Calcium in PDB 1qni: Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution

The structure of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution, PDB code: 1qni was solved by K.Brown, M.Tegoni, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.40
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	211.290, 211.290, 166.457, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 26.1

The structure of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution also contains other interesting chemical elements:

Copper	(Cu)	36 atoms
Chlorine	(Cl)	6 atoms

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution (pdb code 1qni). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution, PDB code: 1qni:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:46.9 occ:1.00 O A:THR215 2.2 54.7 1.0 O A:TYR204 2.3 51.0 1.0 O A:HOH2172 2.4 31.5 1.0 OD1 A:ASN268 2.5 38.5 1.0 OE2 A:GLU207 2.7 43.8 1.0 OD2 A:ASP221 2.7 51.6 1.0 OE1 A:GLU207 2.7 41.2 1.0 OD1 A:ASP221 2.8 49.2 1.0 CD A:GLU207 3.1 43.9 1.0 CG A:ASP221 3.1 51.4 1.0 C A:THR215 3.4 54.8 1.0 CG A:ASN268 3.4 41.2 1.0 C A:TYR204 3.4 50.3 1.0 ND2 A:ASN268 3.9 38.2 1.0 N A:ASN205 4.2 49.6 1.0 N A:MET216 4.2 56.1 1.0 CA A:MET216 4.3 57.5 1.0 CA A:ASN205 4.3 48.6 1.0 CA A:TYR204 4.3 49.1 1.0 CA A:THR215 4.3 53.5 1.0 N A:SER206 4.4 48.8 1.0 N A:ASN268 4.5 48.9 1.0 CB A:ASN268 4.6 43.0 1.0 CG A:GLU207 4.6 46.8 1.0 CA A:ASN268 4.6 46.6 1.0 CB A:ASP221 4.6 53.2 1.0 OG A:SER206 4.6 48.3 1.0 O A:ASN218 4.8 63.2 1.0 C A:MET216 4.8 58.7 1.0 C A:ASN205 4.9 48.3 1.0 CB A:THR215 4.9 52.2 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:41.0 occ:1.00 O A:LYS397 2.2 45.8 1.0 OE1 A:GLU412 2.2 49.6 1.0 O B:HOH2309 2.3 42.0 1.0 O A:HOH2236 2.5 38.8 1.0 O A:HOH2235 2.5 26.4 1.0 O B:HOH2288 2.6 39.7 1.0 OE2 A:GLU412 2.9 50.2 1.0 CD A:GLU412 2.9 50.1 1.0 C A:LYS397 3.3 45.5 1.0 CA A:LYS397 4.1 45.7 1.0 OD1 B:ASP523 4.2 47.5 1.0 N A:PHE398 4.3 45.4 1.0 CG A:GLU412 4.3 48.7 1.0 CA A:PHE398 4.4 44.9 1.0 CD1 B:TRP563 4.4 36.0 1.0 NE1 B:TRP563 4.5 35.6 1.0 CD1 A:PHE398 4.5 43.6 1.0 O A:PRO411 4.6 46.0 1.0 O B:HOH2289 4.6 30.2 1.0 CB A:LYS397 4.6 44.4 1.0 O A:HIS410 4.6 43.3 1.0 O B:HOH2290 4.7 25.7 1.0 CA A:GLU412 4.8 48.1 1.0 O B:PHE564 4.8 41.8 1.0 OE1 A:GLU435 4.9 55.7 1.0 CB A:GLU412 4.9 46.9 1.0 C A:PRO411 5.0 45.9 1.0 O A:HOH2237 5.0 50.2 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:50.3 occ:1.00 O B:THR215 2.4 58.1 1.0 O B:TYR204 2.5 53.9 1.0 OE2 B:GLU207 2.5 54.5 1.0 OD1 B:ASN268 2.5 48.5 1.0 OD1 B:ASP221 2.6 51.8 1.0 OD2 B:ASP221 2.6 52.0 1.0 OE1 B:GLU207 2.7 53.5 1.0 CD B:GLU207 3.0 54.3 1.0 CG B:ASP221 3.0 53.9 1.0 C B:THR215 3.4 58.3 1.0 C B:TYR204 3.4 53.7 1.0 CG B:ASN268 3.5 48.9 1.0 ND2 B:ASN268 4.1 48.2 1.0 N B:ASN205 4.2 53.9 1.0 CA B:ASN205 4.2 53.4 1.0 N B:MET216 4.3 59.3 1.0 CA B:THR215 4.3 57.5 1.0 CA B:TYR204 4.4 52.6 1.0 CA B:MET216 4.4 61.0 1.0 N B:SER206 4.4 54.5 1.0 CG B:GLU207 4.5 53.5 1.0 N B:ASN268 4.5 52.6 1.0 CB B:ASP221 4.5 56.3 1.0 OG B:SER206 4.6 58.0 1.0 CA B:ASN268 4.7 50.4 1.0 CB B:ASN268 4.7 49.8 1.0 C B:MET216 4.8 62.4 1.0 O B:ASN218 4.8 65.2 1.0 C B:ASN205 4.8 53.8 1.0 N B:ARG217 4.9 64.8 1.0 CB B:THR215 5.0 57.0 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:49.3 occ:1.00 O B:HOH2200 2.2 31.1 1.0 O B:HOH2209 2.2 49.0 1.0 O A:HOH2309 2.3 51.0 1.0 OE1 B:GLU412 2.4 52.6 1.0 O B:LYS397 2.4 48.7 1.0 O B:HOH2210 2.5 43.3 1.0 OE2 B:GLU412 2.6 53.5 1.0 CD B:GLU412 2.8 53.6 1.0 C B:LYS397 3.4 48.4 1.0 OD1 A:ASP523 4.0 53.0 1.0 N B:PHE398 4.3 48.1 1.0 CG B:GLU412 4.3 52.1 1.0 CA B:LYS397 4.3 48.8 1.0 CA B:PHE398 4.3 47.9 1.0 O B:HIS410 4.4 48.8 1.0 O A:HOH2310 4.4 59.0 1.0 O B:PRO411 4.4 49.8 1.0 CD1 B:PHE398 4.4 45.2 1.0 CD1 A:TRP563 4.5 38.0 1.0 NE1 A:TRP563 4.6 38.3 1.0 O B:HOH2208 4.6 40.5 1.0 CA B:GLU412 4.6 51.2 1.0 C B:PRO411 4.8 49.6 1.0 CB B:LYS397 4.8 47.7 1.0 O A:PHE564 4.9 46.8 1.0 CB B:GLU412 4.9 50.6 1.0 N B:GLU412 4.9 51.2 1.0 O A:ASP523 4.9 49.4 1.0 CG A:ASP523 4.9 53.6 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:63.7 occ:1.00 OD1 C:ASN268 2.3 55.9 1.0 OD2 C:ASP221 2.5 64.6 1.0 O C:THR215 2.5 60.9 1.0 O C:TYR204 2.5 60.6 1.0 OE2 C:GLU207 2.5 65.8 1.0 OD1 C:ASP221 2.6 63.4 1.0 OE1 C:GLU207 2.7 65.7 1.0 CG C:ASP221 2.9 64.5 1.0 CD C:GLU207 3.0 65.5 1.0 CG C:ASN268 3.4 57.1 1.0 C C:TYR204 3.5 60.0 1.0 C C:THR215 3.6 61.0 1.0 ND2 C:ASN268 4.0 56.8 1.0 OG C:SER206 4.2 59.5 