Manganese in PDB 3fa3: Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Enzymatic activity of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
All present enzymatic activity of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form:
4.1.3.32;
Protein crystallography data
The structure of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form, PDB code: 3fa3
was solved by
B.C.Narayanan,
O.Herzberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.60
|
Space group
|
P 32
|
Cell size a, b, c (Å), α, β, γ (°)
|
160.570,
160.570,
161.410,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19 /
25.5
|
Other elements in 3fa3:
The structure of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form also contains other interesting chemical elements:
Manganese Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Manganese atom in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
(pdb code 3fa3). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the
Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form, PDB code: 3fa3:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 1 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:34.0
occ:1.00
|
O1
|
A:OAF501
|
2.0
|
33.4
|
1.0
|
O3
|
A:OAF501
|
2.0
|
33.8
|
1.0
|
O
|
A:HOH305
|
2.2
|
34.0
|
1.0
|
O
|
A:HOH304
|
2.2
|
31.8
|
1.0
|
OD2
|
A:ASP87
|
2.3
|
42.4
|
1.0
|
O
|
A:HOH306
|
2.4
|
31.8
|
1.0
|
C1
|
A:OAF501
|
2.8
|
34.9
|
1.0
|
C2
|
A:OAF501
|
2.9
|
34.9
|
1.0
|
CG
|
A:ASP87
|
3.4
|
37.9
|
1.0
|
NZ
|
A:LYS122
|
3.5
|
40.2
|
1.0
|
F1
|
A:OAF501
|
3.6
|
35.3
|
1.0
|
C3
|
A:OAF501
|
3.7
|
35.5
|
1.0
|
OD1
|
A:ASP87
|
3.9
|
38.0
|
1.0
|
NH2
|
A:ARG161
|
3.9
|
37.1
|
1.0
|
OD1
|
A:ASP59
|
3.9
|
38.9
|
1.0
|
O4
|
A:OAF501
|
4.0
|
35.3
|
1.0
|
N
|
A:ALA48
|
4.0
|
36.8
|
1.0
|
O5
|
A:OAF501
|
4.0
|
36.7
|
1.0
|
O2
|
A:OAF501
|
4.0
|
34.5
|
1.0
|
CA
|
A:GLY47
|
4.0
|
37.3
|
1.0
|
OD2
|
A:ASP89
|
4.0
|
39.1
|
1.0
|
N
|
A:GLY47
|
4.1
|
37.7
|
1.0
|
OD2
|
A:ASP59
|
4.2
|
40.1
|
1.0
|
C4
|
A:OAF501
|
4.3
|
36.4
|
1.0
|
OH
|
A:TYR44
|
4.4
|
36.1
|
1.0
|
C
|
A:GLY47
|
4.5
|
37.0
|
1.0
|
CE1
|
A:HIS114
|
4.5
|
37.6
|
1.0
|
CB
|
A:ASP87
|
4.5
|
37.3
|
1.0
|
CG
|
A:ASP59
|
4.5
|
38.9
|
1.0
|
CZ
|
A:ARG161
|
4.8
|
37.5
|
1.0
|
OE1
|
A:GLU116
|
4.8
|
39.3
|
1.0
|
CE
|
A:LYS122
|
4.9
|
38.8
|
1.0
|
F2
|
A:OAF501
|
4.9
|
37.0
|
1.0
|
NH1
|
A:ARG161
|
4.9
|
34.2
|
1.0
|
|
Manganese binding site 2 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 2 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn401
b:37.4
occ:1.00
|
O3
|
B:OAF501
|
2.1
|
30.8
|
1.0
|
O1
|
B:OAF501
|
2.1
|
32.6
|
1.0
|
O
|
B:HOH307
|
2.2
|
31.5
|
1.0
|
O
|
B:HOH306
|
2.2
|
29.9
|
1.0
|
OD2
|
B:ASP87
|
2.4
|
35.9
|
1.0
|
O
|
B:HOH308
|
2.4
|
26.0
|
1.0
|
C1
|
B:OAF501
|
2.9
|
34.0
|
1.0
|
C2
|
B:OAF501
|
2.9
|
32.4
|
1.0
|
NZ
|
B:LYS122
|
3.3
|
39.5
|
1.0
|
CG
|
B:ASP87
|
3.4
|
36.3
|
1.0
|
F1
|
B:OAF501
|
3.6
|
36.2
|
1.0
|
OD1
|
B:ASP87
|
3.7
|
35.9
|
1.0
|
C3
|
B:OAF501
|
3.8
|
33.5
|
1.0
|
O5
|
B:OAF501
|
3.8
|
28.9
|
1.0
|
OD1
|
B:ASP59
|
3.9
|
39.9
|
1.0
|
NH2
|
B:ARG161
|
4.0
|
34.9
|
1.0
|
CA
|
B:GLY47
|
4.0
|
36.0
|
1.0
|
N
|
B:ALA48
|
4.0
|
36.1
|
1.0
|
OD1
|
B:ASP89
|
4.1
|
36.4
|
1.0
|
O2
|
B:OAF501
|
4.1
|
36.6
|
1.0
|
O4
|
B:OAF501
|
4.1
|
32.6
|
1.0
|
C4
|
B:OAF501
|
4.2
|
32.6
|
1.0
|
N
|
B:GLY47
|
4.2
|
35.5
|
1.0
|
C
|
B:GLY47
|
4.5
|
36.7
|
1.0
|
OD2
|
B:ASP59
|
4.5
|
37.9
|
1.0
|
OH
|
B:TYR44
|
4.5
|
32.0
|
1.0
|
CE1
|
B:HIS114
|
4.6
|
38.6
|
1.0
|
CE
|
B:LYS122
|
4.6
|
39.6
|
1.0
|
CG
|
B:ASP59
|
4.6
|
39.1
|
1.0
|
OE1
|
B:GLU116
|
4.7
|
37.2
|
1.0
|
CB
|
B:ASP87
|
4.7
|
36.8
|
1.0
|
CZ
|
B:ARG161
|
4.8
|
34.9
|
1.0
|
NH1
|
B:ARG161
|
5.0
|
32.6
|
1.0
|
F2
|
B:OAF501
|
5.0
|
32.9
|
1.0
|
|
Manganese binding site 3 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 3 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn401
b:35.7
occ:1.00
|
O1
|
C:OAF501
|
2.1
|
32.4
|
1.0
|
O3
|
C:OAF501
|
2.1
|
35.1
|
1.0
|
O
|
C:HOH310
|
2.1
|
32.4
|
1.0
|
OD2
|
C:ASP87
|
2.2
|
37.0
|
1.0
|
O
|
C:HOH309
|
2.3
|
33.0
|
1.0
|
O
|
C:HOH311
|
2.3
|
36.5
|
1.0
|
C1
|
C:OAF501
|
2.9
|
33.6
|
1.0
|
C2
|
C:OAF501
|
3.0
|
34.4
|
1.0
|
NZ
|
C:LYS122
|
3.1
|
37.6
|
1.0
|
CG
|
C:ASP87
|
3.3
|
36.8
|
1.0
|
F1
|
C:OAF501
|
3.6
|
36.9
|
1.0
|
OD1
|
C:ASP89
|
3.8
|
39.7
|
1.0
|
OD1
|
C:ASP87
|
3.8
|
36.3
|
1.0
|
C3
|
C:OAF501
|
3.8
|
34.7
|
1.0
|
O5
|
C:OAF501
|
3.9
|
35.0
|
1.0
|
OD1
|
C:ASP59
|
4.0
|
37.2
|
1.0
|
CA
|
C:GLY47
|
4.1
|
36.5
|
1.0
|
O2
|
C:OAF501
|
4.1
|
33.7
|
1.0
|
N
|
C:GLY47
|
4.2
|
36.8
|
1.0
|
N
|
C:ALA48
|
4.2
|
36.0
|
1.0
|
OD2
|
C:ASP59
|
4.2
|
36.2
|
1.0
|
O4
|
C:OAF501
|
4.2
|
34.7
|
1.0
|
NH1
|
C:ARG161
|
4.3
|
36.1
|
1.0
|
C4
|
C:OAF501
|
4.4
|
35.3
|
1.0
|
CE
|
C:LYS122
|
4.4
|
42.4
|
1.0
|
CB
|
C:ASP87
|
4.5
|
37.4
|
1.0
|
C
|
C:GLY47
|
4.5
|
36.0
|
1.0
|
CG
|
C:ASP59
|
4.5
|
36.3
|
1.0
|
OH
|
C:TYR44
|
4.6
|
38.2
|
1.0
|
CE1
|
C:HIS114
|
4.7
|
39.8
|
1.0
|
OE1
|
C:GLU116
|
4.9
|
37.3
|
1.0
|
F2
|
C:OAF501
|
5.0
|
34.0
|
1.0
|
|
Manganese binding site 4 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 4 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn401
b:36.2
occ:1.00
|
O3
|
D:OAF501
|
1.9
|
31.4
|
1.0
|
O
|
D:HOH314
|
2.0
|
32.5
|
1.0
|
O
|
D:HOH313
|
2.2
|
32.1
|
1.0
|
OD2
|
D:ASP87
|
2.2
|
36.2
|
1.0
|
O1
|
D:OAF501
|
2.2
|
31.7
|
1.0
|
O
|
D:HOH312
|
2.5
|
30.9
|
1.0
|
C2
|
D:OAF501
|
2.7
|
32.5
|
1.0
|
C1
|
D:OAF501
|
2.9
|
31.9
|
1.0
|
CG
|
D:ASP87
|
3.3
|
37.4
|
1.0
|
C3
|
D:OAF501
|
3.6
|
32.8
|
1.0
|
F1
|
D:OAF501
|
3.6
|
33.0
|
1.0
|
NZ
|
D:LYS122
|
3.7
|
38.6
|
1.0
|
OD1
|
D:ASP87
|
3.7
|
36.6
|
1.0
|
O4
|
D:OAF501
|
3.8
|
34.1
|
1.0
|
O5
|
D:OAF501
|
3.9
|
30.5
|
1.0
|
NH2
|
D:ARG161
|
3.9
|
35.2
|
1.0
|
OD1
|
D:ASP59
|
3.9
|
37.4
|
1.0
|
OD1
|
D:ASP89
|
4.0
|
34.6
|
1.0
|
CA
|
D:GLY47
|
4.1
|
37.1
|
1.0
|
O2
|
D:OAF501
|
4.1
|
32.3
|
1.0
|
OD2
|
D:ASP59
|
4.1
|
38.0
|
1.0
|
N
|
D:ALA48
|
4.1
|
38.0
|
1.0
|
C4
|
D:OAF501
|
4.1
|
31.6
|
1.0
|
N
|
D:GLY47
|
4.2
|
37.2
|
1.0
|
CG
|
D:ASP59
|
4.4
|
37.9
|
1.0
|
OH
|
D:TYR44
|
4.5
|
39.7
|
1.0
|
CB
|
D:ASP87
|
4.5
|
37.2
|
1.0
|
C
|
D:GLY47
|
4.6
|
38.0
|
1.0
|
CE
|
D:LYS122
|
4.6
|
36.3
|
1.0
|
CZ
|
D:ARG161
|
4.7
|
37.2
|
1.0
|
F2
|
D:OAF501
|
4.7
|
33.6
|
1.0
|
NH1
|
D:ARG161
|
4.7
|
35.2
|
1.0
|
OE2
|
D:GLU116
|
4.7
|
36.8
|
1.0
|
CE1
|
D:HIS114
|
4.8
|
36.9
|
1.0
|
|
Manganese binding site 5 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 5 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn401
b:36.4
occ:1.00
|
O3
|
E:OAF501
|
1.9
|
32.5
|
1.0
|
OD2
|
E:ASP87
|
2.1
|
40.5
|
1.0
|
O1
|
E:OAF501
|
2.1
|
28.4
|
1.0
|
O
|
E:HOH316
|
2.3
|
33.3
|
1.0
|
O
|
E:HOH317
|
2.3
|
26.4
|
1.0
|
O
|
E:HOH315
|
2.4
|
30.3
|
1.0
|
C2
|
E:OAF501
|
2.9
|
32.9
|
1.0
|
C1
|
E:OAF501
|
2.9
|
31.1
|
1.0
|
CG
|
E:ASP87
|
3.2
|
39.4
|
1.0
|
NZ
|
E:LYS122
|
3.6
|
40.7
|
1.0
|
F1
|
E:OAF501
|
3.7
|
34.8
|
1.0
|
C3
|
E:OAF501
|
3.7
|
33.7
|
1.0
|
OD1
|
E:ASP87
|
3.8
|
38.3
|
1.0
|
OD1
|
E:ASP59
|
3.8
|
39.7
|
1.0
|
O5
|
E:OAF501
|
4.0
|
32.8
|
1.0
|
OD2
|
E:ASP89
|
4.0
|
35.4
|
1.0
|
NH2
|
E:ARG161
|
4.0
|
33.6
|
1.0
|
O4
|
E:OAF501
|
4.0
|
33.3
|
1.0
|
O2
|
E:OAF501
|
4.1
|
31.3
|
1.0
|
C4
|
E:OAF501
|
4.2
|
33.6
|
1.0
|
N
|
E:ALA48
|
4.3
|
37.6
|
1.0
|
OD2
|
E:ASP59
|
4.3
|
39.9
|
1.0
|
CE1
|
E:HIS114
|
4.4
|
35.6
|
1.0
|
CA
|
E:GLY47
|
4.4
|
36.9
|
1.0
|
N
|
E:GLY47
|
4.4
|
37.9
|
1.0
|
CB
|
E:ASP87
|
4.5
|
37.8
|
1.0
|
CG
|
E:ASP59
|
4.5
|
39.5
|
1.0
|
OH
|
E:TYR44
|
4.5
|
37.9
|
1.0
|
CE
|
E:LYS122
|
4.6
|
37.5
|
1.0
|
OE1
|
E:GLU116
|
4.7
|
36.2
|
1.0
|
C
|
E:GLY47
|
4.7
|
37.9
|
1.0
|
CZ
|
E:ARG161
|
4.7
|
36.8
|
1.0
|
NH1
|
E:ARG161
|
4.8
|
34.2
|
1.0
|
F2
|
E:OAF501
|
4.9
|
34.2
|
1.0
|
|
Manganese binding site 6 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 6 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn401
b:36.5
occ:1.00
|
O3
|
F:OAF501
|
2.0
|
32.0
|
1.0
|
O1
|
F:OAF501
|
2.2
|
32.6
|
1.0
|
O
|
F:HOH318
|
2.2
|
28.2
|
1.0
|
O
|
F:HOH319
|
2.2
|
28.0
|
1.0
|
OD2
|
F:ASP87
|
2.2
|
38.1
|
1.0
|
O
|
F:HOH320
|
2.4
|
33.0
|
1.0
|
C1
|
F:OAF501
|
2.9
|
33.2
|
1.0
|
C2
|
F:OAF501
|
2.9
|
33.2
|
1.0
|
CG
|
F:ASP87
|
3.2
|
38.7
|
1.0
|
OD1
|
F:ASP87
|
3.5
|
38.7
|
1.0
|
F1
|
F:OAF501
|
3.8
|
35.3
|
1.0
|
C3
|
F:OAF501
|
3.8
|
34.4
|
1.0
|
OD1
|
F:ASP59
|
3.8
|
38.7
|
1.0
|
NZ
|
F:LYS122
|
3.9
|
34.0
|
1.0
|
O5
|
F:OAF501
|
3.9
|
33.2
|
1.0
|
OD1
|
F:ASP89
|
4.0
|
37.5
|
1.0
|
NH2
|
F:ARG161
|
4.0
|
32.7
|
1.0
|
CA
|
F:GLY47
|
4.0
|
35.8
|
1.0
|
O4
|
F:OAF501
|
4.0
|
34.3
|
1.0
|
O2
|
F:OAF501
|
4.1
|
32.2
|
1.0
|
N
|
F:ALA48
|
4.2
|
34.9
|
1.0
|
C4
|
F:OAF501
|
4.2
|
34.4
|
1.0
|
N
|
F:GLY47
|
4.3
|
35.5
|
1.0
|
OD2
|
F:ASP59
|
4.3
|
36.4
|
1.0
|
OH
|
F:TYR44
|
4.4
|
32.4
|
1.0
|
CG
|
F:ASP59
|
4.5
|
37.7
|
1.0
|
CE1
|
F:HIS114
|
4.5
|
36.5
|
1.0
|
CB
|
F:ASP87
|
4.6
|
38.6
|
1.0
|
C
|
F:GLY47
|
4.6
|
35.5
|
1.0
|
CE
|
F:LYS122
|
4.7
|
36.9
|
1.0
|
OE1
|
F:GLU116
|
4.8
|
34.6
|
1.0
|
CZ
|
F:ARG161
|
4.8
|
30.9
|
1.0
|
NH1
|
F:ARG161
|
4.9
|
28.6
|
1.0
|
F2
|
F:OAF501
|
4.9
|
35.2
|
1.0
|
|
Manganese binding site 7 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 7 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn401
b:34.5
occ:1.00
|
O1
|
G:OAF501
|
1.9
|
34.6
|
1.0
|
O3
|
G:OAF501
|
1.9
|
35.0
|
1.0
|
O
|
G:HOH323
|
2.0
|
30.6
|
1.0
|
O
|
G:HOH322
|
2.1
|
28.6
|
1.0
|
OD2
|
G:ASP87
|
2.2
|
37.7
|
1.0
|
O
|
G:HOH321
|
2.5
|
32.2
|
1.0
|
C1
|
G:OAF501
|
2.7
|
33.8
|
1.0
|
C2
|
G:OAF501
|
2.9
|
34.2
|
1.0
|
CG
|
G:ASP87
|
3.2
|
37.4
|
1.0
|
NZ
|
G:LYS122
|
3.4
|
36.3
|
1.0
|
OD1
|
G:ASP87
|
3.6
|
36.6
|
1.0
|
F1
|
G:OAF501
|
3.8
|
38.4
|
1.0
|
O2
|
G:OAF501
|
3.9
|
35.1
|
1.0
|
C3
|
G:OAF501
|
3.9
|
34.6
|
1.0
|
O4
|
G:OAF501
|
3.9
|
35.9
|
1.0
|
OD1
|
G:ASP59
|
3.9
|
37.5
|
1.0
|
OD1
|
G:ASP89
|
4.0
|
36.9
|
1.0
|
O5
|
G:OAF501
|
4.0
|
31.4
|
1.0
|
CA
|
G:GLY47
|
4.0
|
36.4
|
1.0
|
N
|
G:ALA48
|
4.1
|
36.8
|
1.0
|
N
|
G:GLY47
|
4.1
|
36.4
|
1.0
|
CB
|
G:ASP87
|
4.3
|
38.8
|
1.0
|
CE
|
G:LYS122
|
4.4
|
36.5
|
1.0
|
OD2
|
G:ASP59
|
4.4
|
39.5
|
1.0
|
NH2
|
G:ARG161
|
4.4
|
36.8
|
1.0
|
CE1
|
G:HIS114
|
4.4
|
39.7
|
1.0
|
C4
|
G:OAF501
|
4.4
|
33.9
|
1.0
|
OH
|
G:TYR44
|
4.5
|
33.3
|
1.0
|
C
|
G:GLY47
|
4.5
|
36.9
|
1.0
|
CG
|
G:ASP59
|
4.6
|
37.9
|
1.0
|
NH1
|
G:ARG161
|
4.9
|
34.2
|
1.0
|
CZ
|
G:ARG161
|
4.9
|
36.0
|
1.0
|
F2
|
G:OAF501
|
5.0
|
37.0
|
1.0
|
OE1
|
G:GLU116
|
5.0
|
38.0
|
1.0
