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Calcium in PDB 3l1t: E. Coli Nrfa Sulfite Ocmplex

Enzymatic activity of E. Coli Nrfa Sulfite Ocmplex

All present enzymatic activity of E. Coli Nrfa Sulfite Ocmplex:
1.7.2.2;

Protein crystallography data

The structure of E. Coli Nrfa Sulfite Ocmplex, PDB code: 3l1t was solved by T.A.Clarke, A.M.Hemmings, J.N.Butt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.36 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.520, 82.234, 142.172, 90.00, 101.08, 90.00
R / Rfree (%) 17.7 / 23.8

Other elements in 3l1t:

The structure of E. Coli Nrfa Sulfite Ocmplex also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the E. Coli Nrfa Sulfite Ocmplex (pdb code 3l1t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the E. Coli Nrfa Sulfite Ocmplex, PDB code: 3l1t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3l1t

Go back to Calcium Binding Sites List in 3l1t
Calcium binding site 1 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:18.3
occ:1.00
 O A:LYS261 2.2 17.6 1.0
O A:HOH546 2.3 21.6 1.0
O A:TYR216 2.3 20.1 1.0
OE1 A:GLN263 2.5 18.1 1.0
OE1 A:GLU215 2.5 20.0 1.0
O A:HOH497 2.5 14.4 1.0
OE2 A:GLU215 2.6 21.0 1.0
CD A:GLU215 2.9 21.8 1.0
C A:LYS261 3.4 18.2 1.0
C A:TYR216 3.5 20.4 1.0
CD A:GLN263 3.7 21.3 1.0
OH A:TYR242 4.0 16.8 1.0
N A:TYR216 4.1 20.3 1.0
CA A:ALA262 4.2 17.4 1.0
N A:ALA262 4.2 17.4 1.0
OD2 A:ASP249 4.3 22.5 1.0
NE2 A:GLN263 4.3 19.4 1.0
CG A:GLU215 4.4 19.7 1.0
N A:GLN263 4.4 18.2 1.0
CA A:LYS261 4.4 18.4 1.0
CA A:TYR216 4.5 20.6 1.0
N A:TYR217 4.5 20.5 1.0
C A:ALA262 4.5 17.8 1.0
OD1 A:ASP249 4.5 23.0 1.0
CB A:LYS261 4.6 18.3 1.0
CA A:TYR217 4.6 20.8 1.0
CB A:TYR217 4.7 20.3 1.0
N A:LYS261 4.7 18.6 1.0
CG A:ASP249 4.7 23.0 1.0
CZ3 A:TRP379 4.8 13.3 1.0
CG A:GLN263 4.9 19.2 1.0
CZ A:TYR242 4.9 17.0 1.0
CB A:GLN263 4.9 19.0 1.0

Calcium binding site 2 out of 8 in 3l1t

Go back to Calcium Binding Sites List in 3l1t
Calcium binding site 2 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:93.9
occ:1.00
 O1A A:HEC3 2.6 30.8 1.0
O1A A:HEC4 2.7 31.4 1.0
O A:HOH629 2.7 27.9 1.0
O A:PRO91 2.8 26.1 1.0
CGA A:HEC3 3.8 29.8 1.0
CGA A:HEC4 3.8 28.1 1.0
O A:HOH669 3.9 34.0 1.0
C A:PRO91 4.0 25.9 1.0
O2A A:HEC4 4.2 29.2 1.0
O A:HOH559 4.3 33.8 1.0
O2A A:HEC3 4.3 30.9 1.0
CA A:ARG92 4.6 26.0 1.0
CG A:PRO91 4.8 25.1 1.0
N A:ARG92 4.8 25.9 1.0
CA A:PRO91 4.9 25.7 1.0
N A:PRO91 4.9 25.6 1.0
CBA A:HEC3 5.0 27.8 1.0
CAA A:HEC3 5.0 23.4 1.0
CBA A:HEC4 5.0 27.4 1.0

Calcium binding site 3 out of 8 in 3l1t

Go back to Calcium Binding Sites List in 3l1t
Calcium binding site 3 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1

