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Sodium in PDB 4zm9: Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1

Enzymatic activity of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1

All present enzymatic activity of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1:
3.4.19.5; 3.5.1.1;

Protein crystallography data

The structure of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1, PDB code: 4zm9 was solved by W.Z.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.74 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.308, 111.107, 122.517, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 (pdb code 4zm9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1, PDB code: 4zm9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4zm9

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Sodium binding site 1 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:19.9
occ:1.00
 O A:ASP58 2.3 21.6 1.0
O A:CYS65 2.4 22.9 1.0
O A:ALA63 2.4 21.9 1.0
O A:GLU56 2.5 26.8 1.0
O A:PHE61 2.6 19.9 1.0
O A:LEU55 2.7 17.3 1.0
C A:GLU56 3.2 24.1 1.0
C A:ASP58 3.3 23.2 1.0
C A:CYS65 3.5 21.6 1.0
C A:ALA63 3.5 20.9 1.0
C A:PHE61 3.6 19.8 1.0
CA A:GLU56 3.6 21.7 1.0
C A:LEU55 3.7 18.7 1.0
N A:ASP58 3.8 23.1 1.0
CB A:PHE61 4.0 23.1 1.0
N A:CYS65 4.1 22.8 1.0
N A:PHE61 4.1 22.1 1.0
N A:ALA63 4.1 21.3 1.0
CA A:ASP58 4.1 23.3 1.0
N A:PRO59 4.1 26.1 1.0
CA A:PHE61 4.1 21.4 1.0
CA A:PRO59 4.1 25.4 1.0
N A:GLU56 4.2 19.3 1.0
C A:ASP57 4.2 23.3 1.0
N A:ASP57 4.2 22.8 1.0
C A:GLY64 4.3 21.5 1.0
CA A:CYS65 4.3 23.7 1.0
CA A:ALA63 4.3 20.2 1.0
N A:GLY66 4.4 21.8 1.0
N A:GLY64 4.5 21.8 1.0
CA A:GLY66 4.5 21.1 1.0
CA A:GLY64 4.6 20.8 1.0
C A:PRO59 4.6 23.5 1.0
CB A:ALA63 4.6 19.6 1.0
O A:ASP57 4.6 23.2 1.0
CA A:ASP57 4.7 23.4 1.0
O A:GLY64 4.7 20.9 1.0
N A:ASN62 4.8 18.5 1.0
CB A:CYS65 4.8 24.9 1.0
C A:GLY66 4.8 19.9 1.0
CB A:ASP58 4.8 23.0 1.0
N A:GLU60 5.0 23.9 1.0
CB A:GLU56 5.0 20.1 1.0

Sodium binding site 2 out of 7 in 4zm9

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Sodium binding site 2 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:33.6
occ:1.00
 OD2 A:ASP199 2.6 15.9 1.0
OG A:SER200 2.9 16.8 1.0
O A:THR218 2.9 17.3 1.0
N A:GLY402 3.2 27.4 1.0
CG A:ASP199 3.4 15.3 1.0
OD1 A:ASP199 3.4 14.7 1.0
C A:THR218 3.5 17.9 1.0
CG2 A:THR168 3.5 15.2 1.0
CA A:GLY402 3.6 27.4 1.0
OG1 A:THR218 3.6 22.6 1.0
CG2 A:THR184 3.7 16.0 1.0
CA A:THR219 3.8 19.1 1.0
N A:THR219 4.0 19.1 1.0
CB A:SER200 4.0 16.9 1.0
CA A:SER200 4.1 15.8 1.0
CA A:GLY206 4.3 19.5 1.0
N A:SER200 4.3 15.1 1.0
OG1 A:THR168 4.3 17.6 1.0
CB A:THR168 4.5 15.9 1.0
CA A:THR218 4.5 19.1 1.0
CB A:THR218 4.6 21.4 1.0
C A:THR219 4.6 18.2 1.0
O A:GLY206 4.7 18.7 1.0
CB A:ASP199 4.8 14.5 1.0
CD1 A:ILE225 4.8 19.8 1.0
N A:GLY220 4.9 19.4 1.0
CB A:THR219 4.9 19.5 1.0
C A:ASP199 4.9 14.4 1.0
N A:THR218 4.9 16.6 1.0

