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Sodium in PDB 5g3p: Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.

Protein crystallography data

The structure of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site., PDB code: 5g3p was solved by J.A.Gavira, M.Conejero-Muriel, S.Martinez-Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.23 / 1.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 143.764, 150.208, 98.257, 90.00, 98.68, 90.00
R / Rfree (%) 16.4 / 18.1

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. (pdb code 5g3p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site., PDB code: 5g3p:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 5g3p

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Sodium binding site 1 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1333

b:36.2
occ:1.00
 O B:ALA302 3.0 8.5 1.0
O A:HOH2322 3.2 32.9 1.0
ND2 A:ASN293 3.4 20.0 1.0
CB A:ASN293 3.7 20.0 1.0
CB A:LYS299 3.8 10.9 1.0
C B:ALA302 3.8 9.8 1.0
CA B:ALA302 3.9 9.7 1.0
O A:HOH2327 3.9 18.8 1.0
CG A:LYS299 3.9 14.5 1.0
CD A:LYS299 4.0 17.5 1.0
CG A:ASN293 4.1 20.0 1.0
CB B:ALA302 4.2 10.3 1.0
O1 A:PEG1329 4.3 50.0 1.0
O A:HOH2337 4.4 34.7 1.0
CA A:LYS299 4.4 9.6 1.0
O A:HOH2325 4.9 38.9 1.0
CA A:ASN293 4.9 10.8 1.0
N A:LYS299 5.0 8.5 1.0
NZ A:LYS299 5.0 18.9 1.0
O A:ASN293 5.0 9.7 1.0
CE A:LYS299 5.0 22.5 1.0

Sodium binding site 2 out of 15 in 5g3p

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Sodium binding site 2 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1340

b:41.4
occ:1.00
 O A:HOH2327 3.1 18.8 1.0
O B:HOH2298 3.2 28.4 1.0
CA B:GLY304 3.9 9.6 1.0
CB A:GLU292 4.0 10.4 0.6
O A:HOH2325 4.1 38.9 1.0
CA A:GLU292 4.1 9.9 0.6
CA A:GLU292 4.2 10.2 0.4
O B:GLU303 4.2 8.3 1.0
CB A:GLU292 4.3 10.6 0.4
N B:GLY304 4.3 8.9 1.0
CG A:GLU292 4.4 10.9 0.4
C B:GLU303 4.4 8.8 1.0
N A:GLU292 4.8 10.0 0.6
N A:GLU292 4.8 10.2 0.4
O A:HOH2322 4.9 32.9 1.0
C B:GLY304 5.0 10.1 1.0

Sodium binding site 3 out of 15 in 5g3p

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Sodium binding site 3 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1334

b:40.1
occ:1.00
 O B:HOH2004 2.3 38.9 1.0
O B:GLY5 2.8 20.1 1.0
OG B:SER4 3.0 18.1 1.0
O E:GLN194 3.1 10.2 1.0
CB B:SER4 3.6 23.6 1.0
C B:SER4 3.7 23.2 1.0
N B:GLY5 3.8 22.8 1.0
O B:SER4 3.8 21.4 1.0
NE2 E:GLN198 3.8 10.2 1.0
C B:GLY5 3.9 23.9 1.0
OE1 E:GLN198 3.9 11.4 1.0
CG E:GLN194 4.0 23.1 1.0
CD E:GLN198 4.0 10.1 1.0
CH2 F:TRP269 4.0 12.7 1.0
CZ3 F:TRP208 4.1 13.8 1.0
C E:GLN194 4.1 13.1 1.0
CH2 F:TRP208 4.1 13.0 1.0
CA B:SER4 4.2 22.0 1.0
CG1 E:VAL195 4.2 14.1 1.0
CZ3 F:TRP269 4.4 12.4 1.0
NE2 E:GLN194 4.4 28.1 1.0
CA B:GLY5 4.4 23.1 1.0
CA E:VAL195 4.6 11.9 1.0
CD E:GLN194 4.8 27.1 1.0
N E:VAL195 4.8 11.9 1.0
CZ2 F:TRP269 5.0 11.8 1.0