b:19.2
occ:1.00
 O B:HOH567 2.2 21.1 1.0
O B:TYR216 2.3 18.4 1.0
O B:LYS261 2.4 18.9 1.0
O B:HOH623 2.4 15.4 1.0
OE1 B:GLN263 2.5 15.6 1.0
OE2 B:GLU215 2.5 21.3 1.0
OE1 B:GLU215 2.6 20.4 1.0
CD B:GLU215 2.9 21.6 1.0
C B:TYR216 3.6 18.4 1.0
C B:LYS261 3.6 18.2 1.0
CD B:GLN263 3.7 18.1 1.0
OH B:TYR242 4.0 25.3 1.0
N B:TYR216 4.0 17.7 1.0
CA B:ALA262 4.1 17.1 1.0
OD2 B:ASP249 4.2 22.1 1.0
NE2 B:GLN263 4.3 17.3 1.0
N B:ALA262 4.3 17.3 1.0
CG B:GLU215 4.4 17.5 1.0
N B:GLN263 4.4 16.0 1.0
N B:TYR217 4.5 19.0 1.0
CA B:TYR216 4.5 18.0 1.0
C B:ALA262 4.5 17.5 1.0
OD1 B:ASP249 4.5 24.3 1.0
CA B:TYR217 4.5 20.0 1.0
CB B:TYR217 4.6 20.0 1.0
CA B:LYS261 4.7 18.0 1.0
CG B:ASP249 4.7 23.0 1.0
CB B:LYS261 4.7 18.2 1.0
CZ B:TYR242 4.9 27.1 1.0
CZ3 B:TRP379 4.9 19.9 1.0
N B:LYS261 4.9 18.2 1.0
CG B:GLN263 4.9 15.4 1.0
C B:GLU215 5.0 17.2 1.0

Calcium binding site 4 out of 8 in 3l1t

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Calcium binding site 4 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:62.4
occ:1.00
 O B:PRO91 2.5 17.4 1.0
O1A B:HEC4 2.8 23.7 1.0
O1A B:HEC3 3.0 20.8 1.0
O B:HOH536 3.0 31.2 1.0
C B:PRO91 3.6 18.1 1.0
CGA B:HEC4 3.6 23.9 1.0
O2A B:HEC4 3.7 27.1 1.0
O B:HOH566 4.0 23.3 1.0
CD B:PRO91 4.0 18.6 1.0
CGA B:HEC3 4.2 21.7 1.0
N B:PRO91 4.2 18.2 1.0
CB B:LYS90 4.4 19.1 1.0
CA B:PRO91 4.4 18.1 1.0
O B:HOH932 4.5 30.3 1.0
N B:ARG92 4.5 17.4 1.0
CA B:ARG92 4.5 17.5 1.0
CG B:PRO91 4.6 19.1 1.0
C B:LYS90 4.6 18.7 1.0
CB B:PRO91 4.7 18.0 1.0
O2A B:HEC3 4.8 23.7 1.0

Calcium binding site 5 out of 8 in 3l1t

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Calcium binding site 5 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1

b:19.8
occ:1.00
 O C:LYS261 2.2 16.2 1.0
OE2 C:GLU215 2.3 20.4 1.0
OE1 C:GLN263 2.4 23.5 1.0
O C:TYR216 2.4 18.9 1.0
O C:HOH525 2.4 12.4 1.0
OE1 C:GLU215 2.5 18.7 1.0
O C:HOH544 2.5 23.5 1.0
CD C:GLU215 2.7 19.5 1.0
C C:LYS261 3.3 16.1 1.0
CD C:GLN263 3.6 24.3 1.0
C C:TYR216 3.6 19.6 1.0
OH C:TYR242 3.9 23.3 1.0
CA C:ALA262 4.0 16.1 1.0
N C:TYR216 4.1 18.8 1.0
N C:ALA262 4.1 16.0 1.0
NE2 C:GLN263 4.2 25.0 1.0
N C:GLN263 4.2 17.3 1.0
CG C:GLU215 4.2 16.8 1.0
C C:ALA262 4.3 17.2 1.0
OD2 C:ASP249 4.4 23.3 1.0
CA C:LYS261 4.4 16.2 1.0
N C:TYR217 4.5 20.8 1.0
CA C:TYR217 4.5 21.9 1.0
CB C:LYS261 4.5 16.1 1.0
CB C:TYR217 4.5 22.1 1.0
CA C:TYR216 4.5 19.0 1.0
OD1 C:ASP249 4.7 23.5 1.0
N C:LYS261 4.7 17.7 1.0
C2 C:EDO483 4.7 39.9 1.0
CZ C:TYR242 4.8 23.3 1.0
CG C:GLN263 4.8 19.9 1.0
CZ3 C:TRP379 4.9 21.5 1.0
CB C:GLN263 4.9 18.5 1.0
CG C:ASP249 4.9 22.7 1.0

