Sodium in PDB 8bve: MOEA2 From Corynebacterium Glutamicum
Protein crystallography data
The structure of MOEA2 From Corynebacterium Glutamicum, PDB code: 8bve
was solved by
M.Martinez,
A.Haouz,
A.M.Wehenkel,
P.M.Alzari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.20 /
2.14
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.443,
94.443,
230.564,
90,
90,
90
|
R / Rfree (%)
|
20 /
22.7
|
Sodium Binding Sites:
The binding sites of Sodium atom in the MOEA2 From Corynebacterium Glutamicum
(pdb code 8bve). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
MOEA2 From Corynebacterium Glutamicum, PDB code: 8bve:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 8bve
Go back to
Sodium Binding Sites List in 8bve
Sodium binding site 1 out
of 2 in the MOEA2 From Corynebacterium Glutamicum
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of MOEA2 From Corynebacterium Glutamicum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:69.4
occ:1.00
|
O
|
A:VAL401
|
2.4
|
77.8
|
1.0
|
OG
|
A:SER348
|
2.7
|
72.5
|
1.0
|
O
|
A:VAL349
|
2.7
|
84.2
|
1.0
|
O
|
A:PRO398
|
2.7
|
66.3
|
1.0
|
O
|
A:ARG352
|
2.8
|
63.0
|
1.0
|
O
|
A:GLU399
|
2.8
|
73.3
|
1.0
|
C
|
A:GLU399
|
3.4
|
73.1
|
1.0
|
C
|
A:VAL401
|
3.6
|
78.6
|
1.0
|
CA
|
A:GLU399
|
3.7
|
67.9
|
1.0
|
C
|
A:VAL349
|
3.7
|
87.9
|
1.0
|
CB
|
A:SER348
|
3.7
|
73.1
|
1.0
|
C
|
A:PRO398
|
3.8
|
68.3
|
1.0
|
C
|
A:ARG352
|
3.9
|
63.1
|
1.0
|
N
|
A:VAL401
|
4.0
|
78.0
|
1.0
|
CG2
|
A:ILE397
|
4.0
|
65.7
|
1.0
|
N
|
A:ARG352
|
4.2
|
68.5
|
1.0
|
N
|
A:GLU399
|
4.2
|
66.8
|
1.0
|
CA
|
A:VAL401
|
4.3
|
78.5
|
1.0
|
N
|
A:VAL349
|
4.3
|
89.4
|
1.0
|
N
|
A:ASP400
|
4.4
|
72.8
|
1.0
|
N
|
A:GLY351
|
4.4
|
73.9
|
1.0
|
CA
|
A:ALA350
|
4.4
|
78.5
|
1.0
|
N
|
A:ALA350
|
4.5
|
81.6
|
1.0
|
C
|
A:SER348
|
4.5
|
80.2
|
1.0
|
O
|
A:ILE397
|
4.6
|
60.1
|
1.0
|
N
|
A:THR402
|
4.6
|
82.4
|
1.0
|
C
|
A:ASP400
|
4.6
|
81.8
|
1.0
|
CA
|
A:ARG352
|
4.7
|
64.6
|
1.0
|
CA
|
A:VAL349
|
4.7
|
86.4
|
1.0
|
CA
|
A:THR402
|
4.7
|
82.2
|
1.0
|
CA
|
A:SER348
|
4.7
|
76.7
|
1.0
|
C
|
A:ALA350
|
4.8
|
77.1
|
1.0
|
CB
|
A:VAL401
|
4.8
|
76.0
|
1.0
|
N
|
A:LYS353
|
4.8
|
60.4
|
1.0
|
NE2
|
A:HIS285
|
4.9
|
62.8
|
1.0
|
CB
|
A:ILE397
|
4.9
|
63.5
|
1.0
|
C
|
A:ILE397
|
4.9
|
63.5
|
1.0
|
CA
|
A:ASP400
|
4.9
|
78.6
|
1.0
|
