Atomistry » Sodium » PDB 5g3g-5gwa » 5g3p
Atomistry »
  Sodium »
    PDB 5g3g-5gwa »
      5g3p »

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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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

Go back to Sodium Binding Sites List in 5g3p
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: Tue Dec 15 11:01:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy