Magnesium in PDB 6vc7: Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Protein crystallography data
The structure of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vc7
was solved by
U.Gabale,
S.Ressl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.56 /
2.05
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.612,
124.899,
183.296,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.5 /
22.7
|
Other elements in 6vc7:
The structure of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
(pdb code 6vc7). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vc7:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6vc7
Go back to
Magnesium Binding Sites List in 6vc7
Magnesium binding site 1 out
of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1812
b:31.2
occ:1.00
|
O
|
A:HOH2078
|
2.7
|
54.2
|
1.0
|
O
|
A:HOH2066
|
3.0
|
37.4
|
1.0
|
O
|
A:HOH2039
|
3.1
|
30.7
|
1.0
|
N
|
A:THR302
|
3.2
|
25.5
|
1.0
|
OG1
|
A:THR302
|
3.7
|
28.8
|
1.0
|
CA
|
A:THR301
|
3.7
|
28.5
|
1.0
|
CB
|
A:THR301
|
3.7
|
32.9
|
1.0
|
CD
|
A:ARG451
|
3.7
|
25.8
|
1.0
|
NH1
|
A:ARG451
|
3.9
|
32.3
|
1.0
|
CB
|
A:THR302
|
4.0
|
27.8
|
1.0
|
C
|
A:THR301
|
4.0
|
26.9
|
1.0
|
NE
|
A:ARG451
|
4.1
|
27.4
|
1.0
|
CZ
|
A:ARG451
|
4.1
|
30.4
|
1.0
|
CA
|
A:THR302
|
4.2
|
26.0
|
1.0
|
CG2
|
A:THR301
|
4.4
|
27.6
|
1.0
|
OG1
|
A:THR301
|
4.9
|
37.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6vc7
Go back to
Magnesium Binding Sites List in 6vc7
Magnesium binding site 2 out
of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:33.7
occ:1.00
|
O
|
B:HOH885
|
2.6
|
53.4
|
1.0
|
O
|
B:HOH855
|
3.1
|
42.3
|
1.0
|
N
|
B:THR302
|
3.2
|
32.0
|
1.0
|
O
|
B:HOH858
|
3.3
|
54.5
|
1.0
|
OG1
|
B:THR302
|
3.6
|
33.5
|
1.0
|
CD
|
B:ARG451
|
3.7
|
35.3
|
1.0
|
NH1
|
B:ARG451
|
3.7
|
32.6
|
1.0
|
CB
|
B:THR301
|
3.7
|
35.6
|
1.0
|
CA
|
B:THR301
|
3.8
|
36.0
|
1.0
|
CB
|
B:THR302
|
3.9
|
32.9
|
1.0
|
C
|
B:THR301
|
4.0
|
33.7
|
1.0
|
NE
|
B:ARG451
|
4.0
|
38.9
|
1.0
|
CZ
|
B:ARG451
|
4.0
|
38.4
|
1.0
|
CA
|
B:THR302
|
4.1
|
33.9
|
1.0
|
CG2
|
B:THR301
|
4.4
|
35.9
|
1.0
|
OG1
|
B:THR301
|
4.9
|
35.8
|
1.0
|
NH2
|
B:ARG451
|
4.9
|
34.2
|
1.0
|
CG
|
B:ARG451
|
5.0
|
29.2
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6vc7
Go back to
Magnesium Binding Sites List in 6vc7
Magnesium binding site 3 out
of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1709
b:33.5
occ:1.00
|
O
|
C:HOH1997
|
2.9
|
53.4
|
1.0
|
O
|
C:HOH1980
|
3.0
|
44.9
|
1.0
|
N
|
C:THR302
|
3.3
|
25.6
|
1.0
|
O
|
C:HOH1937
|
3.4
|
27.1
|
1.0
|
NH1
|
C:ARG451
|
3.6
|
32.6
|
1.0
|
CD
|
C:ARG451
|
3.7
|
26.6
|
1.0
|
CA
|
C:THR301
|
3.7
|
28.4
|
1.0
|
CB
|
C:THR301
|
3.8
|
30.7
|
1.0
|
OG1
|
C:THR302
|
3.8
|
28.9
|
1.0
|
CZ
|
C:ARG451
|
4.0
|
31.3
|
1.0
|
NE
|
C:ARG451
|
4.0
|
31.2
|
1.0
|
CB
|
C:THR302
|
4.0
|
26.2
|
1.0
|
C
|
C:THR301
|
4.0
|
30.0
|
1.0
|
CA
|
C:THR302
|
4.2
|
24.7
|
1.0
|
CG2
|
C:THR301
|
4.2
|
25.6
|
1.0
|
NH2
|
C:ARG451
|
4.9
|
29.1
|
1.0
|
CG
|
C:ARG451
|
5.0
|
25.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6vc7
Go back to
Magnesium Binding Sites List in 6vc7
Magnesium binding site 4 out
of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg605
b:43.5
occ:1.00
|
O
|
D:HOH834
|
2.6
|
48.3
|
1.0
|
N
|
D:THR302
|
3.1
|
41.2
|
1.0
|
O
|
D:HOH789
|
3.4
|
37.6
|
1.0
|
CA
|
D:THR301
|
3.7
|
40.6
|
1.0
|
CD
|
D:ARG451
|
3.7
|
32.4
|
1.0
|
CB
|
D:THR301
|
3.7
|
42.5
|
1.0
|
OG1
|
D:THR302
|
3.7
|
42.4
|
1.0
|
CB
|
D:THR302
|
3.8
|
37.9
|
1.0
|
NH1
|
D:ARG451
|
3.9
|
40.0
|
1.0
|
C
|
D:THR301
|
3.9
|
41.4
|
1.0
|
NE
|
D:ARG451
|
4.0
|
34.7
|
1.0
|
CA
|
D:THR302
|
4.1
|
38.9
|
1.0
|
CZ
|
D:ARG451
|
4.1
|
38.9
|
1.0
|
CG2
|
D:THR301
|
4.4
|
44.0
|
1.0
|
O
|
D:HOH788
|
4.5
|
51.4
|
1.0
|
OG1
|
D:THR301
|
4.8
|
42.8
|
1.0
|
CG
|
D:ARG451
|
4.9
|
30.7
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6vc7
Go back to
Magnesium Binding Sites List in 6vc7
Magnesium binding site 5 out
of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg608
b:43.8
occ:1.00
|
O
|
E:HOH826
|
2.2
|
53.8
|
1.0
|
N
|
E:THR302
|
2.9
|
37.1
|
1.0
|
O
|
E:HOH813
|
3.3
|
59.0
|
1.0
|
O
|
E:HOH764
|
3.4
|
41.0
|
1.0
|
OG1
|
E:THR302
|
3.4
|
34.6
|
1.0
|
CD
|
E:ARG451
|
3.5
|
34.1
|
1.0
|
CB
|
E:THR302
|
3.6
|
34.6
|
1.0
|
CA
|
E:THR301
|
3.6
|
36.6
|
1.0
|
NH1
|
E:ARG451
|
3.6
|
39.8
|
1.0
|
CB
|
E:THR301
|
3.8
|
37.0
|
1.0
|
C
|
E:THR301
|
3.8
|
35.1
|
1.0
|
CA
|
E:THR302
|
3.9
|
36.7
|
1.0
|
NE
|
E:ARG451
|
3.9
|
37.5
|
1.0
|
CZ
|
E:ARG451
|
4.0
|
41.3
|
1.0
|
CG2
|
E:THR301
|
4.5
|
35.0
|
1.0
|
CG
|
E:ARG451
|
4.7
|
37.2
|
1.0
|
N
|
E:ASP303
|
4.8
|
36.0
|
1.0
|
OG1
|
E:THR301
|
4.9
|
39.9
|
1.0
|
C
|
E:THR302
|
4.9
|
35.9
|
1.0
|
O
|
E:THR301
|
5.0
|
34.5
|
1.0
|
N
|
E:THR301
|
5.0
|
36.9
|
1.0
|
NH2
|
E:ARG451
|
5.0
|
40.7
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6vc7
Go back to
Magnesium Binding Sites List in 6vc7
Magnesium binding site 6 out
of 6 in the Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of the F349A Mutant of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg606
b:45.2
occ:1.00
|
N
|
F:THR302
|
3.3
|
40.6
|
1.0
|
O
|
F:HOH790
|
3.4
|
44.6
|
1.0
|
CD
|
F:ARG451
|
3.4
|
37.2
|
1.0
|
OG1
|
F:THR302
|
3.7
|
41.9
|
1.0
|
NE
|
F:ARG451
|
3.7
|
40.0
|
1.0
|
NH1
|
F:ARG451
|
3.8
|
41.3
|
1.0
|
CA
|
F:THR301
|
3.8
|
40.0
|
1.0
|
CB
|
F:THR301
|
3.9
|
43.5
|
1.0
|
CZ
|
F:ARG451
|
3.9
|
42.4
|
1.0
|
CB
|
F:THR302
|
4.0
|
40.6
|
1.0
|
C
|
F:THR301
|
4.0
|
39.8
|
1.0
|
CA
|
F:THR302
|
4.3
|
38.9
|
1.0
|
CG2
|
F:THR301
|
4.3
|
39.5
|
1.0
|
NH2
|
F:ARG451
|
4.8
|
43.8
|
1.0
|
CG
|
F:ARG451
|
4.8
|
33.1
|
1.0
|
O
|
F:ASN300
|
5.0
|
42.3
|
1.0
|
|
Reference:
U.Gabale,
P.A.Pena Palomino,
H.Kim,
W.Chen,
S.Ressl.
The Essential Inner Membrane Protein Yejm Is A Metalloenzyme. Sci Rep V. 10 17794 2020.
ISSN: ESSN 2045-2322
PubMed: 33082366
DOI: 10.1038/S41598-020-73660-6
Page generated: Tue Oct 1 21:27:17 2024
|