Calcium binding site 6 out of 8 in 3l1t

Go back to Calcium Binding Sites List in 3l1t
Calcium binding site 6 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2

b:81.9
occ:1.00
 O C:PRO91 2.4 19.6 1.0
O1A C:HEC4 2.5 26.6 1.0
O1A C:HEC3 2.5 17.4 1.0
O C:HOH710 3.3 50.0 1.0
C C:PRO91 3.5 19.0 1.0
O C:HOH631 3.5 40.6 1.0
CGA C:HEC4 3.6 25.7 1.0
CGA C:HEC3 3.8 18.1 1.0
O C:HOH568 3.9 32.8 1.0
O2A C:HEC4 3.9 27.4 1.0
CG C:PRO91 4.0 19.4 1.0
CD C:PRO91 4.2 18.9 1.0
CA C:ARG92 4.3 18.3 1.0
O C:HOH621 4.3 41.3 1.0
N C:PRO91 4.3 18.7 1.0
N C:ARG92 4.3 18.9 1.0
CA C:PRO91 4.4 19.0 1.0
O2A C:HEC3 4.4 19.7 1.0
CB C:PRO91 4.6 18.6 1.0
CAA C:HEC3 4.7 17.0 1.0
CB C:LYS90 4.8 19.1 1.0
CBA C:HEC4 4.8 22.3 1.0
CBA C:HEC3 4.9 18.1 1.0
C C:LYS90 4.9 18.6 1.0

Calcium binding site 7 out of 8 in 3l1t

Go back to Calcium Binding Sites List in 3l1t
Calcium binding site 7 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1

b:29.8
occ:1.00
 O D:LYS261 2.2 25.7 1.0
O D:TYR216 2.3 34.9 1.0
O D:HOH973 2.4 26.6 1.0
OE2 D:GLU215 2.4 31.9 1.0
OE1 D:GLU215 2.4 32.9 1.0
O D:HOH959 2.4 30.9 1.0
OE1 D:GLN263 2.5 32.5 1.0
CD D:GLU215 2.7 31.8 1.0
C D:LYS261 3.4 26.3 1.0
C D:TYR216 3.5 34.9 1.0
CD D:GLN263 3.7 32.6 1.0
N D:TYR216 4.0 33.8 1.0
CA D:ALA262 4.0 27.1 1.0
N D:ALA262 4.2 26.2 1.0
OH D:TYR242 4.2 39.4 1.0
CG D:GLU215 4.2 31.9 1.0
NE2 D:GLN263 4.3 32.8 1.0
N D:GLN263 4.3 28.0 1.0
OD2 D:ASP249 4.4 35.8 1.0
C D:ALA262 4.4 27.3 1.0
CA D:TYR216 4.4 34.4 1.0
N D:TYR217 4.4 35.9 1.0
CA D:LYS261 4.4 26.6 1.0
CB D:TYR217 4.5 36.2 1.0
CA D:TYR217 4.5 36.4 1.0
CB D:LYS261 4.6 26.6 1.0
OD1 D:ASP249 4.6 37.7 1.0
N D:LYS261 4.7 27.1 1.0
CZ3 D:TRP379 4.8 24.2 1.0
CG D:ASP249 4.9 34.8 1.0
CG D:GLN263 4.9 29.9 1.0
CB D:GLN263 4.9 28.7 1.0
C D:GLU215 5.0 33.3 1.0

Calcium binding site 8 out of 8 in 3l1t

Go back to Calcium Binding Sites List in 3l1t
Calcium binding site 8 out of 8 in the E. Coli Nrfa Sulfite Ocmplex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of E. Coli Nrfa Sulfite Ocmplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2

b:82.4
occ:1.00
 O1A D:HEC4 2.5 38.6 1.0
O D:PRO91 2.8 33.4 1.0
O D:HOH512 2.9 46.5 1.0
O1A D:HEC3 3.1 35.2 1.0
CGA D:HEC4 3.4 37.4 1.0
O2A D:HEC4 3.7 41.0 1.0
C D:PRO91 3.8 32.5 1.0
CG D:PRO91 4.2 31.6 1.0
O D:HOH535 4.2 40.5 1.0
CGA D:HEC3 4.3 33.8 1.0
N D:PRO91 4.4 31.6 1.0
CD D:PRO91 4.4 31.4 1.0
CB D:LYS90 4.4 31.0 1.0
CA D:PRO91 4.6 31.9 1.0
N D:ARG92 4.6 32.5 1.0
CA D:ARG92 4.6 32.5 1.0
C D:LYS90 4.7 31.2 1.0
CB D:PRO91 4.7 31.8 1.0
O D:HOH796 4.8 44.4 1.0
CBA D:HEC4 4.8 34.5 1.0
O2A D:HEC3 4.9 35.3 1.0

Reference:

G.L.Kemp, T.A.Clarke, S.J.Marritt, C.Lockwood, S.R.Poock, A.M.Hemmings, D.J.Richardson, M.R.Cheesman, J.N.Butt. Kinetic and Thermodynamic Resolution of the Interactions Between Sulfite and the Pentahaem Cytochrome Nrfa From Escherichia Coli Biochem.J. V. 431 73 2010.
ISSN: ISSN 0264-6021
PubMed: 20629638
DOI: 10.1042/BJ20100866
Page generated: Sat Jul 13 12:45:59 2024

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