Sodium binding site 3 out of 7 in 4zm9

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Sodium binding site 3 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:28.9
occ:1.00
 O B:ASP58 2.3 27.7 1.0
O B:CYS65 2.4 20.2 1.0
O B:ALA63 2.5 25.8 1.0
O B:PHE61 2.6 18.8 1.0
O B:GLU56 2.6 21.7 1.0
O B:LEU55 2.6 21.8 1.0
C B:GLU56 3.2 23.4 1.0
C B:ASP58 3.2 28.5 1.0
C B:PHE61 3.6 20.1 1.0
C B:ALA63 3.6 21.8 1.0
C B:CYS65 3.6 22.2 1.0
CA B:GLU56 3.7 22.0 1.0
C B:LEU55 3.7 21.2 1.0
N B:ASP58 3.8 23.9 1.0
CB B:PHE61 3.9 21.7 1.0
N B:PHE61 4.0 20.9 1.0
CA B:PHE61 4.0 21.2 1.0
N B:ALA63 4.1 22.1 1.0
N B:PRO59 4.1 31.2 1.0
CA B:ASP58 4.1 25.9 1.0
N B:CYS65 4.1 26.3 1.0
CA B:PRO59 4.1 29.8 1.0
N B:GLU56 4.2 21.5 1.0
C B:ASP57 4.2 23.4 1.0
N B:ASP57 4.2 23.8 1.0
C B:GLY64 4.3 24.3 1.0
CA B:ALA63 4.3 23.8 1.0
CA B:CYS65 4.4 24.6 1.0
N B:GLY66 4.5 23.0 1.0
N B:GLY64 4.5 21.7 1.0
CA B:GLY66 4.6 24.5 1.0
C B:PRO59 4.6 28.1 1.0
CB B:ALA63 4.6 23.3 1.0
CA B:GLY64 4.7 21.6 1.0
O B:ASP57 4.7 23.0 1.0
N B:ASN62 4.7 21.3 1.0
CA B:ASP57 4.7 24.2 1.0
O B:GLY64 4.8 24.5 1.0
CB B:ASP58 4.8 26.1 1.0
CB B:CYS65 4.8 27.6 1.0
C B:GLY66 4.9 23.6 1.0
CG B:PHE61 5.0 22.8 1.0
N B:GLU60 5.0 28.0 1.0
CA B:LEU55 5.0 20.9 1.0
CD2 B:PHE61 5.0 24.4 1.0

Sodium binding site 4 out of 7 in 4zm9

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Sodium binding site 4 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:21.3
occ:1.00
 O C:ASP58 2.3 24.8 1.0
O C:CYS65 2.3 22.9 1.0
O C:ALA63 2.4 22.8 1.0
O C:GLU56 2.5 23.1 1.0
O C:PHE61 2.6 15.9 1.0
O C:LEU55 2.7 19.6 1.0
C C:GLU56 3.2 23.1 1.0
C C:ASP58 3.2 26.4 1.0
C C:CYS65 3.5 22.8 1.0
C C:ALA63 3.6 22.1 1.0
C C:PHE61 3.6 17.3 1.0
CA C:GLU56 3.7 22.5 1.0
N C:ASP58 3.7 22.0 1.0
C C:LEU55 3.8 20.8 1.0
N C:CYS65 4.0 26.8 1.0
N C:PHE61 4.0 18.2 1.0
CB C:PHE61 4.0 19.0 1.0
CA C:ASP58 4.0 25.1 1.0
N C:PRO59 4.1 28.6 1.0
CA C:PRO59 4.1 28.9 1.0
C C:ASP57 4.1 22.8 1.0
CA C:PHE61 4.1 17.9 1.0
N C:ALA63 4.1 22.1 1.0
N C:ASP57 4.2 23.3 1.0
C C:GLY64 4.2 24.8 1.0
N C:GLU56 4.2 21.6 1.0
CA C:CYS65 4.3 26.4 1.0
CA C:ALA63 4.4 21.5 1.0
N C:GLY66 4.4 20.7 1.0
CA C:GLY66 4.5 20.3 1.0
N C:GLY64 4.5 22.8 1.0
C C:PRO59 4.5 26.2 1.0
O C:ASP57 4.6 20.3 1.0
CA C:GLY64 4.6 23.0 1.0
CA C:ASP57 4.6 24.4 1.0
O C:GLY64 4.7 25.5 1.0
CB C:ALA63 4.7 21.5 1.0
CB C:CYS65 4.7 27.2 1.0
C C:GLY66 4.8 18.9 1.0
N C:ASN62 4.8 17.3 1.0
CB C:ASP58 4.8 25.5 1.0
N C:GLU60 4.9 25.7 1.0

Sodium binding site 5 out of 7 in 4zm9

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Sodium binding site 5 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na408

b:52.2
occ:1.00
 O C:ARG196 2.7 18.2 1.0
OD1 C:ASP78 3.0 27.4 1.0
O C:HOH511 3.1 15.2 1.0
NZ C:LYS192 3.3 21.2 1.0
CA C:ALA94 3.3 18.5 1.0
N C:ALA94 3.5 16.4 1.0
CB C:ALA94 3.6 18.7 1.0
CB C:GLU76 3.7 25.6 1.0
CG C:ASP78 3.8 25.2 1.0
OD2 C:ASP78 3.9 26.2 1.0
CE C:LYS192 3.9 20.6 1.0
C C:ARG196 4.0 19.4 1.0
O C:GLU76 4.0 18.8 1.0
C C:GLU76 4.0 21.8 1.0
N C:MET77 4.2 22.4 1.0
O C:MET77 4.4 18.0 1.0
C C:MET77 4.5 20.9 1.0
CD C:GLU76 4.5 31.6 1.0
CA C:GLU76 4.5 22.6 1.0
OE2 C:GLU76 4.5 36.3 1.0
CA C:VAL197 4.6 17.1 1.0
CG C:GLU76 4.6 28.1 1.0
C C:ALA94 4.7 19.2 1.0
N C:ARG196 4.7 18.4 1.0
C C:SER93 4.7 16.0 1.0
N C:VAL197 4.7 18.7 1.0
CA C:MET77 4.8 21.7 1.0
C C:GLY195 4.8 19.6 1.0
N C:ASP78 4.9 20.8 1.0
OE1 C:GLU76 4.9 28.6 1.0
CD C:LYS192 4.9 21.3 1.0
CG2 C:VAL197 5.0 16.5 1.0

