Magnesium in PDB 3tcs: Crystal Structure of A Putative Racemase From Roseobacter Denitrificans
Protein crystallography data
The structure of Crystal Structure of A Putative Racemase From Roseobacter Denitrificans, PDB code: 3tcs
was solved by
S.Eswaramoorthy,
S.Chamala,
B.Evans,
R.Foti,
A.Gizzi,
B.Hillerich,
A.Kar,
J.Lafleur,
R.Seidel,
G.Villigas,
W.Zencheck,
S.C.Almo,
S.Swaminathan,
Newyork Structural Genomics Research Consortium (Nysgrc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.45 /
1.88
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
182.492,
64.745,
76.449,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.5 /
21.6
|
Other elements in 3tcs:
The structure of Crystal Structure of A Putative Racemase From Roseobacter Denitrificans also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans
(pdb code 3tcs). 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 A Putative Racemase From Roseobacter Denitrificans, PDB code: 3tcs:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 3tcs
Go back to
Magnesium Binding Sites List in 3tcs
Magnesium binding site 1 out
of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans
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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg368
b:18.7
occ:1.00
|
O
|
A:DAL370
|
1.9
|
24.5
|
1.0
|
OE2
|
A:GLU209
|
1.9
|
20.6
|
1.0
|
OE1
|
A:GLU235
|
2.1
|
20.6
|
1.0
|
OD2
|
A:ASP183
|
2.1
|
22.2
|
1.0
|
O
|
A:HOH402
|
2.2
|
18.2
|
1.0
|
N
|
A:DAL370
|
2.2
|
17.5
|
1.0
|
C
|
A:DAL370
|
2.6
|
20.9
|
1.0
|
CA
|
A:DAL370
|
2.8
|
20.7
|
1.0
|
CD
|
A:GLU209
|
3.0
|
23.6
|
1.0
|
CD
|
A:GLU235
|
3.0
|
20.0
|
1.0
|
CG
|
A:ASP183
|
3.2
|
23.2
|
1.0
|
OE2
|
A:GLU235
|
3.4
|
21.0
|
1.0
|
OD1
|
A:ASP183
|
3.6
|
21.5
|
1.0
|
CG
|
A:GLU209
|
3.7
|
22.1
|
1.0
|
O
|
A:HOH438
|
3.8
|
20.6
|
1.0
|
OE1
|
A:GLU209
|
3.9
|
21.6
|
1.0
|
O
|
A:HOH422
|
3.9
|
22.3
|
1.0
|
NZ
|
A:LYS145
|
4.1
|
21.6
|
1.0
|
CB
|
A:DAL370
|
4.2
|
17.3
|
1.0
|
CD2
|
A:HIS285
|
4.2
|
14.4
|
1.0
|
OD1
|
A:ASN185
|
4.2
|
22.4
|
1.0
|
CG
|
A:GLU235
|
4.3
|
20.8
|
1.0
|
NH1
|
A:ARG147
|
4.4
|
21.7
|
1.0
|
CB
|
A:ASP183
|
4.5
|
22.4
|
1.0
|
OE1
|
A:GLU210
|
4.7
|
25.7
|
1.0
|
CB
|
A:GLU209
|
4.7
|
23.4
|
1.0
|
NE2
|
A:HIS285
|
4.9
|
14.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 3tcs
Go back to
Magnesium Binding Sites List in 3tcs
Magnesium binding site 2 out
of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans
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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg369
b:35.2
occ:1.00
|
O
|
A:HOH420
|
2.0
|
27.0
|
1.0
|
O
|
A:HOH419
|
2.1
|
28.4
|
1.0
|
O
|
A:HOH418
|
2.1
|
25.7
|
1.0
|
O
|
A:HOH421
|
2.2
|
31.4
|
1.0
|
O
|
A:THR224
|
2.3
|
34.8
|
1.0
|
O
|
A:LEU227
|
2.3
|
32.4
|
1.0
|
C
|
A:LEU227
|
3.5
|
32.0
|
1.0
|
C
|
A:THR224
|
3.5
|
34.5
|
1.0
|
CA
|
A:ASP228
|
4.2
|
32.6
|
1.0
|
OD1
|
A:ASP253
|
4.2
|
31.7
|
1.0
|
OD2
|
A:ASP253
|
4.2
|
30.1
|
1.0
|
N
|
A:ASP228
|
4.3
|
32.4
|
1.0
|
O
|
A:ASP228
|
4.3
|
32.1
|
1.0
|
CG2
|
A:THR224
|
4.3
|
32.8
|
1.0
|
O
|
A:ILE229
|
4.3
|
28.4
|
1.0
|
CA
|
A:ASP225
|
4.4
|
35.8
|
1.0
|
C
|
A:ASP228
|
4.4
|
31.8
|
1.0
|
N
|
A:ASP225
|
4.4
