Magnesium in PDB 1t0t: Crystallographic Structure of A Putative Chlorite Dismutase
Protein crystallography data
The structure of Crystallographic Structure of A Putative Chlorite Dismutase, PDB code: 1t0t
was solved by
M.Gilski,
D.Borek,
Y.Chen,
F.Collart,
A.Joachimiak,
Z.Otwinowski,
Midwestcenter For Structural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
1.75
|
Space group
|
I 2 3 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
202.839,
202.839,
202.839,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.6 /
19.4
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystallographic Structure of A Putative Chlorite Dismutase
(pdb code 1t0t). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystallographic Structure of A Putative Chlorite Dismutase, PDB code: 1t0t:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1t0t
Go back to
Magnesium Binding Sites List in 1t0t
Magnesium binding site 1 out
of 5 in the Crystallographic Structure of A Putative Chlorite Dismutase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystallographic Structure of A Putative Chlorite Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg4004
b:21.6
occ:1.00
|
O
|
V:HOH4262
|
2.1
|
23.6
|
1.0
|
O
|
V:HOH4263
|
2.1
|
18.6
|
1.0
|
O
|
V:HOH4260
|
2.1
|
21.9
|
1.0
|
O
|
Z:HOH5841
|
2.1
|
20.4
|
1.0
|
O
|
Z:HOH5842
|
2.2
|
22.2
|
1.0
|
O
|
V:HOH4261
|
2.2
|
22.2
|
1.0
|
O
|
V:HOH4134
|
3.9
|
24.7
|
1.0
|
O
|
Z:HOH5653
|
4.0
|
20.5
|
1.0
|
O
|
Z:HOH5603
|
4.0
|
20.4
|
1.0
|
O
|
V:LEU98
|
4.2
|
14.7
|
1.0
|
O
|
Z:HOH5743
|
4.3
|
43.0
|
1.0
|
O
|
Z:HOH5685
|
4.3
|
22.9
|
1.0
|
CD
|
V:PRO100
|
4.3
|
18.5
|
1.0
|
O
|
V:HOH4041
|
4.3
|
17.6
|
1.0
|
O
|
V:HOH4020
|
4.5
|
20.2
|
1.0
|
CG
|
V:PRO100
|
4.5
|
25.1
|
1.0
|
O
|
V:HOH4131
|
4.6
|
28.6
|
1.0
|
NH1
|
V:ARG18
|
4.6
|
16.2
|
1.0
|
O
|
Z:ILE20
|
4.6
|
15.9
|
1.0
|
O
|
V:ALA95
|
4.6
|
18.2
|
1.0
|
OD1
|
V:ASN90
|
4.6
|
21.1
|
1.0
|
CD1
|
Z:TRP22
|
5.0
|
17.3
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1t0t
Go back to
Magnesium Binding Sites List in 1t0t
Magnesium binding site 2 out
of 5 in the Crystallographic Structure of A Putative Chlorite Dismutase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystallographic Structure of A Putative Chlorite Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Mg4003
b:21.0
occ:1.00
|
O
|
W:HOH4255
|
2.0
|
18.1
|
1.0
|
O
|
W:HOH4258
|
2.1
|
19.8
|
1.0
|
O
|
W:HOH4256
|
2.1
|
20.3
|
1.0
|
O
|
W:HOH4257
|
2.1
|
21.8
|
1.0
|
O
|
V:HOH4259
|
2.2
|
24.2
|
1.0
|
O
|
V:HOH4258
|
2.2
|
20.5
|
1.0
|
O
|
W:HOH4033
|
3.9
|
22.7
|
1.0
|
O
|
V:HOH4030
|
4.0
|
20.0
|
1.0
|
O
|
V:HOH4018
|
4.1
|
23.0
|
1.0
|
O
|
W:LEU98
|
4.3
|
18.5
|
1.0
|
O
|
V:HOH4088
|
4.3
|
21.7
|
1.0
|
O
|
W:HOH4024
|
4.3
|
21.0
|
1.0
|
O
|
V:HOH4163
|
4.3
|
38.8
|
1.0
|
O
|
W:HOH4020
|
4.4
|
22.1
|
1.0
|
CD
|
W:PRO100
|
4.4
|
19.8
|
1.0
|
O
|
V:HOH4233
|
4.5
|
31.1
|
1.0
|
O
|
W:ALA95
|
4.6
|
19.9
|
1.0
|
NH1
|
W:ARG18
|
4.6
|
18.2
|
1.0
|
O
|
V:ILE20
|
4.7
|
17.1
|
1.0
|
OD1
|
W:ASN90
|
4.7
|
23.8
|
1.0
|
CG
|
W:PRO100
|
4.8
|
23.8
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1t0t
Go back to
Magnesium Binding Sites List in 1t0t
Magnesium binding site 3 out
of 5 in the Crystallographic Structure of A Putative Chlorite Dismutase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystallographic Structure of A Putative Chlorite Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mg4005