Sodium binding site 6 out of 7 in 4zm9

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Sodium binding site 6 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na409

b:33.5
occ:1.00
 OD2 C:ASP199 2.5 17.5 1.0
OG C:SER200 2.9 16.5 1.0
O C:THR218 3.0 15.9 1.0
N C:GLY402 3.0 28.5 1.0
CG C:ASP199 3.3 14.9 1.0
OD1 C:ASP199 3.3 13.6 1.0
CA C:GLY402 3.4 27.2 1.0
C C:THR218 3.5 17.5 1.0
CG2 C:THR168 3.6 20.6 1.0
OG1 C:THR218 3.6 20.7 1.0
CA C:THR219 3.8 19.2 1.0
CG2 C:THR184 3.8 16.7 1.0
N C:THR219 4.0 18.5 1.0
CB C:SER200 4.0 16.4 1.0
CA C:SER200 4.0 15.9 1.0
N C:SER200 4.3 15.8 1.0
CA C:GLY206 4.3 16.7 1.0
OG1 C:THR168 4.3 23.3 1.0
CB C:THR168 4.5 20.2 1.0
CA C:THR218 4.6 18.3 1.0
C C:THR219 4.6 17.9 1.0
CB C:THR218 4.6 20.5 1.0
O C:GLY206 4.7 18.3 1.0
CB C:ASP199 4.7 14.2 1.0
CD1 C:ILE225 4.7 19.5 1.0
C C:GLY402 4.8 25.3 1.0
C C:ASP199 4.8 14.9 1.0
N C:GLY220 4.8 18.7 1.0
CB C:THR219 4.9 19.2 1.0
N C:THR218 5.0 16.5 1.0

Sodium binding site 7 out of 7 in 4zm9

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Sodium binding site 7 out of 7 in the Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Circularly Permuted Human Asparaginase-Like Protein 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:30.8
occ:1.00
 O D:ASP58 2.3 30.3 1.0
O D:CYS65 2.5 20.5 1.0
O D:ALA63 2.5 21.2 1.0
O D:LEU55 2.5 23.1 1.0
O D:GLU56 2.6 23.4 1.0
O D:PHE61 2.6 19.3 1.0
C D:GLU56 3.2 24.4 1.0
C D:ASP58 3.2 28.0 1.0
C D:ALA63 3.6 21.1 1.0
C D:PHE61 3.6 21.0 1.0
CA D:GLU56 3.6 22.5 1.0
C D:CYS65 3.6 21.9 1.0
C D:LEU55 3.7 21.9 1.0
N D:ASP58 3.8 24.2 1.0
CB D:PHE61 3.9 24.8 1.0
N D:PHE61 4.0 23.2 1.0
CA D:PHE61 4.0 23.6 1.0
CA D:ASP58 4.1 25.0 1.0
N D:ALA63 4.1 19.2 1.0
N D:GLU56 4.1 22.0 1.0
N D:PRO59 4.1 31.9 1.0
N D:CYS65 4.1 27.8 1.0
CA D:PRO59 4.2 30.1 1.0
C D:ASP57 4.2 24.2 1.0
N D:ASP57 4.2 25.3 1.0
CA D:ALA63 4.3 20.1 1.0
C D:GLY64 4.3 26.1 1.0
CA D:CYS65 4.4 24.3 1.0
N D:GLY64 4.5 23.5 1.0
N D:GLY66 4.6 22.2 1.0
CB D:ALA63 4.6 19.9 1.0
CA D:GLY66 4.6 22.2 1.0
C D:PRO59 4.6 28.3 1.0
CA D:GLY64 4.7 24.1 1.0
O D:ASP57 4.7 24.4 1.0
N D:ASN62 4.7 21.6 1.0
CA D:ASP57 4.7 26.2 1.0
CB D:ASP58 4.7 24.1 1.0
O D:GLY64 4.8 25.4 1.0
CB D:CYS65 4.9 27.6 1.0
C D:GLY66 4.9 22.9 1.0
CG D:PHE61 4.9 26.3 1.0
CA D:LEU55 4.9 22.2 1.0
CD2 D:PHE61 5.0 25.8 1.0
N D:GLU60 5.0 28.3 1.0
CB D:GLU56 5.0 21.4 1.0

Reference:

W.Li, S.Irani, A.Crutchfield, K.Hodge, W.Matthews, P.Patel, Y.J.Zhang, E.Stone. Intramolecular Cleavage of the HASRGL1 Homodimer Occurs in Two Stages. Biochemistry V. 55 960 2016.
ISSN: ISSN 0006-2960
PubMed: 26780688
DOI: 10.1021/ACS.BIOCHEM.5B01157
Page generated: Mon Oct 7 19:45:05 2024

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