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Calcium in PDB 3sbp: Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form

Enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form

All present enzymatic activity of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form:
1.7.99.6;

Protein crystallography data

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form, PDB code: 3sbp was solved by A.Pomowski, W.G.Zumft, P.M.H.Kroneck, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.02 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.890, 106.700, 131.139, 111.34, 107.33, 90.74
R / Rfree (%) 17.7 / 23.6

Other elements in 3sbp:

The structure of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form also contains other interesting chemical elements:

Potassium (K) 8 atoms
Chlorine (Cl) 8 atoms
Copper (Cu) 48 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form (pdb code 3sbp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form, PDB code: 3sbp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3sbp

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Calcium binding site 1 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:47.2
occ:1.00
 O A:MET267 2.2 55.2 1.0
OD1 A:ASN324 2.2 45.1 1.0
O A:TYR256 2.6 44.8 1.0
OD1 A:ASP273 2.7 45.4 1.0
OD2 A:ASP273 2.8 45.4 1.0
OE2 A:GLU259 2.8 48.2 1.0
OE1 A:GLU259 2.8 48.6 1.0
CG A:ASP273 3.1 45.5 1.0
CD A:GLU259 3.2 49.6 1.0
CG A:ASN324 3.4 42.4 1.0
C A:MET267 3.4 56.0 1.0
C A:TYR256 3.5 44.4 1.0
ND2 A:ASN324 4.0 42.8 1.0
CA A:MET267 4.3 56.0 1.0
N A:ASN257 4.3 45.6 1.0
N A:MET268 4.4 56.7 1.0
CA A:TYR256 4.4 42.8 1.0
CA A:MET268 4.5 57.1 1.0
CA A:ASN257 4.5 47.1 1.0
CB A:ASN324 4.6 39.8 1.0
N A:SER258 4.6 48.3 1.0
CA A:ASN324 4.6 39.4 1.0
OG A:SER258 4.6 48.8 1.0
N A:ASN324 4.6 39.8 1.0
CB A:ASP273 4.6 45.5 1.0
ND2 A:ASN270 4.7 58.0 1.0
CG A:GLU259 4.7 51.4 1.0
O A:ASN270 4.7 55.7 1.0
N A:ARG269 4.7 58.8 1.0
C A:MET268 4.8 58.1 1.0
CB A:MET267 4.9 55.2 1.0

Calcium binding site 2 out of 8 in 3sbp

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Calcium binding site 2 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:27.4
occ:1.00
 O B:MET267 2.4 32.5 1.0
OE2 B:GLU259 2.4 27.6 1.0
O B:HOH2592 2.4 31.6 1.0
OD1 B:ASP273 2.4 24.1 1.0
O B:TYR256 2.5 26.7 1.0
OE1 B:GLU259 2.6 27.3 1.0
OD2 B:ASP273 2.6 24.4 1.0
OD1 B:ASN324 2.8 23.5 1.0
CD B:GLU259 2.8 28.1 1.0
CG B:ASP273 2.9 25.8 1.0
C B:MET267 3.5 33.0 1.0
C B:TYR256 3.6 26.9 1.0
CG B:ASN324 3.7 23.7 1.0
ND2 B:ASN324 4.3 23.1 1.0
N B:MET268 4.3 33.9 1.0
CG B:GLU259 4.3 29.4 1.0
CB B:ASP273 4.4 26.6 1.0
N B:SER258 4.4 28.7 1.0
N B:ASN257 4.4 27.6 1.0
CA B:MET268 4.4 34.6 1.0
CA B:ASN257 4.4 27.9 1.0
CA B:MET267 4.4 32.9 1.0
OG B:SER258 4.4 28.8 1.0
CA B:TYR256 4.5 26.5 1.0
N B:ASN324 4.6 23.8 1.0
O B:ASN270 4.7 33.7 1.0
C B:MET268 4.7 34.7 1.0
CA B:ASN324 4.8 23.4 1.0
N B:ARG269 4.8 34.9 1.0
CB B:ASN324 4.9 23.5 1.0
N B:ASN270 4.9 33.9 1.0
CB B:ASN270 4.9 33.4 1.0
C B:ASN257 4.9 28.3 1.0
N B:GLU259 5.0 29.9 1.0