Sodium binding site 4 out of 15 in 5g3p

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Sodium binding site 4 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1335

b:30.0
occ:1.00
 O B:HOH2002 2.7 24.0 1.0
O B:HOH2106 3.0 24.0 1.0
N B:THR254 3.1 9.8 1.0
O B:HOH2326 3.1 19.9 1.0
O E:THR193 3.2 11.6 1.0
OG1 B:THR254 3.4 9.1 1.0
C E:THR193 3.5 12.9 1.0
C1 B:PEG1328 3.6 43.9 1.0
O B:THR254 3.6 8.6 1.0
OG1 E:THR193 3.6 13.6 1.0
C2 B:PEG1328 3.7 38.4 1.0
CA B:VAL253 3.7 10.7 1.0
O B:ILE252 3.7 13.8 1.0
CG1 B:VAL243 3.8 10.6 0.5
CB E:THR193 3.8 11.7 1.0
N E:GLN194 3.9 12.1 1.0
C B:VAL253 3.9 10.2 1.0
CA E:GLN194 3.9 14.5 1.0
CA B:THR254 4.0 9.4 1.0
O2 B:PEG1328 4.1 37.7 1.0
C B:THR254 4.3 9.3 1.0
CB B:THR254 4.3 9.3 1.0
CA E:THR193 4.3 11.3 1.0
C B:ILE252 4.6 11.8 1.0
C3 B:PEG1328 4.6 33.2 1.0
N B:VAL253 4.6 10.4 1.0
CG1 B:VAL253 4.6 12.5 1.0
C E:GLN194 4.7 13.1 1.0
CB B:VAL253 4.7 12.9 1.0
O E:GLN194 4.8 10.2 1.0
CG2 B:THR254 4.9 9.4 1.0
O1 B:PEG1328 4.9 57.8 1.0
CG1 B:VAL243 4.9 9.9 0.5
CB B:VAL243 5.0 10.1 0.5

Sodium binding site 5 out of 15 in 5g3p

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Sodium binding site 5 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1336

b:27.8
occ:1.00
 O B:HOH2174 2.6 21.4 1.0
O B:HOH2145 2.6 25.1 1.0
OE2 B:GLU105 2.7 8.9 1.0
N B:VAL80 3.0 10.3 1.0
O B:VAL80 3.4 11.5 1.0
CD B:GLU105 3.6 8.8 1.0
CG B:GLU105 3.6 9.2 1.0
CA B:THR79 3.7 11.5 1.0
C B:THR79 3.9 11.4 1.0
CB B:THR79 3.9 12.4 1.0
O B:LYS106 3.9 8.2 0.5
O B:LYS106 3.9 8.1 0.5
C B:VAL80 3.9 11.4 1.0
CA B:VAL80 4.0 10.8 1.0
NZ B:LYS129 4.2 9.2 1.0
O B:HOH2146 4.3 25.9 1.0
CG B:PRO108 4.4 12.0 1.0
O B:HOH2064 4.4 53.5 1.0
CB B:VAL80 4.4 11.0 1.0
O4 B:PGE1330 4.4 47.8 1.0
CG2 B:THR79 4.6 12.0 1.0
OE1 B:GLU105 4.7 8.6 1.0
CD B:PRO108 4.8 10.9 1.0
NH2 B:ARG131 4.8 8.1 1.0
O B:CYS78 4.9 9.5 1.0
O B:HOH2175 4.9 30.0 1.0

Sodium binding site 6 out of 15 in 5g3p

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Sodium binding site 6 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1337

b:37.9
occ:1.00
 O B:HOH2328 2.6 42.3 1.0
OE1 B:GLU75 2.8 16.5 1.0
OG1 B:THR73 2.9 8.7 1.0
CB B:THR73 3.6 10.9 1.0
CB B:GLU75 3.8 13.8 1.0
CG2 B:THR73 3.8 12.6 1.0
CD B:GLU75 3.8 17.8 1.0
O B:HOH2050 3.9 34.1 1.0
CD1 B:PHE76 3.9 10.1 1.0
CE1 B:PHE76 3.9 9.9 1.0
CD B:LYS70 4.1 19.6 1.0
CG B:LYS70 4.1 16.8 1.0
O B:HOH2133 4.1 27.3 1.0
CB B:LYS70 4.3 13.9 1.0
CG B:GLU75 4.3 15.4 1.0
CE B:LYS70 4.5 22.5 1.0
O B:LYS70 4.7 8.8 1.0
OE2 B:GLU75 4.9 17.6 1.0
CA B:GLU75 5.0 11.9 1.0
CA B:LYS70 5.0 12.4 1.0
O B:HOH2128 5.0 46.8 1.0

