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Zinc in PDB 1ycf: Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica

Protein crystallography data

The structure of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica, PDB code: 1ycf was solved by R.Silaghi-Dumitrescu, D.M.Kurtz, W.N.Lanzilotta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.670, 159.670, 276.798, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 26

Other elements in 1ycf:

The structure of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica (pdb code 1ycf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica, PDB code: 1ycf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1ycf

Go back to Zinc Binding Sites List in 1ycf
Zinc binding site 1 out of 3 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:70.8
occ:1.00
OG A:SER2 1.8 70.6 1.0
N A:SER2 2.6 51.6 1.0
CB A:SER2 2.7 75.0 1.0
CA A:SER2 2.7 65.0 1.0
OE2 A:GLU60 3.0 56.7 1.0
CD A:GLU60 4.2 69.6 1.0
C A:SER2 4.2 62.2 1.0
OE1 A:GLU60 4.7 80.8 1.0
O A:SER2 4.9 70.2 1.0

Zinc binding site 2 out of 3 in 1ycf

Go back to Zinc Binding Sites List in 1ycf
Zinc binding site 2 out of 3 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:71.5
occ:1.00
NE2 A:HIS271 2.2 68.4 1.0
OD2 A:ASP275 2.5 59.5 1.0
CD2 A:HIS271 3.1 61.1 1.0
CE1 A:HIS271 3.2 65.3 1.0
CG A:ASP275 3.3 55.3 1.0
OD1 A:ASP275 3.3 52.5 1.0
CG A:HIS271 4.2 50.3 1.0
ND1 A:HIS271 4.2 57.7 1.0
O A:HOH654 4.5 56.1 1.0
CB A:ASP275 4.7 46.8 1.0

Zinc binding site 3 out of 3 in 1ycf

Go back to Zinc Binding Sites List in 1ycf
Zinc binding site 3 out of 3 in the Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Oxidized (Di-Ferric) Fpra From Moorella Thermoacetica within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn512

b:0.5
occ:1.00
N B:VAL17 3.4 45.8 1.0
O B:VAL17 3.7 40.0 1.0
CB B:VAL17 3.9 29.7 1.0
CA B:VAL17 4.1 34.5 1.0
CG2 B:VAL17 4.2 24.8 1.0
C B:VAL17 4.3 38.0 1.0
CD B:GLU60 4.3 64.9 1.0
OE1 B:GLU60 4.4 65.1 1.0
C B:ALA16 4.4 49.1 1.0
CA B:ALA16 4.4 47.1 1.0
CG B:GLU60 4.4 59.9 1.0
CB B:ALA16 4.5 41.5 1.0
NZ B:LYS64 4.7 38.4 1.0
OE2 B:GLU60 4.7 42.4 1.0
N B:SER2 4.8 71.1 1.0
O B:HOH628 4.9 5.6 1.0
NE1 B:TRP19 4.9 52.7 1.0

Reference:

R.Silaghi-Dumitrescu, D.M.Kurtz Jr, L.G.Ljungdahl, W.N.Lanzilotta. X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase. Biochemistry V. 44 6492 2005.
ISSN: ISSN 0006-2960
PubMed: 15850383
DOI: 10.1021/BI0473049
Page generated: Thu Oct 29 07:42:07 2020
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