Zinc in PDB 2c1d: Crystal Structure of Soxxa From P. Pantotrophus

The structure of Crystal Structure of Soxxa From P. Pantotrophus, PDB code: 2c1d was solved by T.Dambe, A.Quentmeier, D.Rother, C.Friedrich, A.J.Scheidig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	119.52 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.860, 180.010, 117.930, 90.00, 92.83, 90.00
R / Rfree (%)	15.9 / 21.1

The structure of Crystal Structure of Soxxa From P. Pantotrophus also contains other interesting chemical elements:

Iron

(Fe)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Soxxa From P. Pantotrophus (pdb code 2c1d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Soxxa From P. Pantotrophus, PDB code: 2c1d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:32.1 occ:1.00 OD1 A:ASP266 1.8 2.0 1.0 NE2 A:HIS190 2.1 33.4 1.0 OD2 A:ASP266 2.6 31.7 1.0 CG A:ASP266 2.7 20.9 1.0 CE1 A:HIS190 3.0 33.1 1.0 CD2 A:HIS190 3.1 30.8 1.0 ND1 A:HIS190 4.1 32.9 1.0 CB A:ASP266 4.2 26.0 1.0 CG A:HIS190 4.2 30.5 1.0 O A:HOH2310 4.4 64.1 1.0 O A:HOH2236 4.6 36.9 1.0 CA A:ASP266 4.8 25.9 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1294 b:25.4 occ:1.00 O1D A:HEC1291 1.9 25.3 1.0 NE2 A:HIS129 2.0 23.3 1.0 O A:HOH2335 2.2 25.3 1.0 CGD A:HEC1291 2.6 23.8 1.0 O2D A:HEC1291 2.8 25.1 1.0 CE1 A:HIS129 3.0 26.0 1.0 CD2 A:HIS129 3.0 22.1 1.0 OE2 A:GLU128 3.7 28.5 1.0 CBD A:HEC1291 4.1 23.6 1.0 ND1 A:HIS129 4.1 23.4 1.0 CG A:HIS129 4.2 24.7 1.0 O A:HOH2156 4.2 25.9 1.0 CD A:GLU128 4.2 27.5 1.0 O A:HOH2336 4.3 29.2 1.0 CG A:GLU128 4.6 25.1 1.0 OE1 A:GLU128 4.9 29.6 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1295 b:65.8 occ:1.00 OD2 A:ASP81 1.8 35.6 1.0 OD2 A:ASP78 2.7 46.7 1.0 O A:HOH2081 2.7 59.2 1.0 CG A:ASP81 2.8 36.3 1.0 OD1 A:ASP78 2.8 45.2 1.0 CG A:ASP78 3.0 38.3 1.0 OD1 A:ASP81 3.1 41.8 1.0 O A:HOH2086 3.7 39.9 1.0 CB A:ASP81 4.1 33.9 1.0 CB A:ASP78 4.3 35.3 1.0 O A:HOH2080 4.8 50.2 1.0 N A:ASP81 4.8 33.6 1.0 O A:HOH2011 4.8 43.2 1.0 O A:HOH2013 4.9 36.0 1.0 CB A:PHE80 5.0 35.2 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1296 b:24.1 occ:1.00 O2A A:HEC1291 1.9 22.4 1.0 O A:HOH2336 2.1 29.2 1.0 CGA A:HEC1291 2.9 26.6 1.0 CBA A:HEC1291 3.4 25.4 1.0 O1A A:HEC1291 3.9 24.8 1.0 O A:HOH2335 4.3 25.3 1.0 O A:HOH2139 4.3 35.9 1.0 NH2 A:ARG125 4.7 23.4 1.0 CAA A:HEC1291 4.9 25.9 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1293 b:32.2 occ:1.00 OD1 C:ASP266 1.9 35.3 1.0 NE2 C:HIS190 2.1 31.6 1.0 OD2 C:ASP266 2.6 38.5 1.0 CG C:ASP266 2.6 30.8 1.0 CE1 C:HIS190 2.9 31.5 1.0 CD2 C:HIS190 3.2 29.8 1.0 O C:HOH2339 3.5 45.9 1.0 ND1 C:HIS190 4.1 31.6 1.0 CB C:ASP266 4.1 29.4 1.0 CG C:HIS190 4.2 29.1 1.0 O C:HOH2252 4.5 34.2 1.0 O C:HOH2338 4.6 45.9 1.0 CA C:ASP266 4.7 28.