Magnesium in PDB 1rlm: Crystal Structure of Ybiv From Escherichia Coli K12
Protein crystallography data
The structure of Crystal Structure of Ybiv From Escherichia Coli K12, PDB code: 1rlm
was solved by
A.Roberts,
S.Y.Lee,
E.Mccullagh,
R.E.Silversmith,
D.E.Wemmer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.96 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
71.823,
91.605,
186.563,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.9 /
24.8
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Ybiv From Escherichia Coli K12
(pdb code 1rlm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of Ybiv From Escherichia Coli K12, PDB code: 1rlm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1rlm
Go back to
Magnesium Binding Sites List in 1rlm
Magnesium binding site 1 out
of 4 in the Crystal Structure of Ybiv From Escherichia Coli K12
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Ybiv From Escherichia Coli K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg800
b:18.6
occ:1.00
|
OD1
|
A:ASP215
|
2.2
|
25.5
|
1.0
|
OD2
|
A:ASP9
|
2.2
|
26.8
|
1.0
|
O
|
A:ASP11
|
2.2
|
16.9
|
1.0
|
O
|
A:HOH946
|
2.4
|
40.0
|
1.0
|
O
|
A:HOH949
|
2.4
|
39.6
|
1.0
|
O
|
A:HOH926
|
3.1
|
38.5
|
1.0
|
OG
|
A:SER216
|
3.1
|
35.9
|
1.0
|
CG
|
A:ASP215
|
3.2
|
22.9
|
1.0
|
CG
|
A:ASP9
|
3.3
|
23.6
|
1.0
|
C
|
A:ASP11
|
3.4
|
18.0
|
1.0
|
OD2
|
A:ASP215
|
3.6
|
22.5
|
1.0
|
OD1
|
A:ASP9
|
3.6
|
22.2
|
1.0
|
CB
|
A:ASP11
|
4.1
|
19.4
|
1.0
|
CA
|
A:ASP11
|
4.1
|
17.7
|
1.0
|
OD2
|
A:ASP219
|
4.2
|
19.7
|
1.0
|
O
|
A:SER178
|
4.2
|
41.0
|
1.0
|
CB
|
A:SER216
|
4.3
|
28.1
|
1.0
|
N
|
A:ASP11
|
4.3
|
16.9
|
1.0
|
OG1
|
A:THR13
|
4.4
|
17.6
|
1.0
|
N
|
A:GLY12
|
4.4
|
17.8
|
1.0
|
N
|
A:SER216
|
4.4
|
22.4
|
1.0
|
CB
|
A:ASP215
|
4.5
|
21.4
|
1.0
|
CA
|
A:GLY12
|
4.6
|
17.4
|
1.0
|
CB
|
A:ASP9
|
4.6
|
19.0
|
1.0
|
C
|
A:GLY12
|
4.8
|
16.6
|
1.0
|
OD1
|
A:ASN218
|
4.8
|
23.6
|
1.0
|
N
|
A:ASP215
|
4.8
|
19.6
|
1.0
|
C
|
A:ASP215
|
5.0
|
22.2
|
1.0
|
C
|
A:SER178
|
5.0
|
39.5
|
1.0
|
CA
|
A:SER216
|
5.0
|
25.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1rlm
Go back to
Magnesium Binding Sites List in 1rlm
Magnesium binding site 2 out
of 4 in the Crystal Structure of Ybiv From Escherichia Coli K12
