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Zinc in PDB 1ych: X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase

Protein crystallography data

The structure of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ych 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) 43.91 / 2.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 160.327, 160.327, 279.144, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.5

Other elements in 1ych:

The structure of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase also contains other interesting chemical elements:

Iron (Fe) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb code 1ych). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ych:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1ych

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Zinc binding site 1 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:91.6
occ:1.00
OE2 A:GLU60 2.7 66.2 1.0
OG A:SER2 3.0 77.5 1.0
CB A:SER2 3.2 76.3 1.0
CD A:GLU60 3.8 68.2 1.0
CA A:SER2 3.8 74.7 1.0
OE1 A:GLU60 4.2 70.0 1.0
N A:SER2 4.3 75.1 1.0
O A:HOH768 4.9 66.2 1.0

Zinc binding site 2 out of 8 in 1ych

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Zinc binding site 2 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:82.8
occ:1.00
NE2 A:HIS271 2.5 59.8 1.0
OD2 A:ASP275 3.0 60.6 1.0
OD1 A:ASP275 3.0 61.1 1.0
CE1 A:HIS271 3.2 59.7 1.0
CG A:ASP275 3.4 60.0 1.0
CD2 A:HIS271 3.7 58.7 1.0
ND1 A:HIS271 4.4 58.4 1.0
CG A:HIS271 4.7 57.2 1.0
CB A:ASP275 4.8 56.2 1.0

Zinc binding site 3 out of 8 in 1ych

Go back to Zinc Binding Sites List in 1ych
Zinc binding site 3 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn610

b:90.9
occ:1.00
OE2 B:GLU60 2.9 62.9 1.0
CB B:SER2 3.2 76.3 1.0
OG B:SER2 3.4 78.0 1.0
CA B:SER2 3.8 76.1 1.0
CD B:GLU60 3.8 63.6 1.0
OE1 B:GLU60 4.0 63.5 1.0
N B:SER2 4.5 75.0 1.0

Zinc binding site 4 out of 8 in 1ych

Go back to Zinc Binding Sites List in 1ych
Zinc binding site 4 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn611

b:86.5
occ:1.00
NE2 B:HIS271 2.5 65.1 1.0
OD2 B:ASP275 2.6 62.7 1.0
OD1 B:ASP275 2.8 62.7 1.0
CG B:ASP275 3.1 63.1 1.0
CE1 B:HIS271 3.3 65.8 1.0
CD2 B:HIS271 3.5 64.7 1.0
ND1 B:HIS271 4.5 65.6 1.0
CB B:ASP275 4.6 60.4 1.0
CG B:HIS271 4.6 64.7 1.0

Zinc binding site 5 out of 8 in 1ych

Go back to Zinc Binding Sites List in 1ych
Zinc binding site 5 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn620

b:80.5
occ:1.00
OE2 C:GLU60 2.7 50.0 1.0
CB C:SER2 3.0 72.8 1.0
OG C:SER2 3.0 75.5 1.0
CA C:SER2 3.6 69.8 1.0
CD C:GLU60 3.7 53.0 1.0
OE1 C:GLU60 4.0 55.1 1.0
N C:SER2 4.2 69.3 1.0

Zinc binding site 6 out of 8 in 1ych

Go back to Zinc Binding Sites List in 1ych
Zinc binding site 6 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn621

b:96.1
occ:1.00
NE2 C:HIS271 2.5 54.3 1.0
OD2 C:ASP275 3.0 64.0 1.0
OD1 C:ASP275 3.2 64.4 1.0
CE1 C:HIS271 3.4 55.6 1.0
CG C:ASP275 3.5 64.4 1.0
CD2 C:HIS271 3.6 53.7 1.0
ND1 C:HIS271 4.6 55.1 1.0
CG C:HIS271 4.7 54.9 1.0
CB C:ASP275 5.0 62.4 1.0

Zinc binding site 7 out of 8 in 1ych

Go back to Zinc Binding Sites List in 1ych
Zinc binding site 7 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn630

b:81.8
occ:1.00
OE2 D:GLU60 2.7 63.8 1.0
CB D:SER2 2.9 75.1 1.0
OG D:SER2 3.2 75.3 1.0
CA D:SER2 3.7 73.8 1.0
CD D:GLU60 3.8 63.6 1.0
N D:SER2 4.2 74.2 1.0
OE1 D:GLU60 4.3 65.1 1.0

Zinc binding site 8 out of 8 in 1ych

Go back to Zinc Binding Sites List in 1ych
Zinc binding site 8 out of 8 in the X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of X-Ray Crystal Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn631

b:93.0
occ:1.00
NE2 D:HIS271 2.7 53.3 1.0
OD1 D:ASP275 3.0 65.3 1.0
OD2 D:ASP275 3.3 68.6 1.0
CG D:ASP275 3.5 64.6 1.0
CE1 D:HIS271 3.6 54.4 1.0
CD2 D:HIS271 3.7 51.0 1.0
ND1 D:HIS271 4.7 52.6 1.0
CG D:HIS271 4.8 50.5 1.0
CB D:ASP275 4.9 61.2 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: Wed Oct 16 20:50:43 2024

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