Sodium in PDB 3gvk: Crystal Structure of Endo-Neuraminidase Nf Mutant
Enzymatic activity of Crystal Structure of Endo-Neuraminidase Nf Mutant
All present enzymatic activity of Crystal Structure of Endo-Neuraminidase Nf Mutant:
3.2.1.129;
Protein crystallography data
The structure of Crystal Structure of Endo-Neuraminidase Nf Mutant, PDB code: 3gvk
was solved by
E.C.Schulz,
A.Dickmanns,
R.Ficner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
1.84
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.400,
153.700,
157.800,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.5 /
28.2
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Endo-Neuraminidase Nf Mutant
(pdb code 3gvk). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Crystal Structure of Endo-Neuraminidase Nf Mutant, PDB code: 3gvk:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 3gvk
Go back to
Sodium Binding Sites List in 3gvk
Sodium binding site 1 out
of 3 in the Crystal Structure of Endo-Neuraminidase Nf Mutant
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 Endo-Neuraminidase Nf Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na916
b:14.8
occ:1.00
|
O
|
A:HIS743
|
2.3
|
13.3
|
1.0
|
O
|
A:THR322
|
2.4
|
12.5
|
1.0
|
O
|
A:TYR324
|
2.5
|
13.8
|
1.0
|
O
|
A:SER745
|
2.5
|
12.2
|
1.0
|
OD2
|
A:ASP746
|
2.8
|
12.7
|
1.0
|
CG
|
A:ASP746
|
3.3
|
12.5
|
1.0
|
NH2
|
B:ARG772
|
3.4
|
15.0
|
1.0
|
C
|
A:HIS743
|
3.5
|
12.9
|
1.0
|
OD1
|
A:ASP746
|
3.5
|
11.8
|
1.0
|
C
|
A:SER745
|
3.5
|
12.1
|
1.0
|
OD1
|
A:ASN326
|
3.6
|
15.2
|
1.0
|
C
|
A:THR322
|
3.6
|
12.7
|
1.0
|
C
|
A:TYR324
|
3.7
|
14.0
|
1.0
|
N
|
A:SER745
|
4.0
|
12.0
|
1.0
|
C
|
A:PRO323
|
4.0
|
13.3
|
1.0
|
C
|
A:PRO744
|
4.0
|
12.3
|
1.0
|
CZ
|
B:ARG772
|
4.1
|
14.6
|
1.0
|
N
|
A:TYR324
|
4.2
|
13.6
|
1.0
|
O
|
A:PRO323
|
4.2
|
13.2
|
1.0
|
CA
|
A:PRO323
|
4.3
|
13.1
|
1.0
|
CG
|
A:ASN326
|
4.3
|
13.8
|
1.0
|
N
|
A:ASN326
|
4.3
|
13.9
|
1.0
|
O
|
A:PRO744
|
4.3
|
12.2
|
1.0
|
N
|
A:PRO744
|
4.3
|
12.7
|
1.0
|
CA
|
A:SER745
|
4.4
|
12.3
|
0.5
|
CA
|
A:SER745
|
4.4
|
11.8
|
0.5
|
N
|
A:PRO323
|
4.4
|
12.8
|
1.0
|
N
|
A:ASP746
|
4.4
|
12.0
|
1.0
|
CA
|
A:PRO744
|
4.4
|
12.3
|
1.0
|
CA
|
A:HIS743
|
4.4
|
13.4
|
1.0
|
CB
|
A:ASP746
|
4.5
|
11.8
|
1.0
|
N
|
A:THR322
|
