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Calcium in PDB 2xce: Structure of Yncf in Complex with Dupnhpp

Enzymatic activity of Structure of Yncf in Complex with Dupnhpp

All present enzymatic activity of Structure of Yncf in Complex with Dupnhpp:
3.6.1.23;

Protein crystallography data

The structure of Structure of Yncf in Complex with Dupnhpp, PDB code: 2xce was solved by J.Garcia-Nafria, L.Burchell, M.Takezawa, N.Rzechorzek, M.Fogg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.116, 99.345, 99.252, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 18.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Yncf in Complex with Dupnhpp (pdb code 2xce). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of Yncf in Complex with Dupnhpp, PDB code: 2xce:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 2xce

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Calcium binding site 1 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1132

b:23.9
occ:0.50
 O A:HOH2036 2.2 21.4 1.0
O1G B:DUP1131 2.2 26.6 0.8
O A:HOH2130 2.3 28.4 1.0
O2 A:GOL1133 2.4 41.8 1.0
O3 A:GOL1133 2.5 35.3 1.0
O A:HOH2035 2.5 33.1 1.0
OE1 A:GLN112 2.8 27.5 1.0
C3 A:GOL1133 3.3 35.8 1.0
C2 A:GOL1133 3.4 40.1 1.0
PG B:DUP1131 3.5 30.2 0.8
O3G B:DUP1131 3.8 30.6 0.8
CD A:GLN112 3.9 24.0 1.0
O B:HOH2120 4.0 41.2 1.0
O B:HOH2121 4.0 17.8 1.0
OD1 A:ASP27 4.2 19.8 1.0
C1 A:GOL1133 4.2 40.7 1.0
O1B B:DUP1131 4.2 31.2 1.0
O A:HOH2131 4.3 20.0 1.0
O A:TRP25 4.4 20.7 1.0
O A:HOH2030 4.5 32.0 1.0
O2G B:DUP1131 4.5 30.0 0.8
NE2 A:GLN112 4.5 24.4 1.0
O3B B:DUP1131 4.6 28.9 1.0
CB A:TRP25 4.6 18.4 1.0
O1 A:GOL1133 4.9 43.1 1.0
O B:HOH2117 4.9 26.5 1.0
C A:TRP25 4.9 19.1 1.0
PB B:DUP1131 5.0 31.1 1.0

Calcium binding site 2 out of 8 in 2xce

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Calcium binding site 2 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1134

b:23.4
occ:0.75
 O2 A:GOL1135 2.3 31.3 1.0
O C:HOH2035 2.3 19.7 1.0
O1G A:DUP1131 2.3 20.1 0.8
O A:HOH2133 2.3 25.7 1.0
O C:HOH2034 2.4 27.7 1.0
O1 A:GOL1135 2.4 28.4 1.0
OE1 C:GLN112 2.4 21.4 1.0
C1 A:GOL1135 3.2 28.6 1.0
C2 A:GOL1135 3.3 31.8 1.0
CD C:GLN112 3.6 20.2 1.0
PG A:DUP1131 3.6 23.6 0.8
O3G A:DUP1131 3.9 23.1 0.8
O A:HOH2122 3.9 39.1 1.0
OD2 C:ASP27 4.0 21.7 1.0
O A:HOH2126 4.1 15.2 1.0
NE2 C:GLN112 4.1 19.4 1.0
C3 A:GOL1135 4.1 31.0 1.0
O2B A:DUP1131 4.2 24.2 1.0
O C:TRP25 4.3 19.9 1.0
O A:HOH2134 4.4 17.9 1.0
CB C:TRP25 4.5 17.9 1.0
O3B A:DUP1131 4.6 25.9 1.0
O C:HOH2031 4.7 21.2 1.0
O2G A:DUP1131 4.7 20.8 0.8
CG C:GLN112 4.8 15.3 1.0
C C:TRP25 4.8 20.1 1.0
CB C:GLN112 4.8 16.8 1.0
O3 A:GOL1135 4.9 35.8 1.0
CG C:ASP27 4.9 21.3 1.0