Calcium binding site 3 out of 8 in 3sbp

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Calcium binding site 3 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:15.8
occ:1.00
 O C:HOH2673 2.3 18.8 1.0
OD1 C:ASN324 2.3 16.1 1.0
O C:TYR256 2.4 11.3 1.0
OD1 C:ASP273 2.4 13.5 1.0
OE2 C:GLU259 2.4 15.8 1.0
O C:MET267 2.5 16.9 1.0
OE1 C:GLU259 2.6 15.2 1.0
OD2 C:ASP273 2.8 15.6 1.0
CD C:GLU259 2.9 15.8 1.0
CG C:ASP273 3.0 15.5 1.0
CG C:ASN324 3.4 15.4 1.0
C C:TYR256 3.5 11.0 1.0
C C:MET267 3.6 17.6 1.0
ND2 C:ASN324 4.0 12.3 1.0
N C:MET268 4.4 18.4 1.0
CA C:MET268 4.4 18.9 1.0
CA C:TYR256 4.4 11.5 1.0
CG C:GLU259 4.4 15.6 1.0
N C:SER258 4.4 12.6 1.0
N C:ASN257 4.4 11.0 1.0
CA C:ASN257 4.4 11.2 1.0
N C:ASN324 4.5 14.3 1.0
CB C:ASP273 4.5 13.9 1.0
OG C:SER258 4.5 14.9 1.0
CA C:MET267 4.5 17.5 1.0
CA C:ASN324 4.6 13.7 1.0
CB C:ASN324 4.6 13.8 1.0
O C:ASN270 4.8 20.4 1.0
C C:MET268 4.8 19.6 1.0
N C:ARG269 4.8 20.1 1.0
N C:ASN270 4.9 20.4 1.0
CB C:ASN270 4.9 20.3 1.0
C C:ASN257 4.9 11.6 1.0

Calcium binding site 4 out of 8 in 3sbp

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Calcium binding site 4 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:25.4
occ:1.00
 O D:MET267 2.2 31.4 1.0
O D:HOH2725 2.4 32.3 1.0
OD1 D:ASN324 2.4 26.2 1.0
O D:TYR256 2.4 22.5 1.0
OE2 D:GLU259 2.5 31.6 1.0
OD1 D:ASP273 2.5 24.7 1.0
OD2 D:ASP273 2.7 28.5 1.0
OE1 D:GLU259 2.9 30.1 1.0
CG D:ASP273 3.0 27.5 1.0
CD D:GLU259 3.0 31.4 1.0
CG D:ASN324 3.3 24.9 1.0
C D:MET267 3.4 31.8 1.0
C D:TYR256 3.5 22.7 1.0
ND2 D:ASN324 3.8 22.7 1.0
CA D:MET268 4.2 32.6 1.0
N D:MET268 4.2 32.0 1.0
N D:ASN257 4.4 23.3 1.0
CA D:TYR256 4.4 22.2 1.0
CA D:MET267 4.4 32.1 1.0
O D:ASN270 4.4 34.2 1.0
CA D:ASN257 4.4 24.4 1.0
CB D:ASP273 4.5 27.7 1.0
N D:ASN324 4.5 24.6 1.0
CG D:GLU259 4.5 30.2 1.0
CB D:ASN324 4.6 23.9 1.0
N D:SER258 4.6 25.8 1.0
CA D:ASN324 4.6 23.9 1.0
OG D:SER258 4.6 26.5 1.0
C D:MET268 4.7 33.0 1.0
N D:ARG269 4.8 33.8 1.0
N D:ASN270 4.9 34.3 1.0
CB D:TYR256 5.0 21.7 1.0

Calcium binding site 5 out of 8 in 3sbp

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Calcium binding site 5 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca703

b:18.1
occ:1.00
 O E:MET267 2.4 20.3 1.0
O E:HOH709 2.4 11.6 1.0
O E:TYR256 2.4 13.3 1.0
OD1 E:ASN324 2.4 13.2 1.0
OE2 E:GLU259 2.5 15.9 1.0
OD1 E:ASP273 2.6 17.9 1.0
OD2 E:ASP273 2.6 15.8 1.0
OE1 E:GLU259 2.7 20.2 1.0
CD E:GLU259 2.9 18.6 1.0
CG E:ASP273 2.9 16.7 1.0
CG E:ASN324 3.4 12.8 1.0
C E:TYR256 3.5 14.6 1.0
C E:MET267 3.5 20.8 1.0
ND2 E:ASN324 4.0 15.0 1.0
N E:MET268 4.3 21.0 1.0
CA E:MET268 4.3 20.8 1.0
N E:ASN257 4.3 14.9 1.0
OG E:SER258 4.3 20.1 1.0
CA E:TYR256 4.4 14.1 1.0
CA E:ASN257 4.4 16.0 1.0
N E:ASN324 4.4 12.9 1.0
CG E:GLU259 4.5 18.7 1.0
CB E:ASP273 4.5 16.2 1.0
N E:SER258 4.5 17.9 1.0
CA E:MET267 4.5 20.9 1.0
O E:ASN270 4.5 19.2 1.0
CA E:ASN324 4.5 12.7 1.0
CB E:ASN324 4.6 12.5 1.0
C E:MET268 4.8 20.7 1.0
CB E:ASN270 4.9 19.7 1.0
N E:ASN270 4.9 20.3 1.0
N E:ARG269 4.9 20.9 1.0
C E:ASN257 5.0 17.1 1.0

Calcium binding site 6 out of 8 in 3sbp

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Calcium binding site 6 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca703

b:17.6
occ:1.00
 OD1 F:ASN324 2.3 19.4 1.0
O F:HOH2077 2.3 14.9 1.0
O F:TYR256 2.4 17.0 1.0
O F:MET267 2.4 20.1 1.0
OD1 F:ASP273 2.4 17.9 1.0
OE2 F:GLU259 2.5 18.2 1.0
OE1 F:GLU259 2.6 17.1 1.0
OD2 F:ASP273 2.7 16.2 1.0
CD F:GLU259 2.9 17.6 1.0
CG F:ASP273 2.9 18.0 1.0
CG F:ASN324 3.4 15.9 1.0
C F:TYR256 3.5 17.0 1.0
C F:MET267 3.5 20.5 1.0
ND2 F:ASN324 4.0 16.7 1.0
N F:ASN257 4.3 17.7 1.0
CA F:TYR256 4.3 16.3 1.0
OG F:SER258 4.3 20.0 1.0
N F:MET268 4.3 20.2 1.0
CA F:MET268 4.4 20.9 1.0
CA F:ASN257 4.4 18.1 1.0
N F:SER258 4.4 19.1 1.0
CG F:GLU259 4.4 18.3 1.0
CB F:ASP273 4.5 17.9 1.0
CA F:MET267 4.5 20.4 1.0
N F:ASN324 4.5 15.2 1.0
CA F:ASN324 4.6 14.4 1.0
CB F:ASN324 4.6 14.8 1.0
O F:ASN270 4.6 20.7 1.0
C F:MET268 4.8 20.8 1.0
N F:ARG269 4.9 20.9 1.0
C F:ASN257 4.9 18.8 1.0
CB F:TYR256 5.0 16.1 1.0
N F:ASN270 5.0 21.5 1.0