4.5
|
12.7
|
1.0
|
N
|
A:TYR325
|
4.6
|
14.1
|
1.0
|
CA
|
A:TYR324
|
4.6
|
14.1
|
1.0
|
CA
|
A:ASP746
|
4.6
|
11.8
|
1.0
|
CB
|
A:HIS743
|
4.6
|
13.4
|
1.0
|
NH1
|
B:ARG772
|
4.6
|
14.1
|
1.0
|
N
|
A:HIS743
|
4.7
|
13.3
|
1.0
|
CA
|
A:TYR325
|
4.7
|
14.2
|
1.0
|
CB
|
A:ASN326
|
4.7
|
13.7
|
1.0
|
CA
|
A:THR322
|
4.7
|
12.6
|
1.0
|
NE
|
B:ARG772
|
4.7
|
14.3
|
1.0
|
O
|
A:HOH143
|
4.9
|
13.9
|
1.0
|
OG1
|
A:THR322
|
4.9
|
12.7
|
1.0
|
|
Sodium binding site 2 out
of 3 in 3gvk
Go back to
Sodium Binding Sites List in 3gvk
Sodium binding site 2 out
of 3 in the Crystal Structure of Endo-Neuraminidase Nf Mutant
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 Endo-Neuraminidase Nf Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na916
b:14.0
occ:1.00
|
O
|
B:THR322
|
2.4
|
12.8
|
1.0
|
O
|
B:HIS743
|
2.4
|
13.0
|
1.0
|
O
|
B:TYR324
|
2.4
|
12.9
|
1.0
|
O
|
B:SER745
|
2.5
|
11.8
|
1.0
|
OD2
|
B:ASP746
|
2.8
|
12.9
|
1.0
|
CG
|
B:ASP746
|
3.3
|
12.3
|
1.0
|
NH2
|
C:ARG772
|
3.4
|
14.0
|
1.0
|
OD1
|
B:ASN326
|
3.5
|
14.5
|
1.0
|
C
|
B:SER745
|
3.5
|
12.3
|
1.0
|
OD1
|
B:ASP746
|
3.5
|
12.4
|
1.0
|
C
|
B:HIS743
|
3.5
|
12.7
|
1.0
|
C
|
B:THR322
|
3.6
|
12.9
|
1.0
|
C
|
B:TYR324
|
3.6
|
13.1
|
1.0
|
C
|
B:PRO323
|
3.9
|
12.8
|
1.0
|
N
|
B:SER745
|
4.0
|
12.5
|
1.0
|
CZ
|
C:ARG772
|
4.1
|
14.2
|
1.0
|
C
|
B:PRO744
|
4.1
|
12.6
|
1.0
|
N
|
B:TYR324
|
4.1
|
12.9
|
1.0
|
O
|
B:PRO323
|
4.1
|
12.6
|
1.0
|
CA
|
B:PRO323
|
4.2
|
12.8
|
1.0
|
CG
|
B:ASN326
|
4.3
|
12.8
|
1.0
|
N
|
B:ASN326
|
4.3
|
11.9
|
1.0
|
O
|
B:PRO744
|
4.3
|
12.7
|
1.0
|
CA
|
B:SER745
|
4.4
|
12.4
|
1.0
|
N
|
B:PRO323
|
4.4
|
12.8
|
1.0
|
N
|
B:ASP746
|
4.4
|
12.2
|
1.0
|
N
|
B:PRO744
|
4.4
|
12.7
|
1.0
|
CB
|
B:ASP746
|
4.4
|
12.2
|
1.0
|
CA
|
B:HIS743
|
4.5
|
13.0
|
1.0
|
N
|
B:THR322
|
4.5
|
12.4
|
1.0
|
CA
|
B:PRO744
|
4.5
|
12.7
|
1.0
|
CA
|
B:TYR324
|
4.5
|
13.0
|
1.0
|
N
|
B:TYR325
|
4.6
|
12.7
|
1.0
|
CA
|
B:ASP746
|
4.6
|
12.2
|
1.0
|
NH1
|
C:ARG772
|
4.6
|
14.2
|
1.0
|
CA
|
B:THR322
|
4.6
|
12.7
|
1.0
|
CB
|
B:HIS743
|
4.6
|
12.8
|
1.0
|
CB
|
B:ASN326
|
4.7
|
12.0
|
1.0
|
N
|
B:HIS743
|
4.7
|
13.5
|
1.0
|
CA
|
B:TYR325
|
4.7
|
12.7
|
1.0
|
NE
|
C:ARG772
|
4.7
|
13.7
|
1.0
|
OG1
|
B:THR322
|
4.9
|
13.3
|
1.0
|
O
|
B:HOH953
|
4.9
|
11.6