Sodium binding site 7 out of 15 in 5g3p

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Sodium binding site 7 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1331

b:33.5
occ:1.00
 O B:HOH2232 2.4 49.4 1.0
O C:GLY5 2.7 23.6 1.0
O B:GLN194 3.0 9.4 1.0
OG C:SER4 3.1 19.4 1.0
CB C:SER4 3.6 23.9 1.0
C C:SER4 3.6 23.4 1.0
O C:SER4 3.8 19.0 1.0
N C:GLY5 3.8 22.0 1.0
CG B:GLN194 3.8 18.9 1.0
C C:GLY5 3.9 25.9 1.0
NE2 B:GLN198 3.9 10.2 1.0
OE1 B:GLN198 3.9 11.0 1.0
C B:GLN194 4.0 11.2 1.0
CD B:GLN198 4.1 10.5 1.0
CH2 A:TRP269 4.1 13.6 1.0
CZ3 A:TRP208 4.2 11.2 1.0
CA C:SER4 4.2 23.7 1.0
CG1 B:VAL195 4.2 12.9 1.0
CH2 A:TRP208 4.2 10.5 1.0
NE2 B:GLN194 4.3 22.8 1.0
CA C:GLY5 4.4 23.2 1.0
CZ3 A:TRP269 4.4 12.1 1.0
CA B:VAL195 4.6 11.4 1.0
CD B:GLN194 4.7 23.2 1.0
N B:VAL195 4.7 10.5 1.0
CA B:GLN194 4.9 12.9 1.0
CB B:GLN194 4.9 15.6 1.0
O B:HOH2231 4.9 21.5 1.0
CB B:VAL195 5.0 12.4 1.0
CZ2 A:TRP269 5.0 13.9 1.0

Sodium binding site 8 out of 15 in 5g3p

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Sodium binding site 8 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1332

b:23.5
occ:1.00
 OD1 C:ASN206 2.7 11.1 1.0
OE1 C:GLN209 2.7 9.3 1.0
OG C:SER205 2.8 9.9 1.0
NE2 D:GLN209 2.9 11.8 1.0
O C:HOH2211 3.3 14.5 1.0
N C:ASN206 3.4 9.3 1.0
CB C:SER205 3.5 10.6 1.0
CD C:GLN209 3.5 8.3 1.0
C C:SER205 3.5 9.4 1.0
CG C:ASN206 3.7 10.1 1.0
CA C:ASN206 3.8 8.9 1.0
CB C:PRO171 3.8 8.3 1.0
NE2 C:GLN209 3.8 8.8 1.0
O C:SER205 3.9 9.5 1.0
O C:HOH2214 4.0 15.1 1.0
CA C:PRO171 4.1 8.3 1.0
CD D:GLN209 4.1 10.6 1.0
CA C:SER205 4.1 9.5 1.0
CB C:ASN206 4.4 9.2 1.0
O C:THR202 4.4 8.2 1.0
OE1 D:GLN209 4.4 10.6 1.0
O C:HOH2249 4.5 14.1 1.0
CG C:GLN209 4.7 8.0 1.0
N C:PRO171 4.8 8.3 1.0
ND2 C:ASN206 4.8 10.6 1.0
CG C:PRO171 4.8 8.3 1.0
CD C:PRO171 5.0 8.5 1.0