Calcium binding site 7 out of 8 in 3sbp

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Calcium binding site 7 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca703

b:27.0
occ:1.00
 O G:MET267 2.3 33.4 1.0
OD1 G:ASN324 2.4 27.3 1.0
O G:HOH2175 2.4 20.2 1.0
OD1 G:ASP273 2.4 25.8 1.0
O G:TYR256 2.5 25.7 1.0
OE2 G:GLU259 2.5 31.0 1.0
OE1 G:GLU259 2.6 31.5 1.0
OD2 G:ASP273 2.8 26.3 1.0
CD G:GLU259 2.9 31.3 1.0
CG G:ASP273 3.0 27.6 1.0
CG G:ASN324 3.4 25.8 1.0
C G:TYR256 3.5 26.0 1.0
C G:MET267 3.5 33.7 1.0
ND2 G:ASN324 3.9 24.8 1.0
N G:MET268 4.3 33.9 1.0
CA G:MET268 4.3 34.2 1.0
CA G:TYR256 4.4 25.4 1.0
N G:ASN257 4.4 26.6 1.0
CG G:GLU259 4.5 31.2 1.0
OG G:SER258 4.5 27.4 1.0
CA G:ASN257 4.5 27.5 1.0
CB G:ASP273 4.5 28.1 1.0
CA G:MET267 4.5 33.6 1.0
N G:SER258 4.6 28.6 1.0
N G:ASN324 4.6 25.3 1.0
CB G:ASN324 4.6 25.0 1.0
CA G:ASN324 4.6 25.0 1.0
O G:ASN270 4.7 33.8 1.0
N G:ARG269 4.7 34.8 1.0
C G:MET268 4.7 34.4 1.0
N G:ASN270 4.9 34.6 1.0
CB G:ASN270 5.0 34.1 1.0

Calcium binding site 8 out of 8 in 3sbp

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Calcium binding site 8 out of 8 in the Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca703

b:15.3
occ:1.00
 OE2 H:GLU259 2.3 16.4 1.0
O H:TYR256 2.4 12.1 1.0
O H:HOH2947 2.4 18.0 1.0
O H:MET267 2.4 14.5 1.0
OD1 H:ASN324 2.5 12.8 1.0
OD1 H:ASP273 2.5 13.6 1.0
OE1 H:GLU259 2.6 17.7 1.0
OD2 H:ASP273 2.7 13.8 1.0
CD H:GLU259 2.8 16.7 1.0
CG H:ASP273 2.9 13.9 1.0
CG H:ASN324 3.4 12.8 1.0
C H:TYR256 3.5 11.9 1.0
C H:MET267 3.5 14.9 1.0
ND2 H:ASN324 3.9 11.9 1.0
CA H:MET268 4.2 15.8 1.0
N H:ASN257 4.3 12.5 1.0
N H:MET268 4.3 15.0 1.0
CG H:GLU259 4.3 17.1 1.0
CA H:TYR256 4.4 12.2 1.0
CA H:ASN257 4.4 13.1 1.0
N H:SER258 4.4 14.6 1.0
CB H:ASP273 4.4 14.6 1.0
CA H:MET267 4.5 14.9 1.0
N H:ASN324 4.5 12.0 1.0
OG H:SER258 4.5 18.5 1.0
CB H:ASN324 4.6 12.2 1.0
CA H:ASN324 4.6 12.6 1.0
C H:MET268 4.7 15.4 1.0
N H:ARG269 4.7 15.7 1.0
O H:ASN270 4.7 16.6 1.0
N H:ASN270 4.8 16.2 1.0
CB H:ASN270 4.9 16.3 1.0
C H:ASN257 4.9 14.1 1.0

Reference:

A.Pomowski, W.G.Zumft, P.M.Kroneck, O.Einsle. N2O Binding at A [4CU:2S] Copper-Sulphur Cluster in Nitrous Oxide Reductase. Nature V. 477 234 2011.
ISSN: ISSN 0028-0836
PubMed: 21841804
DOI: 10.1038/NATURE10332
Page generated: Sat Jul 13 19:09:44 2024

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