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1294 b:62.9 occ:1.00 OD2 C:ASP81 1.8 26.9 1.0 OD2 C:ASP78 2.7 41.7 1.0 CG C:ASP81 2.7 32.8 1.0 OD1 C:ASP78 2.8 42.2 1.0 CG C:ASP78 3.0 34.3 1.0 OD1 C:ASP81 3.0 34.0 1.0 O C:HOH2096 3.9 40.9 1.0 CB C:ASP81 4.1 30.3 1.0 CB C:ASP78 4.2 32.3 1.0 O C:HOH2014 4.6 43.9 1.0 N C:ASP81 4.7 31.2 1.0 O C:HOH2013 4.8 40.8 1.0 O C:HOH2089 4.8 47.5 1.0 CD2 C:PHE80 4.9 38.5 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1295 b:25.0 occ:1.00 O2D C:HEC1291 1.9 17.9 1.0 O2A G:HEC1291 2.0 23.1 1.0 NE2 C:HIS129 2.1 22.7 1.0 CGD C:HEC1291 2.7 2.0 1.0 O1D C:HEC1291 2.9 20.2 1.0 CGA G:HEC1291 2.9 22.2 1.0 CD2 C:HIS129 3.0 22.3 1.0 CE1 C:HIS129 3.1 23.4 1.0 O C:HOH2352 3.2 73.0 1.0 CBA G:HEC1291 3.4 22.6 1.0 OE2 C:GLU128 3.8 28.8 1.0 O1A G:HEC1291 4.0 20.3 1.0 CBD C:HEC1291 4.1 2.0 1.0 CD C:GLU128 4.1 28.9 1.0 ND1 C:HIS129 4.2 23.6 1.0 CG C:HIS129 4.2 23.6 1.0 O G:HOH2143 4.2 42.9 1.0 O C:HOH2175 4.3 26.6 1.0 O G:HOH2332 4.3 29.1 1.0 CG C:GLU128 4.5 25.8 1.0 OE1 C:GLU128 4.7 30.2 1.0 NH2 G:ARG125 4.7 25.3 1.0 CAA G:HEC1291 4.9 22.1 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1293 b:33.4 occ:1.00 OD1 E:ASP266 2.0 33.8 1.0 NE2 E:HIS190 2.1 32.5 1.0 CG E:ASP266 3.0 30.4 1.0 CE1 E:HIS190 3.0 31.4 1.0 O E:HOH2350 3.1 51.6 1.0 CD2 E:HIS190 3.2 30.6 1.0 OD2 E:ASP266 3.3 36.2 1.0 ND1 E:HIS190 4.2 30.7 1.0 CG E:HIS190 4.3 28.4 1.0 CB E:ASP266 4.3 28.1 1.0 CA E:ASP266 4.7 27.5 1.0 O E:HOH2240 4.8 35.4 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1294 b:64.2 occ:1.00 OD2 E:ASP81 1.9 28.2 1.0 OD2 E:ASP78 2.6 42.8 1.0 OD1 E:ASP78 2.8 43.3 1.0 CG E:ASP81 2.8 34.1 1.0 CG E:ASP78 3.0 36.6 1.0 OD1 E:ASP81 3.1 37.5 1.0 O E:HOH2085 4.1 44.4 1.0 CB E:ASP81 4.2 31.3 1.0 CB E:ASP78 4.3 34.0 1.0 O E:HOH2007 4.7 35.9 1.0 N E:ASP81 4.8 32.4 1.0 CB E:PHE80 4.8 34.9 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Soxxa From P. Pantotrophus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Soxxa From P. Pantotrophus within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1293 b:31.4 occ:1.00 OD1 G:ASP266 2.0 36.5 1.0 NE2 G:HIS190 2.1 31.0 1.0 OD2 G:ASP266 2.5 37.5 1.0 CG G:ASP266 2.6 28.2 1.0 CE1 G:HIS190 3.0 30.7 1.0 CD2 G:HIS190 3.2 27.6 1.0 O G:HOH2312 3.4 45.6 1.0 CB G:ASP266 4.1 27.9 1.0 ND1 G:HIS190 4.1 31.2 1.0 CG G:HIS190 4.3 27.4 1.0 O G:HOH2311 4.6 38.4 1.0 CA G:ASP266 4.7 27.2 1.0 O G:HOH2232 4.8 33.7 1.0

T.Dambe, A.Quentmeier, D.Rother, C.Friedrich, A.J.Scheidig. Structure of the Cytochrome Complex Soxxa of Paracoccus Pantotrophus, A Heme Enzyme Initiating Chemotrophic Sulfur Oxidation. J.Struct.Biol. V. 152 229 2005.
ISSN: ISSN 1047-8477
PubMed: 16297640
DOI: 10.1016/J.JSB.2005.09.002