbium (Er) 4 atoms
Terbium (Tb) 1 atom
Chlorine (Cl) 1 atom
Copper (Cu) 2 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium 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 Ytterbium atom.
In total 3 binding sites of Ytterbium 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 Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 6the

Go back to Ytterbium Binding Sites List in 6the
Ytterbium binding site 1 out of 3 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 Ytterbium with other atoms in the Yb 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:Yb503

b:33.4
occ:1.00
OE1 A:GLU104 4.2 24.9 1.0
OE2 A:GLU104 4.6 24.9 1.0
CD1 A:ILE83 4.6 26.8 1.0
CD A:GLU104 4.8 24.8 1.0
CG1 A:ILE83 4.9 26.8 1.0

Ytterbium binding site 2 out of 3 in 6the

Go back to Ytterbium Binding Sites List in 6the
Ytterbium binding site 2 out of 3 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 Ytterbium with other atoms in the Yb 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:Yb504

b:24.3
occ:0.20
N A:THR275 3.8 24.7 1.0
OG1 A:THR275 3.9 24.3 1.0
CB A:THR275 4.1 24.4 1.0
CA A:GLY274 4.3 25.2 1.0
C A:GLY274 4.5 24.9 1.0
CA A:THR275 4.6 24.4 1.0

Ytterbium binding site 3 out of 3 in 6the

Go back to Ytterbium Binding Sites List in 6the
Ytterbium binding site 3 out of 3 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 Ytterbium with other atoms in the Yb binding site number 3 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:Yb505

b:32.9
occ:0.20
O A:HOH650 2.8 18.7 1.0
N A:ARG63 3.5 21.6 1.0
O01 A:9JE517 3.8 42.3 1.0
O A:ARG63 3.8 22.1 1.0
CA A:LEU62 3.9 21.1 1.0
CD2 A:LEU62 4.1 21.1 1.0
CB A:LEU62 4.1 21.1 1.0
C A:LEU62 4.2 21.3 1.0
C A:ARG63 4.4 22.1 1.0
CA A:ARG63 4.4 21.9 1.0
C03 A:9JE517 4.4 42.1 1.0
CG2 A:VAL31 4.7 25.3 1.0
C02 A:9JE517 4.7 42.2 1.0
CG1 A:VAL29 4.7 25.5 1.0
CG A:LEU62 4.8 21.1 1.0
CB A:ARG63 4.9 21.9 1.0
O A:LEU61 4.9 20.8 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 02:42:19 2020

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