1.0 CA C:TYR204 4.3 59.9 1.0 N C:ASN205 4.3 59.5 1.0 N C:SER206 4.3 59.0 1.0 N C:ASN268 4.3 58.7 1.0 CA C:MET216 4.4 64.2 1.0 CB C:ASP221 4.4 64.2 1.0 N C:MET216 4.4 62.3 1.0 CA C:ASN205 4.4 59.1 1.0 CG C:GLU207 4.5 63.8 1.0 O C:ASN218 4.5 68.8 1.0 CA C:ASN268 4.5 56.6 1.0 CA C:THR215 4.6 60.2 1.0 CB C:ASN268 4.6 57.4 1.0 C C:MET216 4.8 65.1 1.0 C C:ASN205 4.9 59.3 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca903 b:63.5 occ:1.00 O D:HOH2100 2.5 59.5 1.0 OE1 C:GLU412 2.5 57.5 1.0 O C:LYS397 2.5 55.0 1.0 OE2 C:GLU412 2.8 57.4 1.0 CD C:GLU412 3.1 57.4 1.0 C C:LYS397 3.6 54.5 1.0 CD1 D:TRP563 4.1 52.8 1.0 OD1 D:ASP523 4.1 61.7 1.0 NE1 D:TRP563 4.3 53.1 1.0 CD1 C:PHE398 4.3 57.0 1.0 CA C:LYS397 4.3 54.5 1.0 O D:PHE564 4.4 52.6 1.0 N C:PHE398 4.5 54.9 1.0 O D:ASP523 4.5 55.4 1.0 OE1 C:GLU435 4.5 64.7 1.0 CG C:GLU412 4.6 56.7 1.0 O C:HIS410 4.6 53.1 1.0 CA C:PHE398 4.6 54.6 1.0 CE1 C:PHE398 4.6 57.5 1.0 CB C:LYS397 4.7 54.8 1.0 CG D:ASP523 4.9 59.9 1.0 OD2 D:ASP523 5.0 61.0 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca901 b:64.2 occ:1.00 OE2 D:GLU207 2.4 64.6 1.0 O D:TYR204 2.4 60.4 1.0 OD1 D:ASN268 2.4 51.8 1.0 O D:THR215 2.4 60.3 1.0 OE1 D:GLU207 2.5 63.6 1.0 OD2 D:ASP221 2.6 60.7 1.0 OD1 D:ASP221 2.6 60.7 1.0 CD D:GLU207 2.8 63.4 1.0 CG D:ASP221 2.9 62.5 1.0 C D:TYR204 3.4 59.5 1.0 CG D:ASN268 3.5 53.6 1.0 C D:THR215 3.5 61.0 1.0 ND2 D:ASN268 4.0 53.7 1.0 N D:ASN205 4.2 58.5 1.0 CA D:ASN205 4.2 57.7 1.0 N D:SER206 4.2 58.6 1.0 CA D:TYR204 4.3 60.1 1.0 OG D:SER206 4.3 62.2 1.0 CG D:GLU207 4.3 60.7 1.0 N D:MET216 4.4 62.1 1.0 CA D:THR215 4.4 60.2 1.0 CB D:ASP221 4.5 63.2 1.0 CA D:MET216 4.5 63.4 1.0 N D:ASN268 4.5 56.3 1.0 CB D:ASN268 4.7 52.5 1.0 CA D:ASN268 4.7 54.1 1.0 C D:ASN205 4.7 57.8 1.0 O D:ASN218 4.7 69.3 1.0 C D:MET216 5.0 64.8 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca903 b:70.4 occ:1.00 O C:HOH2089 2.3 65.3 1.0 OE1 D:GLU412 2.4 63.9 1.0 O D:HOH2068 2.4 47.2 1.0 O D:LYS397 2.6 56.6 1.0 OE2 D:GLU412 2.8 64.9 1.0 CD D:GLU412 2.9 64.1 1.0 C D:LYS397 3.6 55.5 1.0 OD1 C:ASP523 3.7 58.2 1.0 O D:HIS410 4.1 54.7 1.0 CD1 C:TRP563 4.3 53.5 1.0 CG D:GLU412 4.5 61.6 1.0 NE1 C:TRP563 4.5 54.9 1.0 O C:ASP523 4.5 