|
34.1
|
1.0
|
CA
|
A:THR224
|
4.4
|
33.1
|
1.0
|
N
|
A:LEU227
|
4.5
|
32.6
|
1.0
|
CA
|
A:LEU227
|
4.5
|
32.3
|
1.0
|
CG
|
A:ASP253
|
4.6
|
28.3
|
1.0
|
C
|
A:ASP225
|
4.7
|
34.9
|
1.0
|
O
|
A:ASP225
|
5.0
|
35.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 3tcs
Go back to
Magnesium Binding Sites List in 3tcs
Magnesium binding site 3 out
of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans
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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg368
b:11.0
occ:1.00
|
O
|
B:DAL370
|
2.0
|
20.3
|
1.0
|
OE2
|
B:GLU209
|
2.0
|
9.8
|
1.0
|
OE1
|
B:GLU235
|
2.0
|
11.1
|
1.0
|
OD2
|
B:ASP183
|
2.1
|
9.2
|
1.0
|
O
|
B:HOH379
|
2.1
|
10.8
|
1.0
|
N
|
B:DAL370
|
2.4
|
11.0
|
1.0
|
C
|
B:DAL370
|
2.6
|
13.4
|
1.0
|
CA
|
B:DAL370
|
2.9
|
13.7
|
1.0
|
CD
|
B:GLU209
|
3.0
|
11.7
|
1.0
|
CD
|
B:GLU235
|
3.0
|
13.3
|
1.0
|
CG
|
B:ASP183
|
3.1
|
9.1
|
1.0
|
OE2
|
B:GLU235
|
3.3
|
13.8
|
1.0
|
OD1
|
B:ASP183
|
3.5
|
8.6
|
1.0
|
CG
|
B:GLU209
|
3.7
|
11.0
|
1.0
|
O
|
B:HOH422
|
3.8
|
11.7
|
1.0
|
OE1
|
B:GLU209
|
3.9
|
11.8
|
1.0
|
O
|
B:HOH424
|
3.9
|
14.2
|
1.0
|
OD1
|
B:ASN185
|
4.1
|
14.7
|
1.0
|
NZ
|
B:LYS145
|
4.1
|
7.9
|
1.0
|
CD2
|
B:HIS285
|
4.2
|
10.0
|
1.0
|
CG
|
B:GLU235
|
4.3
|
11.6
|
1.0
|
NH1
|
B:ARG147
|
4.3
|
9.7
|
1.0
|
CB
|
B:DAL370
|
4.3
|
9.3
|
1.0
|
CB
|
B:ASP183
|
4.4
|
8.4
|
1.0
|
OE1
|
B:GLU210
|
4.5
|
12.2
|
1.0
|
CB
|
B:GLU209
|
4.7
|
7.5
|
1.0
|
CG
|
B:ASN185
|
4.9
|
13.8
|
1.0
|
CB
|
B:GLU235
|
4.9
|
8.3
|
1.0
|
CE
|
B:LYS145
|
5.0
|
9.5
|
1.0
|
NE2
|
B:HIS285
|
5.0
|
9.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 3tcs
Go back to
Magnesium Binding Sites List in 3tcs
Magnesium binding site 4 out
of 4 in the Crystal Structure of A Putative Racemase From Roseobacter Denitrificans
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 A Putative Racemase From Roseobacter Denitrificans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg369
b:14.6
occ:1.00
|
O
|
B:HOH412
|
2.0
|
11.6
|
1.0
|
O
|
B:THR224
|
2.0
|
11.4
|
1.0
|
O
|
B:LEU227
|
2.0
|
12.9
|
1.0
|
O
|
B:HOH398
|
2.1
|
12.9
|
1.0
|
O
|
B:HOH406
|
2.2
|
13.2
|
1.0
|
O
|
B:HOH416
|
2.3
|
15.4
|
1.0
|
C
|
B:THR224
|
3.2
|
12.3
|
1.0
|
C
|
B:LEU227
|
3.3
|
13.6
|
1.0
|
CA
|
B:THR224
|
4.1
|
11.3
|
1.0
|
CG2
|
B:THR224
|
4.1
|
11.7
|
1.0
|
N
|
B:LEU227
|
4.2
|
11.7
|
1.0
|
N
|
B:ASP228
|
4.2
|
14.1
|
1.0
|
N
|
B:ASP225
|
4.2
|
12.8
|
1.0
|
CA
|
B:LEU227
|
4.2
|
13.1
|
1.0
|
OD2
|
B:ASP253
|
4.3
|
11.8
|
1.0
|
CA
|
B:ASP228
|
4.3
|
14.6
|
1.0
|
CA
|
B:ASP225
|
4.3
|
14.3
|
1.0
|
C
|
B:ASP225
|
4.4
|
14.2
|
1.0
|
O
|
B:ASP228
|
4.4
|
13.2
|
1.0
|
O
|
B:ASP225
|
4.4
|
14.8
|
1.0
|
O
|
B:ILE229
|
4.4
|
10.5
|
1.0
|
C
|
B:ASP228
|
4.5
|
14.0
|
1.0
|
OD1
|
B:ASP253
|
4.5
|
11.8
|
1.0
|
CB
|
B:THR224
|
4.8
|
12.3
|
1.0
|
CB
|
B:LEU227
|
4.8
|
11.7
|
1.0
|
CG
|
B:ASP253
|
4.8
|
13.3
|
1.0
|
O
|
B:HOH510
|
4.8
|
23.2
|
1.0
|
O
|
B:VAL223
|
4.8
|
9.9
|
1.0
|
N
|
B:ALA226
|
4.9
|
14.1
|
1.0
|
|
Reference:
S.Eswaramoorthy,
S.C.Almo,
S.Swaminathan.
Crystal Structure of A Putative Racemase From Roseobacter Denitrificans To Be Published.
Page generated: Thu Aug 15 12:03:16 2024
|