|
1.0
|
|
Sodium binding site 3 out
of 3 in 3gvk
Go back to
Sodium Binding Sites List in 3gvk
Sodium binding site 3 out
of 3 in the Crystal Structure of Endo-Neuraminidase Nf Mutant
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 Endo-Neuraminidase Nf Mutant within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na916
b:17.1
occ:1.00
|
O
|
C:HIS743
|
2.3
|
16.1
|
1.0
|
O
|
C:THR322
|
2.3
|
14.6
|
1.0
|
O
|
C:TYR324
|
2.4
|
15.1
|
1.0
|
O
|
C:SER745
|
2.5
|
16.0
|
1.0
|
OD2
|
C:ASP746
|
2.9
|
16.1
|
1.0
|
NH2
|
A:ARG772
|
3.3
|
16.9
|
1.0
|
CG
|
C:ASP746
|
3.4
|
15.4
|
1.0
|
C
|
C:SER745
|
3.5
|
16.0
|
1.0
|
C
|
C:HIS743
|
3.5
|
16.2
|
1.0
|
OD1
|
C:ASP746
|
3.5
|
14.8
|
1.0
|
OD1
|
C:ASN326
|
3.5
|
15.7
|
1.0
|
C
|
C:THR322
|
3.6
|
14.9
|
1.0
|
C
|
C:TYR324
|
3.6
|
15.2
|
1.0
|
N
|
C:SER745
|
3.9
|
16.1
|
1.0
|
C
|
C:PRO323
|
4.0
|
15.1
|
1.0
|
C
|
C:PRO744
|
4.0
|
16.3
|
1.0
|
CZ
|
A:ARG772
|
4.1
|
16.1
|
1.0
|
N
|
C:TYR324
|
4.1
|
15.2
|
1.0
|
CG
|
C:ASN326
|
4.3
|
15.1
|
1.0
|
CA
|
C:PRO323
|
4.3
|
14.9
|
1.0
|
CA
|
C:SER745
|
4.3
|
16.1
|
1.0
|
O
|
C:PRO323
|
4.3
|
14.9
|
1.0
|
N
|
C:ASN326
|
4.3
|
14.9
|
1.0
|
O
|
C:PRO744
|
4.3
|
16.4
|
1.0
|
N
|
C:PRO323
|
4.4
|
14.6
|
1.0
|
N
|
C:PRO744
|
4.4
|
16.1
|
1.0
|
N
|
C:ASP746
|
4.4
|
15.8
|
1.0
|
CA
|
C:HIS743
|
4.4
|
16.3
|
1.0
|
CA
|
C:PRO744
|
4.5
|
16.2
|
1.0
|
N
|
C:THR322
|
4.5
|
15.1
|
1.0
|
CB
|
C:ASP746
|
4.5
|
15.6
|
1.0
|
CA
|
C:TYR324
|
4.5
|
15.3
|
1.0
|
N
|
C:TYR325
|
4.5
|
15.2
|
1.0
|
CA
|
C:THR322
|
4.6
|
15.2
|
1.0
|
CB
|
C:HIS743
|
4.6
|
16.4
|
1.0
|
NH1
|
A:ARG772
|
4.6
|
16.3
|
1.0
|
CA
|
C:ASP746
|
4.6
|
15.8
|
1.0
|
CA
|
C:TYR325
|
4.6
|
15.0
|
1.0
|
N
|
C:HIS743
|
4.7
|
16.4
|
1.0
|
CB
|
C:ASN326
|
4.7
|
14.6
|
1.0
|
NE
|
A:ARG772
|
4.7
|
15.7
|
1.0
|
O
|
C:HOH1008
|
4.9
|
17.4
|
1.0
|
CB
|
C:THR322
|
4.9
|
15.7
|
1.0
|
C
|
C:TYR325
|
5.0
|
14.9
|
1.0
|
|
Reference:
E.C.Schulz,
D.Schwarzer,
M.Frank,
K.Stummeyer,
M.Muhlenhoff,
A.Dickmanns,
R.Gerardy-Schahn,
R.Ficner.
Structural Basis For the Recognition and Cleavage of Polysialic Acid By the Bacteriophage K1F Tailspike Protein Endonf. J.Mol.Biol. V. 397 341 2010.
ISSN: ISSN 0022-2836
PubMed: 20096705
DOI: 10.1016/J.JMB.2010.01.028
Page generated: Mon Oct 7 10:18:08 2024
|