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Ybiv From Escherichia Coli K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg801
b:20.1
occ:1.00
|
O
|
B:ASP11
|
2.2
|
16.4
|
1.0
|
OD2
|
B:ASP9
|
2.3
|
19.1
|
1.0
|
OD1
|
B:ASP215
|
2.3
|
18.2
|
1.0
|
O
|
B:HOH858
|
2.4
|
21.0
|
1.0
|
O
|
B:HOH828
|
2.6
|
24.1
|
1.0
|
OG
|
B:SER216
|
2.7
|
24.6
|
1.0
|
CG
|
B:ASP215
|
3.3
|
21.1
|
1.0
|
CG
|
B:ASP9
|
3.3
|
18.2
|
1.0
|
C
|
B:ASP11
|
3.4
|
17.8
|
1.0
|
OD2
|
B:ASP215
|
3.5
|
17.1
|
1.0
|
CB
|
B:SER216
|
3.6
|
20.5
|
1.0
|
OD1
|
B:ASP9
|
3.8
|
17.5
|
1.0
|
OD2
|
B:ASP219
|
4.0
|
18.3
|
1.0
|
N
|
B:SER216
|
4.1
|
20.8
|
1.0
|
CB
|
B:ASP11
|
4.2
|
21.3
|
1.0
|
CA
|
B:ASP11
|
4.2
|
17.6
|
1.0
|
OG1
|
B:THR13
|
4.3
|
12.5
|
1.0
|
N
|
B:GLY12
|
4.4
|
16.4
|
1.0
|
CA
|
B:GLY12
|
4.5
|
15.0
|
1.0
|
CB
|
B:ASP9
|
4.5
|
16.1
|
1.0
|
N
|
B:ASP11
|
4.5
|
17.0
|
1.0
|
CA
|
B:SER216
|
4.5
|
21.6
|
1.0
|
O
|
B:HOH857
|
4.6
|
22.3
|
1.0
|
C
|
B:GLY12
|
4.6
|
14.7
|
1.0
|
O
|
B:HOH861
|
4.7
|
30.6
|
1.0
|
CB
|
B:ASP215
|
4.7
|
18.4
|
1.0
|
O
|
B:HOH934
|
4.7
|
30.5
|
1.0
|
O
|
B:HOH813
|
4.7
|
13.1
|
1.0
|
O
|
B:HOH950
|
4.8
|
32.3
|
1.0
|
OD1
|
B:ASN218
|
4.8
|
27.2
|
1.0
|
O
|
B:GLY12
|
4.9
|
15.8
|
1.0
|
N
|
B:ASP215
|
4.9
|
18.4
|
1.0
|
CG
|
B:ASP219
|
4.9
|
19.9
|
1.0
|
C
|
B:ASP215
|
5.0
|
19.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1rlm
Go back to
Magnesium Binding Sites List in 1rlm
Magnesium binding site 3 out
of 4 in the Crystal Structure of Ybiv From Escherichia Coli K12
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Ybiv From Escherichia Coli K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg803
b:24.9
occ:1.00
|
O
|
C:HOH912
|
2.1
|
39.5
|
1.0
|
O
|
C:ASP11
|
2.2
|
27.7
|
1.0
|
OD2
|
C:ASP9
|
2.2
|
24.3
|
1.0
|
OD1
|
C:ASP215
|
2.5
|
37.1
|
1.0
|
O
|
C:HOH832
|
2.7
|
36.6
|
1.0
|
OG
|
C:SER216
|
2.7
|
38.8
|
1.0
|
CG
|
C:ASP9
|
3.3
|
22.9
|
1.0
|
C
|
C:ASP11
|
3.4
|
28.2
|
1.0
|
CG
|
C:ASP215
|
3.4
|
34.7
|
1.0
|
OD2
|
C:ASP215
|
3.6
|
34.0
|
1.0
|
CB
|
C:SER216
|
3.7
|
39.8
|
1.0
|
OD1
|
C:ASP9
|
3.8
|
23.3
|
1.0
|
OD2
|
C:ASP219
|
3.9
|
29.6
|
1.0
|
C1
|
C:GOL809
|
4.0
|
29.4
|
1.0
|
N
|
C:SER216
|
4.2
|
37.1
|
1.0
|
CB
|
C:ASP11
|
4.2
|
30.1
|
1.0
|
CA
|
C:ASP11
|
4.2
|
27.4
|
1.0
|
N
|
C:GLY12
|
4.3
|
27.9
|
1.0
|
O3
|
C:GOL809
|