55.2 1.0 CD1 D:PHE398 4.5 59.2 1.0 CA D:LYS397 4.5 55.5 1.0 N D:PHE398 4.5 55.3 1.0 CA D:PHE398 4.5 55.9 1.0 CG C:ASP523 4.6 59.0 1.0 O D:PRO411 4.8 55.9 1.0 OD2 C:ASP523 4.9 59.2 1.0 CE1 D:PHE398 4.9 58.7 1.0 O C:PHE564 4.9 51.7 1.0 CA D:GLU412 4.9 56.5 1.0 CB D:LYS397 5.0 56.6 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca901 b:41.4 occ:1.00 O E:THR215 2.2 53.6 1.0 OD1 E:ASN268 2.4 38.6 1.0 O E:TYR204 2.4 51.7 1.0 OE2 E:GLU207 2.4 47.9 1.0 OD2 E:ASP221 2.7 46.4 1.0 OE1 E:GLU207 2.7 49.2 1.0 OD1 E:ASP221 2.9 46.1 1.0 CD E:GLU207 2.9 49.3 1.0 CG E:ASP221 3.1 48.3 1.0 C E:THR215 3.3 53.3 1.0 CG E:ASN268 3.4 39.6 1.0 C E:TYR204 3.5 50.6 1.0 ND2 E:ASN268 3.8 36.8 1.0 N E:MET216 4.1 54.8 1.0 CA E:MET216 4.1 55.6 1.0 CA E:THR215 4.2 52.5 1.0 N E:ASN205 4.3 50.7 1.0 CA E:ASN205 4.3 50.5 1.0 N E:SER206 4.4 51.2 1.0 CA E:TYR204 4.4 50.1 1.0 CG E:GLU207 4.5 49.2 1.0 N E:ASN268 4.6 47.9 1.0 CB E:ASN268 4.6 41.7 1.0 OG E:SER206 4.6 52.6 1.0 C E:MET216 4.7 57.7 1.0 CB E:ASP221 4.7 51.1 1.0 O E:ASN218 4.7 61.6 1.0 CA E:ASN268 4.7 45.1 1.0 CB E:THR215 4.8 51.1 1.0 C E:ASN205 4.9 50.7 1.0 N E:ARG217 4.9 59.9 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Nitrous Oxide Reductase From Pseudomonas Nautica, at 2.4A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca903 b:47.1 occ:1.00 OE1 E:GLU412 2.2 50.9 1.0 O E:LYS397 2.3 45.6 1.0 O F:HOH2200 2.5 34.2 1.0 O E:HOH2172 2.5 38.7 1.0 O E:HOH2181 2.6 38.0 1.0 CD E:GLU412 2.9 52.3 1.0 OE2 E:GLU412 2.9 50.9 1.0 C E:LYS397 3.5 45.8 1.0 CD1 F:TRP563 4.1 39.6 1.0 O F:HOH2216 4.2 28.4 1.0 OD1 F:ASP523 4.2 45.4 1.0 CA E:LYS397 4.2 46.0 1.0 NE1 F:TRP563 4.3 39.3 1.0 CG E:GLU412 4.4 51.5 1.0 N E:PHE398 4.5 46.6 1.0 O F:PHE564 4.5 41.0 1.0 CB E:LYS397 4.5 45.2 1.0 CD1 E:PHE398 4.5 46.0 1.0 OE1 E:GLU435 4.6 55.5 1.0 O F:HOH2201 4.6 38.6 1.0 CA E:PHE398 4.6 46.1 1.0 O E:HIS410 4.6 43.7 1.0 CE1 E:PHE398 5.0 46.5 1.0 O F:ASP523 5.0 44.8 1.0 O E:HOH2182 5.0 59.3 1.0

K.Brown, M.Tegoni, M.Prudencio, A.S.Pereira, S.Besson, J.J.Moura, I.Moura, C.Cambillau. A Novel Type of Catalytic Copper Cluster in Nitrous Oxide Reductase. Nat.Struct.Biol. V. 7 191 2000.
ISSN: ISSN 1072-8368
PubMed: 10700275
DOI: 10.1038/73288