b:18.9
occ:1.00
|
O
|
X:HOH5600
|
2.1
|
18.9
|
1.0
|
O
|
X:HOH5599
|
2.1
|
17.0
|
1.0
|
O
|
X:HOH5601
|
2.1
|
17.4
|
1.0
|
O
|
X:HOH5602
|
2.1
|
19.4
|
1.0
|
O
|
Y:HOH5598
|
2.2
|
17.3
|
1.0
|
O
|
Y:HOH5597
|
2.2
|
18.1
|
1.0
|
O
|
X:HOH592
|
4.0
|
19.1
|
1.0
|
O
|
Y:HOH777
|
4.0
|
17.4
|
1.0
|
O
|
Y:HOH773
|
4.0
|
19.0
|
1.0
|
O
|
Y:HOH893
|
4.2
|
36.2
|
1.0
|
O
|
X:HOH531
|
4.2
|
19.5
|
1.0
|
O
|
X:LEU98
|
4.2
|
15.6
|
1.0
|
O
|
Y:HOH838
|
4.3
|
18.1
|
1.0
|
CD
|
X:PRO100
|
4.3
|
15.8
|
1.0
|
O
|
X:HOH664
|
4.4
|
30.8
|
1.0
|
O
|
X:HOH502
|
4.4
|
20.8
|
1.0
|
O
|
Y:ILE20
|
4.6
|
16.9
|
1.0
|
CG
|
X:PRO100
|
4.6
|
18.6
|
1.0
|
NH1
|
X:ARG18
|
4.7
|
18.5
|
1.0
|
O
|
X:ALA95
|
4.7
|
17.2
|
1.0
|
OD1
|
X:ASN90
|
4.8
|
22.7
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1t0t
Go back to
Magnesium Binding Sites List in 1t0t
Magnesium binding site 4 out
of 5 in the Crystallographic Structure of A Putative Chlorite Dismutase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystallographic Structure of A Putative Chlorite Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg4002
b:26.9
occ:1.00
|
O
|
W:HOH4254
|
2.0
|
28.0
|
1.0
|
O
|
Y:HOH5582
|
2.1
|
24.7
|
1.0
|
O
|
W:HOH4253
|
2.1
|
27.5
|
1.0
|
O
|
W:HOH4252
|
2.2
|
29.2
|
1.0
|
O
|
Y:HOH5581
|
2.2
|
23.1
|
1.0
|
O
|
Y:HOH5583
|
2.3
|
27.9
|
1.0
|
O
|
W:HOH4136
|
3.8
|
48.5
|
1.0
|
O
|
W:HOH4023
|
3.9
|
24.4
|
1.0
|
O
|
Y:HOH839
|
3.9
|
29.9
|
1.0
|
O
|
W:HOH4019
|
4.0
|
23.0
|
1.0
|
O
|
W:HOH4093
|
4.3
|
26.4
|
1.0
|
O
|
Y:LEU98
|
4.3
|
17.5
|
1.0
|
CD
|
Y:PRO100
|
4.3
|
26.4
|
1.0
|
O
|
W:HOH4242
|
4.3
|
42.6
|
1.0
|
O
|
Y:HOH790
|
4.4
|
25.5
|
1.0
|
NH1
|
Y:ARG18
|
4.6
|
20.0
|
1.0
|
O
|
Y:HOH778
|
4.6
|
20.0
|
1.0
|
O
|
W:ILE20
|
4.7
|
16.9
|
1.0
|
CG
|
Y:PRO100
|
4.7
|
29.3
|
1.0
|
OD1
|
Y:ASN90
|
4.7
|
24.3
|
1.0
|
N
|
Y:PRO100
|
4.8
|
23.4
|
1.0
|
O
|
Y:ALA95
|
4.9
|
16.7
|
1.0
|
CD1
|
W:TRP22
|
4.9
|
14.4
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1t0t
Go back to
Magnesium Binding Sites List in 1t0t
Magnesium binding site 5 out
of 5 in the Crystallographic Structure of A Putative Chlorite Dismutase
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystallographic Structure of A Putative Chlorite Dismutase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mg4001
b:22.5
occ:1.00
|
O
|
Z:HOH5839
|
2.1
|
19.2
|
1.0
|
O
|
Z:HOH5837
|
2.1
|
31.3
|
1.0
|
O
|
X:HOH5575
|
2.1
|
30.7
|
1.0
|
O
|
Z:HOH5838
|
2.1
|
26.4
|
1.0
|
O
|
Z:HOH5840
|
2.1
|
31.0
|
1.0
|
O
|
X:HOH5577
|
2.1
|
25.9
|
1.0
|
O
|
Z:HOH5611
|
3.8
|
32.2
|
1.0
|
O
|
X:HOH507
|
4.0
|
22.2
|
1.0
|
O
|
X:HOH508
|
4.0
|
23.6
|
1.0
|
O
|
X:HOH616
|
4.3
|
44.0
|
1.0
|
O
|
X:HOH581
|
4.3
|
27.0
|
1.0
|
O
|
Z:HOH5609
|
4.4
|
21.2
|
1.0
|
O
|
Z:HOH5711
|
4.4
|
33.3
|
1.0
|
O
|
Z:LEU98
|
4.4
|
18.2
|
1.0
|
CD
|
Z:PRO100
|
4.4
|
23.4
|
1.0
|
O
|
Z:HOH5600
|
4.5
|
19.5
|
1.0
|
NH1
|
Z:ARG18
|
4.7
|
20.9
|
1.0
|
OD1
|
Z:ASN90
|
4.7
|
22.0
|
1.0
|
O
|
X:ILE20
|
4.7
|
18.6
|
1.0
|
O
|
Z:ALA95
|
4.8
|
17.4
|
1.0
|
CG
|
Z:PRO100
|
4.8
|
25.5
|
1.0
|
CD1
|
X:TRP22
|
4.9
|
15.5
|
1.0
|
|
Reference:
M.Gilski,
D.Borek,
Y.Chen,
F.Collart,
A.Joachimiak,
Z.Otwinowski.
Crystal Structure of APC35880 Protein From Bacillus Stearothermophilus To Be Published.
Page generated: Tue Aug 13 14:24:53 2024
|