Atomistry » Sodium » PDB 8u30-8uze » 8ur1
Atomistry »
  Sodium »
    PDB 8u30-8uze »
      8ur1 »

Sodium in PDB 8ur1: Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)

Protein crystallography data

The structure of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site), PDB code: 8ur1 was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.93 / 2.10
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 96.4, 96.4, 205.596, 90, 90, 120
R / Rfree (%) 18.3 / 21.4

Other elements in 8ur1:

The structure of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) (pdb code 8ur1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site), PDB code: 8ur1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8ur1

Go back to Sodium Binding Sites List in 8ur1
Sodium binding site 1 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:31.0
occ:1.00
O A:HOH546 2.2 27.3 1.0
OG1 A:THR75 2.3 27.3 1.0
O A:HOH500 2.3 34.4 1.0
O A:ASP40 2.3 29.6 1.0
O A:HOH541 2.4 27.7 1.0
O A:HOH444 2.4 31.6 1.0
CB A:THR75 3.3 27.7 1.0
C A:ASP40 3.4 27.0 1.0
N A:THR75 3.7 29.0 1.0
CB A:ASP40 3.8 27.5 1.0
CA A:ASP40 3.9 27.5 1.0
O A:HIS4 3.9 36.3 1.0
O A:HOH572 4.1 40.9 1.0
O A:HOH555 4.1 46.1 1.0
CA A:THR75 4.1 28.7 1.0
O A:HOH556 4.4 44.0 1.0
CG2 A:THR75 4.5 26.0 1.0
N A:GLY41 4.5 24.7 1.0
O A:HOH509 4.6 37.9 1.0
CE A:MET9 4.7 30.9 1.0
C A:ILE74 4.8 36.4 1.0
O A:ARG6 4.8 30.4 1.0
CG A:ASP40 4.8 27.2 1.0
CA A:GLY41 4.9 30.3 1.0
OD1 A:ASP40 4.9 34.4 1.0
CA A:ILE74 5.0 28.8 1.0

Sodium binding site 2 out of 4 in 8ur1

Go back to Sodium Binding Sites List in 8ur1
Sodium binding site 2 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:31.2
occ:1.00
OG A:SER143 2.6 22.9 1.0
OG1 A:THR107 2.8 20.5 1.0
N A:ILE139 2.9 20.6 1.0
OD1 A:ASN138 3.0 24.0 1.0
O A:VAL145 3.2 36.1 1.0
C A:ILE139 3.4 24.7 1.0
CB A:SER143 3.5 22.8 1.0
O A:ILE139 3.6 23.9 1.0
N A:PRO140 3.6 28.2 1.0
CA A:ASN138 3.7 26.4 1.0
C A:ASN138 3.7 24.7 1.0
CA A:ILE139 3.7 24.8 1.0
CG2 A:THR107 3.9 22.8 1.0
CB A:THR107 3.9 22.3 1.0
CA A:PRO140 3.9 23.8 1.0
CB A:VAL145 4.0 23.7 1.0
CD A:PRO140 4.0 23.4 1.0
CG A:ASN138 4.0 27.0 1.0
C A:VAL145 4.2 30.2 1.0
CG2 A:ILE139 4.3 22.2 1.0
O A:TYR137 4.3 23.7 1.0
CB A:ASN138 4.4 26.8 1.0
CG A:PRO140 4.5 24.8 1.0
CA A:VAL145 4.5 24.0 1.0
CG1 A:VAL145 4.6 21.2 1.0
N A:VAL145 4.6 26.9 1.0
CB A:ILE139 4.7 19.7 1.0
CB A:PRO140 4.8 22.1 1.0
N A:THR107 4.8 26.5 1.0
N A:ASN138 4.8 26.8 1.0
CA A:SER143 4.8 26.8 1.0
O A:ASN138 4.9 23.1 1.0
CG2 A:VAL145 5.0 30.0 1.0
CA A:THR107 5.0 25.2 1.0