CA
|
A:LYS353
|
4.9
|
60.4
|
1.0
|
N
|
A:GLY354
|
5.0
|
58.4
|
1.0
|
|
Sodium binding site 2 out
of 2 in 8bve
Go back to
Sodium Binding Sites List in 8bve
Sodium binding site 2 out
of 2 in the MOEA2 From Corynebacterium Glutamicum
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of MOEA2 From Corynebacterium Glutamicum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na501
b:33.2
occ:1.00
|
O
|
B:VAL349
|
2.5
|
38.4
|
1.0
|
O
|
B:VAL401
|
2.6
|
40.8
|
1.0
|
O
|
B:ARG352
|
2.6
|
38.4
|
1.0
|
OG
|
B:SER348
|
2.6
|
37.6
|
1.0
|
O
|
B:GLU399
|
2.7
|
41.1
|
1.0
|
O
|
B:PRO398
|
2.8
|
37.5
|
1.0
|
C
|
B:GLU399
|
3.3
|
43.1
|
1.0
|
CB
|
B:SER348
|
3.6
|
38.4
|
1.0
|
C
|
B:VAL349
|
3.6
|
39.2
|
1.0
|
CA
|
B:GLU399
|
3.7
|
42.9
|
1.0
|
C
|
B:VAL401
|
3.7
|
42.2
|
1.0
|
C
|
B:ARG352
|
3.7
|
40.5
|
1.0
|
C
|
B:PRO398
|
3.8
|
41.9
|
1.0
|
N
|
B:VAL401
|
4.0
|
39.5
|
1.0
|
N
|
B:VAL349
|
4.0
|
37.1
|
1.0
|
N
|
B:ARG352
|
4.1
|
40.4
|
1.0
|
C
|
B:SER348
|
4.2
|
39.9
|
1.0
|
N
|
B:GLU399
|
4.2
|
38.7
|
1.0
|
CG2
|
B:ILE397
|
4.2
|
39.9
|
1.0
|
N
|
B:ASP400
|
4.3
|
41.5
|
1.0
|
CA
|
B:VAL401
|
4.4
|
43.1
|
1.0
|
O
|
B:ILE397
|
4.4
|
40.0
|
1.0
|
CA
|
B:VAL349
|
4.5
|
37.6
|
1.0
|
N
|
B:GLY351
|
4.5
|
41.5
|
1.0
|
N
|
B:ALA350
|
4.5
|
37.9
|
1.0
|
C
|
B:ASP400
|
4.5
|
42.4
|
1.0
|
CA
|
B:SER348
|
4.5
|
38.5
|
1.0
|
CA
|
B:ARG352
|
4.5
|
42.9
|
1.0
|
NE2
|
B:HIS285
|
4.6
|
38.9
|
1.0
|
CA
|
B:ALA350
|
4.6
|
40.0
|
1.0
|
O
|
B:SER348
|
4.6
|
40.1
|
1.0
|
N
|
B:LYS353
|
4.7
|
40.8
|
1.0
|
N
|
B:GLY354
|
4.7
|
38.5
|
1.0
|
N
|
B:THR402
|
4.8
|
41.0
|
1.0
|
CA
|
B:LYS353
|
4.8
|
41.0
|
1.0
|
CA
|
B:ASP400
|
4.8
|
45.4
|
1.0
|
C
|
B:ILE397
|
4.8
|
38.6
|
1.0
|
CB
|
B:ILE397
|
4.9
|
38.9
|
1.0
|
CB
|
B:VAL401
|
4.9
|
40.5
|
1.0
|
C
|
B:ALA350
|
4.9
|
40.9
|
1.0
|
CD2
|
B:HIS285
|
4.9
|
38.5
|
1.0
|
CA
|
B:THR402
|
5.0
|
42.6
|
1.0
|
|
Reference:
M.Martinez,
J.Petit,
A.Leyva,
A.Sogues,
D.Megrian,
A.Rodriguez,
Q.Gaday,
M.Ben Assaya,
M.Portela,
A.Haouz,
A.Ducret,
C.Grangeasse,
P.M.Alzari,
R.Dur N,
A.Wehenkel.
Eukaryotic-Like Gephyrin and Cognate Membrane Receptor Coordinate Corynebacterial Cell Division and Polar Elongation. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36778425
DOI: 10.1101/2023.02.01.526586
Page generated: Fri Apr 7 17:59:32 2023
|