|
|
Manganese binding site 8 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 8 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mn401
b:36.0
occ:1.00
|
O3
|
H:OAF501
|
1.9
|
33.9
|
1.0
|
OD2
|
H:ASP87
|
2.0
|
38.6
|
1.0
|
O
|
H:HOH326
|
2.1
|
33.0
|
1.0
|
O
|
H:HOH325
|
2.1
|
33.7
|
1.0
|
O1
|
H:OAF501
|
2.2
|
36.7
|
1.0
|
O
|
H:HOH324
|
2.4
|
33.4
|
1.0
|
C2
|
H:OAF501
|
2.8
|
35.6
|
1.0
|
C1
|
H:OAF501
|
2.8
|
36.1
|
1.0
|
CG
|
H:ASP87
|
3.1
|
35.8
|
1.0
|
NZ
|
H:LYS122
|
3.4
|
36.4
|
1.0
|
OD1
|
H:ASP87
|
3.5
|
40.5
|
1.0
|
F1
|
H:OAF501
|
3.6
|
35.6
|
1.0
|
C3
|
H:OAF501
|
3.7
|
36.8
|
1.0
|
NH2
|
H:ARG161
|
3.8
|
34.4
|
1.0
|
O4
|
H:OAF501
|
3.8
|
34.6
|
1.0
|
OD1
|
H:ASP89
|
3.9
|
36.6
|
1.0
|
OD1
|
H:ASP59
|
4.0
|
35.4
|
1.0
|
O5
|
H:OAF501
|
4.0
|
36.1
|
1.0
|
CA
|
H:GLY47
|
4.1
|
38.1
|
1.0
|
O2
|
H:OAF501
|
4.1
|
35.9
|
1.0
|
OD2
|
H:ASP59
|
4.1
|
40.9
|
1.0
|
N
|
H:ALA48
|
4.2
|
38.5
|
1.0
|
N
|
H:GLY47
|
4.2
|
38.6
|
1.0
|
C4
|
H:OAF501
|
4.2
|
36.3
|
1.0
|
CB
|
H:ASP87
|
4.4
|
36.7
|
1.0
|
CG
|
H:ASP59
|
4.5
|
37.1
|
1.0
|
CE
|
H:LYS122
|
4.5
|
37.6
|
1.0
|
C
|
H:GLY47
|
4.5
|
38.9
|
1.0
|
OH
|
H:TYR44
|
4.5
|
40.5
|
1.0
|
CE1
|
H:HIS114
|
4.7
|
40.5
|
1.0
|
CZ
|
H:ARG161
|
4.7
|
34.5
|
1.0
|
OE2
|
H:GLU116
|
4.7
|
38.2
|
1.0
|
NH1
|
H:ARG161
|
4.8
|
37.0
|
1.0
|
F2
|
H:OAF501
|
4.8
|
39.3
|
1.0
|
|
Manganese binding site 9 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 9 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mn401
b:39.8
occ:1.00
|
O1
|
I:OAF501
|
2.0
|
36.3
|
1.0
|
O
|
I:HOH329
|
2.2
|
30.6
|
1.0
|
O
|
I:HOH328
|
2.2
|
37.6
|
1.0
|
O3
|
I:OAF501
|
2.2
|
36.6
|
1.0
|
OD2
|
I:ASP87
|
2.3
|
39.0
|
1.0
|
O
|
I:HOH327
|
2.4
|
36.0
|
1.0
|
C1
|
I:OAF501
|
2.7
|
37.2
|
1.0
|
C2
|
I:OAF501
|
2.9
|
36.3
|
1.0
|
CG
|
I:ASP87
|
3.2
|
39.6
|
1.0
|
NZ
|
I:LYS122
|
3.4
|
37.8
|
1.0
|
OD1
|
I:ASP87
|
3.6
|
39.4
|
1.0
|
F1
|
I:OAF501
|
3.6
|
38.5
|
1.0
|
NH2
|
I:ARG161
|
3.8
|
36.7
|
1.0
|
O2
|
I:OAF501
|
3.8
|
41.2
|
1.0
|
C3
|
I:OAF501
|
3.8
|
36.9
|
1.0
|
OD2
|
I:ASP89
|
3.9
|
41.4
|
1.0
|
O4