Sodium binding site 3 out of 4 in 8ur1

Go back to Sodium Binding Sites List in 8ur1
Sodium binding site 3 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:30.1
occ:1.00
OD1 A:ASP191 2.7 22.0 1.0
O A:ASN188 2.8 20.5 1.0
OH A:TYR210 2.8 24.8 1.0
ND2 A:ASN188 3.2 20.2 1.0
N A:ASP191 3.4 22.9 1.0
CA A:ASP191 3.5 21.7 1.0
C A:GLY189 3.5 31.1 1.0
CZ A:TYR210 3.6 25.6 1.0
C A:TYR190 3.6 23.4 1.0
C A:ASN188 3.6 27.5 1.0
O A:GLY189 3.6 22.2 1.0
O A:ILE206 3.6 29.8 1.0
CG A:ASP191 3.7 26.0 1.0
CE1 A:TYR210 3.8 23.4 1.0
N A:TYR190 3.8 22.9 1.0
CA A:GLY189 3.9 23.0 1.0
O A:TYR190 3.9 20.4 1.0
N A:GLY189 4.1 23.0 1.0
C A:ILE206 4.1 26.9 1.0
CB A:ASP191 4.1 24.4 1.0
CD1 A:PHE194 4.1 34.0 1.0
CA A:GLY207 4.2 26.9 1.0
CA A:TYR190 4.2 22.3 1.0
CG A:ASN188 4.3 21.0 1.0
N A:ILE206 4.3 28.4 1.0
N A:GLY207 4.4 28.5 1.0
CB A:ASN188 4.5 20.1 1.0
CA A:GLY205 4.6 28.2 1.0
CA A:ASN188 4.7 20.6 1.0
CE2 A:TYR210 4.7 27.0 1.0
OD2 A:ASP191 4.7 23.4 1.0
C A:ASP191 4.7 23.0 1.0
CE1 A:PHE194 4.8 31.2 1.0
C A:GLY205 4.8 24.5 1.0
OH7 A:1PE318 4.9 47.4 1.0
CA A:ILE206 4.9 28.6 1.0
CB A:PHE194 4.9 28.3 1.0
CG A:PHE194 5.0 22.4 1.0

Sodium binding site 4 out of 4 in 8ur1

Go back to Sodium Binding Sites List in 8ur1
Sodium binding site 4 out of 4 in the Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:32.8
occ:1.00
O A:VAL267 2.7 26.6 1.0
O A:LEU269 2.7 17.5 1.0
N A:PHE16 3.0 23.4 1.0
N A:LEU269 3.3 30.8 1.0
NZ A:LYS256 3.4 22.5 1.0
O A:PHE16 3.4 29.1 1.0
CD A:LYS256 3.4 22.3 1.0
CA A:PRO15 3.6 25.5 1.0
C A:PRO268 3.6 25.2 1.0
CE A:LYS256 3.7 24.4 1.0
C A:LEU269 3.7 25.9 1.0
C A:VAL267 3.7 29.7 1.0
C A:PRO15 3.8 27.6 1.0
CA A:PRO268 3.8 31.6 1.0
CA A:PHE16 3.9 28.5 1.0
CA A:LEU269 4.0 23.5 1.0
C A:PHE16 4.1 24.3 1.0
CB A:PHE16 4.2 25.5 1.0
N A:PRO268 4.2 29.1 1.0
O A:HOH460 4.3 24.0 1.0
CG A:LYS256 4.3 21.1 1.0
O A:PRO268 4.3 26.1 1.0
CB A:PRO15 4.3 25.0 1.0
O A:THR14 4.4 21.9 1.0
CD1 A:LEU265 4.4 29.1 1.0
CD2 A:PHE16 4.5 29.9 1.0
CB A:LYS256 4.6 20.7 1.0
CB A:LEU269 4.7 25.2 1.0
CG A:PHE16 4.7 22.6 1.0
N A:PRO15 4.8 27.8 1.0
N A:CYS270 4.9 26.7 1.0
CA A:VAL267 4.9 22.4 1.0

Reference:

S.Lovell, L.Liu, S.Seibold, M.R.Mian. Crystal Structure N-Acetylneuraminate Lyase (Nana) From Klebsiella Aerogenes (Pyruvate Bound Halide Free Active Site) To Be Published.
Page generated: Wed Oct 9 13:54:50 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy