Magnesium in PDB 4hcd: Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium
Protein crystallography data
The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, PDB code: 4hcd
was solved by
A.A.Fedorov,
E.V.Fedorov,
A.Sakai,
C.Millikin,
J.A.Gerlt,
S.C.Almo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.91 /
1.70
|
Space group
|
I 4 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
118.733,
118.733,
133.199,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.3 /
18.5
|
Other elements in 4hcd:
The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium
(pdb code 4hcd). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, PDB code: 4hcd:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 4hcd
Go back to
Magnesium Binding Sites List in 4hcd
Magnesium binding site 1 out
of 3 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium
 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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:5.4
occ:1.00
|
OE2
|
A:GLU232
|
2.0
|
8.7
|
1.0
|
OE1
|
A:GLU258
|
2.0
|
6.0
|
1.0
|
OD1
|
A:ASP206
|
2.0
|
8.0
|
1.0
|
O
|
A:HOH966
|
2.0
|
6.4
|
1.0
|
O
|
A:HOH964
|
2.2
|
8.8
|
1.0
|
O
|
A:HOH963
|
2.2
|
8.7
|
1.0
|
CD
|
A:GLU258
|
3.0
|
9.4
|
1.0
|
CG
|
A:ASP206
|
3.1
|
7.5
|
1.0
|
CD
|
A:GLU232
|
3.1
|
7.2
|
1.0
|
OE2
|
A:GLU258
|
3.3
|
7.3
|
1.0
|
OD2
|
A:ASP206
|
3.6
|
7.0
|
1.0
|
CG
|
A:GLU232
|
3.8
|
4.2
|
1.0
|
NH1
|
A:ARG280
|
4.0
|
5.0
|
1.0
|
OE1
|
A:GLU232
|
4.1
|
7.1
|
1.0
|
NZ
|
A:LYS169
|
4.1
|
5.1
|
1.0
|
NE2
|
A:HIS171
|
4.1
|
7.0
|
1.0
|
NE
|
A:ARG280
|
4.2
|
4.5
|
1.0
|
CB
|
A:ASP206
|
4.3
|
6.3
|
1.0
|
CG
|
A:GLU258
|
4.3
|
7.0
|
1.0
|
O
|
A:HOH637
|
4.3
|
12.3
|
1.0
|
OE2
|
A:GLU233
|
4.4
|
6.9
|
1.0
|
CB
|
A:GLU258
|
4.5
|
6.3
|
1.0
|
CZ
|
A:ARG280
|
4.6
|
5.2
|
1.0
|
CD2
|
A:HIS309
|
4.6
|
7.7
|
1.0
|
O
|
A:HOH581
|
4.6
|
15.9
|
1.0
|
CD2
|
A:HIS171
|
4.7
|
10.9
|
1.0
|
CE1
|
A:HIS209
|
4.7
|
5.8
|
1.0
|
CE
|
A:LYS169
|
4.9
|
4.2
|
1.0
|
NE2
|
A:HIS309
|
4.9
|
9.3
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 4hcd
Go back to
Magnesium Binding Sites List in 4hcd
Magnesium binding site 2 out
of 3 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium
 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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:7.1
occ:1.00
|
O
|
A:LEU250
|
2.1
|
10.5
|
1.0
|
O
|
A:SER247
|
2.2
|
8.0
|
0.6
|
O
|
A:SER247
|
2.2
|
8.0
|
0.4
|
O
|
A:HOH972
|
2.2
|
12.7
|
1.0
|
O
|
A:HOH514
|
2.3
|
8.3
|
1.0
|
O
|
A:HOH786
|
2.3
|
13.2
|
1.0
|
O
|
A:HOH721
|
2.3
|
18.6
|
1.0
|
C
|
A:LEU250
|
3.3
|
7.6
|
1.0
|
C
|
A:SER247
|
3.3
|
7.6
|
0.6
|
C
|
A:SER247
|
3.3
|
7.6
|
0.4
|
CA
|
A:SER247
|
4.0
|
6.1
|
0.6
|
CA
|
A:SER247
|
4.0
|
6.2
|
0.4
|
O
|
A:HOH1012
|
4.0
|
30.2
|
1.0
|
O
|
A:HOH551
|
4.1
|
12.6
|
1.0
|
N
|
A:LEU250
|
4.1
|
6.8
|
1.0
|
CA
|
A:LEU250
|
4.2
|
6.0
|
1.0
|
N
|
A:ASP251
|
4.2
|
9.6
|
1.0
|
OD2
|
A:ASP277
|
4.2
|
5.7
|
1.0
|
CA
|
A:ASP251
|
4.3
|
11.6
|
1.0
|
N
|
A:ASP248
|
4.4
|
7.6
|
1.0
|
O
|
A:ASP251
|
4.4
|
11.6
|
1.0
|
OD1
|
A:ASP277
|
4.4
|
7.7
|
1.0
|
C
|
A:ASP251
|
4.4
|
9.2
|
1.0
|
CB
|
A:SER247
|
4.5
|
9.2
|
0.6
|
O
|
A:ILE252
|
4.5
|
6.5
|
1.0
|
CB
|
A:LEU250
|
4.5
|
5.5
|
1.0
|
CB
|
A:SER247
|
4.6
|
9.3
|
0.4
|
CA
|
A:ASP248
|
4.7
|
9.4
|
1.0
|
C
|
A:ASP248
|
4.7
|
13.7
|
1.0
|
CG
|
A:ASP277
|
4.7
|
6.7
|
1.0
|
O
|
A:ASP248
|
4.9
|
17.0
|
1.0
|
N
|
A:ASN249
|
5.0
|
6.5
|
1.0
|
O
|
A:LEU246
|
5.0
|
5.2
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 4hcd
Go back to
Magnesium Binding Sites List in 4hcd
Magnesium binding site 3 out
of 3 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium
 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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:25.0
occ:1.00
|
O
|
A:LEU346
|
2.1
|
15.7
|
1.0
|
O
|
A:HOH994
|
2.2
|
31.5
|
1.0
|
O
|
A:HIS343
|
2.3
|
10.5
|
1.0
|
O
|
A:HOH752
|
2.5
|
25.3
|
1.0
|
O
|
A:HOH973
|
2.7
|
13.2
|
1.0
|
C
|
A:LEU346
|
3.3
|
9.7
|
1.0
|
C
|
A:HIS343
|
3.4
|
10.3
|
1.0
|
N
|
A:HIS343
|
3.8
|
12.1
|
1.0
|
O
|
A:HOH877
|
3.8
|
40.8
|
1.0
|
O
|
A:HOH661
|
4.1
|
15.0
|
1.0
|
N
|
A:LEU346
|
4.2
|
8.5
|
1.0
|
O
|
A:HOH953
|
4.2
|
27.7
|
1.0
|
CA
|
A:LEU346
|
4.2
|
8.2
|
1.0
|
N
|
A:ASP344
|
4.2
|
10.5
|
1.0
|
CA
|
A:HIS343
|
4.2
|
13.4
|
1.0
|
N
|
A:LYS347
|
4.2
|
12.1
|
1.0
|
O
|
A:ASP341
|
4.3
|
20.5
|
1.0
|
CA
|
A:ASP344
|
4.3
|
14.0
|
1.0
|
O
|
A:HOH582
|
4.3
|
12.9
|
1.0
|
C
|
A:LYS347
|
4.3
|
13.6
|
1.0
|
CA
|
A:LYS347
|
4.3
|
9.6
|
1.0
|
C
|
A:ASP344
|
4.4
|
13.7
|
1.0
|
O
|
A:LYS347
|
4.5
|
13.7
|
1.0
|
C
|
A:GLY342
|
4.5
|
13.1
|
1.0
|
CB
|
A:LEU346
|
4.6
|
11.2
|
1.0
|
O
|
A:ASP344
|
4.6
|
14.6
|
1.0
|
N
|
A:SER348
|
4.6
|
9.1
|
0.7
|
N
|
A:SER348
|
4.7
|
9.2
|
0.3
|
O
|
A:HOH812
|
4.8
|
19.4
|
1.0
|
CA
|
A:GLY342
|
4.9
|
13.6
|
1.0
|
N
|
A:TYR345
|
5.0
|
11.0
|
1.0
|
|
Reference:
A.A.Fedorov,
E.V.Fedorov,
A.Sakai,
C.Millikin,
J.A.Gerlt,
S.C.Almo.
Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium To Be Published.
Page generated: Fri Aug 16 16:14:47 2024
|