4.4
|
31.2
|
1.0
|
CA
|
C:GLY12
|
4.4
|
27.7
|
1.0
|
N
|
C:ASP11
|
4.4
|
25.4
|
1.0
|
C3
|
C:GOL809
|
4.5
|
30.5
|
1.0
|
OG1
|
C:THR13
|
4.5
|
30.2
|
1.0
|
CB
|
C:ASP9
|
4.5
|
22.8
|
1.0
|
CA
|
C:SER216
|
4.6
|
40.6
|
1.0
|
C2
|
C:GOL809
|
4.6
|
32.1
|
1.0
|
OD1
|
C:ASN218
|
4.7
|
39.3
|
1.0
|
N
|
C:THR13
|
4.7
|
25.7
|
1.0
|
C
|
C:GLY12
|
4.8
|
26.4
|
1.0
|
CB
|
C:ASP215
|
4.8
|
34.1
|
1.0
|
O1
|
C:GOL809
|
4.8
|
30.9
|
1.0
|
CG
|
C:ASP219
|
4.9
|
28.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1rlm
Go back to
Magnesium Binding Sites List in 1rlm
Magnesium binding site 4 out
of 4 in the Crystal Structure of Ybiv From Escherichia Coli K12
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Ybiv From Escherichia Coli K12 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg802
b:18.8
occ:1.00
|
O
|
D:HOH976
|
2.3
|
26.0
|
1.0
|
O
|
D:HOH972
|
2.3
|
26.1
|
1.0
|
OD2
|
D:ASP9
|
2.3
|
21.5
|
1.0
|
OG
|
D:SER216
|
2.4
|
22.0
|
1.0
|
O
|
D:ASP11
|
2.4
|
21.0
|
1.0
|
OD1
|
D:ASP215
|
2.5
|
24.8
|
1.0
|
CB
|
D:SER216
|
3.4
|
21.9
|
1.0
|
CG
|
D:ASP215
|
3.4
|
21.8
|
1.0
|
CG
|
D:ASP9
|
3.4
|
17.7
|
1.0
|
C
|
D:ASP11
|
3.4
|
20.4
|
1.0
|
OD2
|
D:ASP215
|
3.6
|
21.8
|
1.0
|
OD2
|
D:ASP219
|
3.9
|
17.8
|
1.0
|
OD1
|
D:ASP9
|
4.0
|
16.9
|
1.0
|
N
|
D:SER216
|
4.1
|
20.5
|
1.0
|
CB
|
D:ASP11
|
4.2
|
23.9
|
1.0
|
CA
|
D:ASP11
|
4.3
|
21.6
|
1.0
|
N
|
D:GLY12
|
4.3
|
20.7
|
1.0
|
O
|
D:HOH973
|
4.4
|
21.0
|
1.0
|
CA
|
D:GLY12
|
4.4
|
18.7
|
1.0
|
CA
|
D:SER216
|
4.4
|
22.4
|
1.0
|
O
|
D:HOH859
|
4.5
|
28.1
|
1.0
|
O
|
D:HOH862
|
4.5
|
32.1
|
1.0
|
CB
|
D:ASP9
|
4.6
|
17.7
|
1.0
|
N
|
D:ASP11
|
4.6
|
19.1
|
1.0
|
O
|
D:HOH820
|
4.7
|
21.7
|
1.0
|
OD1
|
D:ASN218
|
4.7
|
30.7
|
1.0
|
OG1
|
D:THR13
|
4.7
|
27.3
|
1.0
|
C
|
D:GLY12
|
4.7
|
19.4
|
1.0
|
CG
|
D:ASP219
|
4.8
|
20.5
|
1.0
|
CB
|
D:ASP215
|
4.8
|
20.7
|
1.0
|
N
|
D:THR13
|
4.9
|
19.4
|
1.0
|
O
|
D:HOH868
|
4.9
|
38.2
|
1.0
|
O
|
D:HOH835
|
5.0
|
30.4
|
1.0
|
C
|
D:ASP215
|
5.0
|
19.8
|
1.0
|
N
|
D:ASP215
|
5.0
|
19.2
|
1.0
|
|
Reference:
A.Roberts,
S.Y.Lee,
E.Mccullagh,
R.E.Silversmith,
D.E.Wemmer.
Ybiv From Escherichia Coli K12 Is A Had Phosphatase. Proteins V. 58 790 2005.
ISSN: ISSN 0887-3585
PubMed: 15657928
DOI: 10.1002/PROT.20267
Page generated: Tue Aug 13 13:02:49 2024
|