Sodium binding site 9 out of 15 in 5g3p

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Sodium binding site 9 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1331

b:26.2
occ:1.00
 OE2 F:GLU172 2.7 11.5 1.0
O E:HOH2186 2.9 15.5 1.0
CD F:GLU172 3.3 11.8 1.0
N E:GLU172 3.4 8.7 1.0
O E:PRO171 3.5 8.6 1.0
C E:PRO171 3.5 8.3 1.0
CA E:GLU172 3.5 8.7 1.0
CZ F:PHE297 3.7 8.9 1.0
CG F:PRO171 3.7 9.1 1.0
CG E:GLU172 3.8 9.4 1.0
CB E:ARG175 3.8 8.0 1.0
CG F:GLU172 3.8 10.5 1.0
CB E:PRO171 3.9 8.8 1.0
CD E:GLU172 4.1 9.9 1.0
OE1 F:GLU172 4.1 11.7 1.0
CB E:GLU172 4.2 9.0 1.0
CG E:ARG175 4.2 8.1 1.0
CG E:PRO171 4.3 8.6 1.0
CB F:PRO171 4.3 9.6 1.0
OE2 E:GLU172 4.3 9.3 1.0
NE E:ARG175 4.3 9.0 1.0
CA E:PRO171 4.3 8.8 1.0
CE1 F:PHE297 4.4 8.2 1.0
CE2 F:PHE297 4.5 8.1 1.0
N F:GLU172 4.6 8.6 1.0
C E:GLU172 4.7 8.9 1.0
OE1 E:GLU172 4.8 10.5 1.0
O E:HOH2185 4.8 15.2 1.0
CD E:ARG175 4.9 8.7 1.0
CD F:PRO171 4.9 8.6 1.0
C F:PRO171 4.9 9.2 1.0

Sodium binding site 10 out of 15 in 5g3p

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Sodium binding site 10 out of 15 in the Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Bacillus Cereus Formamidase (Bceamif) Acetylated at the Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1332

b:49.4
occ:1.00
 O E:GLY156 2.4 12.4 1.0
O E:HOH2009 2.8 42.8 1.0
OE1 E:GLU260 3.1 9.3 0.2
O E:SER12 3.3 14.0 0.7
C E:GLY156 3.4 11.4 1.0
N E:GLU260 3.7 9.9 0.2
N E:GLU260 3.7 11.3 0.8
OE2 E:GLU260 3.7 25.0 0.8
CD E:PRO259 3.8 10.0 1.0
CG E:GLU260 3.8 20.3 0.8
CB E:GLU260 3.9 15.8 0.8
CB E:GLU260 3.9 9.8 0.2
C E:SER12 3.9 17.4 0.7
N E:GLY13 3.9 14.9 0.3
O E:HOH2178 4.0 46.4 1.0
O E:HOH2180 4.0 23.4 1.0
CA E:GLY157 4.0 12.2 1.0
N E:GLY13 4.0 14.4 0.7
N E:GLY157 4.0 11.5 1.0
CD E:GLU260 4.1 9.8 0.2
N E:PRO259 4.1 9.9 1.0
CA E:GLY13 4.1 13.7 0.3
CD E:GLU260 4.2 24.4 0.8
CA E:GLY13 4.2 13.8 0.7
CB E:PRO259 4.2 10.4 1.0
CG E:PRO259 4.3 10.4 1.0
CA E:GLU260 4.3 9.9 0.2
CA E:GLU260 4.4 12.2 0.8
CA E:GLY156 4.4 11.6 1.0
CG E:GLU260 4.5 9.8 0.2
CA E:PRO259 4.5 9.7 1.0
C E:PRO259 4.5 10.3 1.0
C E:GLY157 4.6 12.2 1.0
C E:TYR258 4.7 9.9 1.0
C E:SER12 4.8 17.2 0.3
O E:GLY157 4.9 12.1 1.0
CA E:SER12 4.9 21.1 0.7

Reference:

S.Martinez-Rodriguez, M.Conejero-Muriel, J.A.Gavira. A Novel Cysteine Carbamoyl-Switch Is Responsible For the Inhibition of Formamidase, A Nitrilase Superfamily Member. Arch.Biochem.Biophys. V. 662 151 2019.
ISSN: ESSN 1096-0384
PubMed: 30528776
DOI: 10.1016/J.ABB.2018.12.008
Page generated: Sun Aug 17 23:55:00 2025

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