|
I:OAF501
|
4.0
|
36.2
|
1.0
|
OD1
|
I:ASP59
|
4.1
|
37.6
|
1.0
|
O5
|
I:OAF501
|
4.2
|
35.1
|
1.0
|
CE
|
I:LYS122
|
4.2
|
37.5
|
1.0
|
N
|
I:ALA48
|
4.3
|
35.2
|
1.0
|
CE1
|
I:HIS114
|
4.3
|
38.4
|
1.0
|
C4
|
I:OAF501
|
4.4
|
35.5
|
1.0
|
CB
|
I:ASP87
|
4.5
|
39.0
|
1.0
|
N
|
I:GLY47
|
4.5
|
35.7
|
1.0
|
OH
|
I:TYR44
|
4.5
|
38.0
|
1.0
|
OE1
|
I:GLU116
|
4.6
|
37.3
|
1.0
|
CA
|
I:GLY47
|
4.6
|
35.2
|
1.0
|
CZ
|
I:ARG161
|
4.6
|
36.6
|
1.0
|
OD2
|
I:ASP59
|
4.7
|
39.5
|
1.0
|
CG
|
I:ASP59
|
4.8
|
38.0
|
1.0
|
NH1
|
I:ARG161
|
4.9
|
34.4
|
1.0
|
C
|
I:GLY47
|
4.9
|
35.1
|
1.0
|
NE2
|
I:HIS114
|
4.9
|
36.6
|
1.0
|
F2
|
I:OAF501
|
5.0
|
36.0
|
1.0
|
CB
|
I:ALA48
|
5.0
|
35.4
|
1.0
|
|
Manganese binding site 10 out
of 16 in 3fa3
Go back to
Manganese Binding Sites List in 3fa3
Manganese binding site 10 out
of 16 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Trigonal Crystal Form within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mn401
b:43.5
occ:1.00
|
O
|
J:HOH330
|
2.1
|
40.7
|
1.0
|
O
|
J:HOH331
|
2.3
|
39.9
|
1.0
|
OD2
|
J:ASP87
|
2.3
|
42.0
|
1.0
|
OD1
|
J:ASP89
|
2.7
|
41.9
|
1.0
|
O
|
J:HOH809
|
3.0
|
31.6
|
1.0
|
CG
|
J:ASP87
|
3.2
|
40.2
|
1.0
|
CG
|
J:ASP89
|
3.3
|
38.6
|
1.0
|
OD1
|
J:ASP87
|
3.4
|
39.3
|
1.0
|
OD2
|
J:ASP89
|
3.6
|
35.6
|
1.0
|
OE1
|
J:GLU116
|
4.1
|
39.2
|
1.0
|
CA
|
J:GLY47
|
4.1
|
38.0
|
1.0
|
OD2
|
J:ASP59
|
4.2
|
41.0
|
1.0
|
CA
|
J:ASP89
|
4.3
|
38.0
|
1.0
|
OD1
|
J:ASP59
|
4.4
|
40.0
|
1.0
|
CB
|
J:ASP89
|
4.4
|
38.6
|
1.0
|
CB
|
J:ASP87
|
4.6
|
39.8
|
1.0
|
N
|
J:ASP89
|
4.6
|
38.2
|
1.0
|
C
|
J:GLY47
|
4.6
|
37.1
|
1.0
|
O
|
J:HOH656
|
4.7
|
36.2
|
1.0
|
CG
|
J:ASP59
|
4.8
|
40.5
|
1.0
|
N
|
J:ALA48
|
4.9
|
36.7
|
1.0
|
N
|
J:GLY47
|
4.9
|
37.7
|
1.0
|
|
Reference:
B.Narayanan,
W.Niu,
H.J.Joosten,
Z.Li,
R.K.Kuipers,
P.J.Schaap,
D.Dunaway-Mariano,
O.Herzberg.
Structure and Function of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member. J.Mol.Biol. V. 386 486 2009.
ISSN: ISSN 0022-2836
PubMed: 19133276
DOI: 10.1016/J.JMB.2008.12.037
Page generated: Sat Oct 5 16:16:03 2024
|