Calcium binding site 3 out of 8 in 2xce

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Calcium binding site 3 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1132

b:24.3
occ:1.00
 O1G C:DUP1131 2.2 23.4 1.0
O1B C:DUP1131 2.2 20.6 1.0
O B:HOH2030 2.3 13.5 1.0
O2A C:DUP1131 2.3 17.7 1.0
O C:HOH2124 2.4 21.8 1.0
O B:HOH2029 2.4 16.4 1.0
PB C:DUP1131 3.3 21.7 1.0
PG C:DUP1131 3.4 27.4 1.0
PA C:DUP1131 3.6 21.8 1.0
O3B C:DUP1131 3.6 22.7 1.0
N3A C:DUP1131 3.9 17.6 1.0
O F:HOH2112 4.1 30.6 1.0
O C:HOH2127 4.1 16.5 1.0
O2G C:DUP1131 4.2 27.7 1.0
NE B:ARG63 4.4 19.6 1.0
O B:HOH2103 4.4 18.3 1.0
OD1 B:ASP27 4.5 21.3 1.0
OD2 B:ASP27 4.5 24.4 1.0
O C:HOH2087 4.5 25.0 1.0
O1A C:DUP1131 4.6 24.7 1.0
O5' C:DUP1131 4.6 23.4 1.0
OE1 B:GLN112 4.6 19.8 1.0
O3G C:DUP1131 4.6 28.7 1.0
O2B C:DUP1131 4.7 18.3 1.0
C5' C:DUP1131 4.8 23.9 1.0
CG B:ARG63 4.8 21.0 1.0
CD B:ARG63 4.9 20.8 1.0
CG B:ASP27 4.9 21.7 1.0

Calcium binding site 4 out of 8 in 2xce

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Calcium binding site 4 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1132

b:29.4
occ:1.00
 O B:HOH2045 2.1 28.4 1.0
O A:HOH2046 2.4 26.1 1.0
O C:HOH2051 2.5 28.8 1.0
OD2 A:ASP39 4.4 30.1 1.0
OD2 B:ASP39 4.4 28.0 1.0
OD1 A:ASP39 4.4 27.0 1.0
O A:HOH2044 4.4 34.8 1.0
NZ C:LYS38 4.4 44.5 1.0
OD2 C:ASP39 4.4 28.4 1.0
OD1 B:ASP39 4.5 29.7 1.0
O C:HOH2100 4.5 34.1 1.0
OD1 C:ASP39 4.6 30.2 1.0
CG A:ASP39 4.8 29.4 1.0
CG B:ASP39 4.9 26.6 1.0
CG C:ASP39 5.0 28.2 1.0

Calcium binding site 5 out of 8 in 2xce

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Calcium binding site 5 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1133

b:21.8
occ:0.75
 O2 D:GOL1134 2.3 30.9 1.0
O2G D:DUP1131 2.3 21.9 0.8
O F:HOH2032 2.4 15.3 1.0
O1 D:GOL1134 2.4 27.0 1.0
O D:HOH2140 2.4 17.1 1.0
OE1 F:GLN112 2.5 22.6 1.0
O F:HOH2030 2.5 25.0 1.0
C1 D:GOL1134 3.2 28.6 1.0
C2 D:GOL1134 3.4 30.0 1.0
PG D:DUP1131 3.6 22.1 0.8
CD F:GLN112 3.6 20.4 1.0
O1G D:DUP1131 3.9 22.7 0.8
O D:HOH2128 4.0 46.6 1.0
O D:HOH2133 4.0 30.4 1.0
O D:HOH2132 4.1 16.0 1.0
OD2 F:ASP27 4.1 20.2 1.0
NE2 F:GLN112 4.2 19.9 1.0
C3 D:GOL1134 4.2 33.2 1.0
O1B D:DUP1131 4.2 25.8 1.0
O D:HOH2139 4.4 16.1 1.0
O F:TRP25 4.4 22.0 1.0
CB F:TRP25 4.6 19.8 1.0
O3B D:DUP1131 4.6 28.8 1.0
O3G D:DUP1131 4.7 21.6 0.8
O F:HOH2028 4.8 22.4 1.0
O3 D:GOL1134 4.8 32.4 1.0
CG F:GLN112 4.9 16.0 1.0
CB F:GLN112 4.9 16.9 1.0
C F:TRP25 4.9 20.5 1.0
PB D:DUP1131 4.9 25.2 1.0

