Atomistry » Calcium » PDB 1qls-1ra1 » 1qni
Atomistry »
  Calcium »
    PDB 1qls-1ra1 »
      1qni »

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

Protein crystallography data

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

Other elements in 1qni:

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

Calcium Binding Sites:

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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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 1qni

Go back to Calcium Binding Sites List in 1qni
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

Reference:

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
Page generated: Thu Jul 11 21:54:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy