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

The structure of X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ycg 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 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	159.680, 159.680, 278.136, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 24.5

The structure of X-Ray 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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase (pdb code 1ycg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the X-Ray Structures of Moorella Thermoacetica Fpra. Novel Diiron Site Structure and Mechanistic Insights Into A Scavenging Nitric Oxide Reductase, PDB code: 1ycg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the X-Ray 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 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:Zn401 b:81.0 occ:1.00 OE2 A:GLU60 2.8 61.0 1.0 CB A:SER2 2.9 68.0 1.0 OG A:SER2 3.0 70.1 1.0 CA A:SER2 3.5 67.0 1.0 CD A:GLU60 3.8 60.8 1.0 N A:SER2 4.1 66.7 1.0 OE1 A:GLU60 4.1 62.1 1.0 C A:SER2 4.8 66.1 1.0

Zinc binding site 2 out of 14 in the X-Ray 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 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:Zn402 b:87.1 occ:1.00 NE2 A:HIS271 2.5 53.5 1.0 OD2 A:ASP275 3.0 54.0 1.0 OD1 A:ASP275 3.1 53.7 1.0 CE1 A:HIS271 3.1 53.4 1.0 CG A:ASP275 3.4 52.2 1.0 CD2 A:HIS271 3.6 51.5 1.0 ND1 A:HIS271 4.3 51.1 1.0 CG A:HIS271 4.6 49.2 1.0 CB A:ASP275 4.8 49.9 1.0

Zinc binding site 3 out of 14 in the X-Ray 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 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:Zn403 b:0.6 occ:1.00 O D:HOH761 1.6 89.9 1.0 OE2 D:GLU388 1.8 60.9 1.0 O A:HOH729 2.2 42.9 1.0 ND1 A:HIS118 2.7 81.8 1.0 CD D:GLU388 2.9 60.2 1.0 CG A:HIS118 3.2 79.7 1.0 CB A:HIS118 3.3 77.3 1.0 OE1 D:GLU388 3.4 60.7 1.0 CE1 A:HIS118 3.6 82.4 1.0 CG D:GLN384 4.0 57.6 1.0 CG D:GLU388 4.1 57.7 1.0 CD2 A:HIS118 4.1 80.4 1.0 O A:HIS118 4.2 76.7 1.0 NE2 D:GLN384 4.3 58.0 1.0 NE2 A:HIS118 4.3 82.0 1.0 CA A:HIS118 4.4 76.1 1.0 C A:HIS118 4.6 75.1 1.0 CD D:GLN384 4.6 60.0 1.0

Zinc binding site 4 out of 14 in the X-Ray 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 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:Zn404 b:1.0 occ:1.00 O A:HOH732 1.4 0.9 1.0 O A:HOH730 1.5 70.3 1.0 O A:HOH731 1.8 67.0 1.0 OE2 A:GLU59 3.1 65.3 1.0 OE2 A:GLU55 3.9 62.5 1.0 CD A:GLU59 4.0 63.9 1.0 O A:PRO56 4.1 48.7 1.0 OE1 A:GLU59 4.3 65.0 1.0 CA A:PRO56 4.4 48.2 1.0 CE A:LYS58 4.5 57.3 1.0 C A:PRO56 4.6 47.9 1.0 OE1 A:GLU55 4.6 63.7 1.0 CD A:GLU55 4.7 62.0 1.0 O A:GLU55 4.8 51.7 1.0

Zinc binding site 5 out of 14 in the X-Ray 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 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:Zn411 b:92.9 occ:1.00 CB B:SER2 2.9 71.5 1.0 OE2 B:GLU60 3.1 62.9 1.0 OG B:SER2 3.5 75.1 1.0 CA B:SER2 3.6 70.5 1.0 CD B:GLU60 4.0 63.4 1.0 OE1 B:GLU60 4.0 63.8 1.0 N B:SER2 4.1 70.2 1.0 C B:SER2 4.9 69.8 1.0

Zinc binding site 6 out of 14 in the X-Ray 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 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:Zn412 b:91.6 occ:1.00 NE2 B:HIS271 2.4 59.9 1.0 OD2 B:ASP275 2.8 55.9 1.0 OD1 B:ASP275 3.0 56.4 1.0 CE1 B:HIS271 3.2 60.4 1.0 CG B:ASP275 3.3 55.4 1.0 CD2 B:HIS271 3.5 58.4 1.0 ND1 B:HIS271 4.4 59.7 1.0 CG B:HIS271 4.5 57.9 1.0 CB B:ASP275 4.8 53.2 1.0

Zinc binding site 7 out of 14 in the X-Ray 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 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:Zn413 b:0.3 occ:1.00 O B:HOH731 1.8 79.9 1.0 O B:HOH733 1.9 67.3 1.0 OD2 B:ASP120 1.9 96.8 1.0 O B:HOH732 1.9 0.1 1.0 O B:HOH734 2.1 61.5 1.0 CG B:ASP120 2.9 95.8 1.0 OD1 B:ASP120 3.2 97.3 1.0 CB B:ASP120 4.3 93.0 1.0

Zinc binding site 8 out of 14 in the X-Ray 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 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:Zn414 b:0.1 occ:1.00 O B:HOH737 1.6 90.0 1.0 O B:HOH735 2.0 97.0 1.0 O B:HOH736 2.2 78.4 1.0 OE2 B:GLU59 3.4 74.4 1.0 OE2 B:GLU55 3.7 64.2 1.0 O B:PRO56 4.1 49.8 1.0 CA B:PRO56 4.1 51.2 1.0 CD B:GLU59 4.3 71.3 1.0 OE1 B:GLU59 4.3 72.2 1.0 C B:PRO56 4.5 50.6 1.0 CD B:GLU55 4.5 64.5 1.0 OE1 B:GLU55 4.5 66.1 1.0 CE B:LYS58 4.5 58.0 1.0 O B:GLU55 4.6 54.7 1.0 NZ B:LYS58 4.9 59.9 1.0 CB B:PRO56 4.9 50.0 1.0

Zinc binding site 9 out of 14 in the X-Ray 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 9 of X-Ray 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:Zn421 b:77.0 occ:1.00 OE2 C:GLU60 2.7 52.5 1.0 CB C:SER2 2.9 65.5 1.0 OG C:SER2 3.1 68.9 1.0 CA C:SER2 3.5 62.6 1.0 CD C:GLU60 3.7 51.7 1.0 OE1 C:GLU60 3.9 53.3 1.0 N C:SER2 4.1 62.4 1.0 C C:SER2 4.9 61.1 1.0

Zinc binding site 10 out of 14 in the X-Ray 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 10 of X-Ray 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:Zn422 b:96.6 occ:1.00 NE2 C:HIS271 2.4 47.6 1.0 OD2 C:ASP275 3.1 56.4 1.0 OD1 C:ASP275 3.2 56.9 1.0 CE1 C:HIS271 3.2 48.0 1.0 CG C:ASP275 3.5 56.5 1.0 CD2 C:HIS271 3.6 46.1 1.0 ND1 C:HIS271 4.4 47.0 1.0 CG C:HIS271 4.6 46.6 1.0

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