Calcium binding site 6 out of 8 in 2xce

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Calcium binding site 6 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1146

b:22.9
occ:1.00
 O3G E:DUP1131 2.2 21.4 1.0
O1B E:DUP1131 2.2 20.8 1.0
O E:HOH2119 2.3 20.5 1.0
O D:HOH2034 2.4 14.8 1.0
O1A E:DUP1131 2.4 21.9 1.0
O D:HOH2033 2.4 13.9 1.0
PB E:DUP1131 3.3 21.6 1.0
PG E:DUP1131 3.4 26.6 1.0
PA E:DUP1131 3.6 22.4 1.0
O3B E:DUP1131 3.6 21.5 1.0
N3A E:DUP1131 3.9 21.3 1.0
O1G E:DUP1131 4.1 27.5 1.0
O E:HOH2122 4.2 16.9 1.0
O D:HOH2032 4.3 21.3 1.0
O D:HOH2114 4.4 19.4 1.0
NE D:ARG63 4.5 22.8 1.0
O E:HOH2079 4.5 20.2 1.0
OD1 D:ASP27 4.5 22.4 1.0
O2G E:DUP1131 4.5 25.3 1.0
O2A E:DUP1131 4.5 22.2 1.0
OD2 D:ASP27 4.6 22.7 1.0
O5' E:DUP1131 4.6 21.5 1.0
NE2 D:GLN112 4.6 14.9 1.0
O2B E:DUP1131 4.7 22.3 1.0
C5' E:DUP1131 4.7 24.3 1.0
CG D:ARG63 4.9 20.4 1.0
O D:HOH2006 4.9 41.3 1.0

Calcium binding site 7 out of 8 in 2xce

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Calcium binding site 7 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1146

b:23.4
occ:1.00
 O2G F:DUP1131 2.2 22.1 1.0
O F:HOH2133 2.2 20.7 1.0
O E:HOH2032 2.3 12.8 1.0
O E:HOH2030 2.3 13.4 1.0
O2B F:DUP1131 2.3 21.2 1.0
O1A F:DUP1131 2.4 19.9 1.0
PB F:DUP1131 3.4 22.6 1.0
PG F:DUP1131 3.4 27.7 1.0
O3B F:DUP1131 3.6 24.7 1.0
PA F:DUP1131 3.6 23.1 1.0
N3A F:DUP1131 3.9 18.2 1.0
O1G F:DUP1131 4.2 28.0 1.0
O F:HOH2139 4.2 16.3 1.0
O E:HOH2027 4.4 25.6 1.0
O F:HOH2089 4.5 24.2 1.0
NE E:ARG63 4.5 20.7 1.0
OD1 E:ASP27 4.5 19.9 1.0
O E:HOH2106 4.5 17.7 1.0
OD2 E:ASP27 4.5 21.2 1.0
O3G F:DUP1131 4.5 24.9 1.0
O5' F:DUP1131 4.6 22.8 1.0
NE2 E:GLN112 4.6 14.0 1.0
O1B F:DUP1131 4.7 22.0 1.0
O2A F:DUP1131 4.7 23.7 1.0
C5' F:DUP1131 4.9 24.3 1.0
CG E:ARG63 4.9 18.5 1.0
CG E:ASP27 5.0 19.2 1.0

Calcium binding site 8 out of 8 in 2xce

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Calcium binding site 8 out of 8 in the Structure of Yncf in Complex with Dupnhpp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Yncf in Complex with Dupnhpp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1147

b:25.9
occ:1.00
 O D:HOH2055 2.2 25.8 1.0
O E:HOH2052 2.4 26.7 1.0
O F:HOH2052 2.5 27.4 1.0
O F:HOH2050 4.3 32.2 1.0
OD1 D:ASP39 4.3 25.4 1.0
OD2 E:ASP39 4.3 29.5 1.0
OD2 F:ASP39 4.4 29.5 1.0
OD2 D:ASP39 4.4 27.0 1.0
O D:HOH2096 4.5 29.4 1.0
O E:HOH2092 4.5 35.1 1.0
OD1 E:ASP39 4.6 30.0 1.0
OD1 F:ASP39 4.6 29.3 1.0
NZ E:LYS38 4.6 46.3 1.0
CG D:ASP39 4.8 27.8 1.0
CG E:ASP39 4.9 27.6 1.0
CG F:ASP39 4.9 28.9 1.0

Reference:

J.Garcia-Nafria, L.Burchell, M.Takezawa, N.Rzechorzek, M.Fogg, K.S.Wilson. The Structure of the Genomic Bacillus Subtilis Dutpase: Novel Features in the Phe-Lid. Acta Crystallogr.,Sect.D V. 66 953 2010.
ISSN: ISSN 0907-4449
PubMed: 20823546
DOI: 10.1107/S0907444910026272
Page generated: Fri Jul 12 19:04:00 2024

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