Manganese in PDB 1nvm: Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
Enzymatic activity of Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
All present enzymatic activity of Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate:
1.2.1.10;
Protein crystallography data
The structure of Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate, PDB code: 1nvm
was solved by
A.B.Manjasetty,
J.Powlowski,
A.Vrielink,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.200,
140.000,
191.400,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.9 /
23
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
(pdb code 1nvm). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate, PDB code: 1nvm:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1nvm
Go back to
Manganese Binding Sites List in 1nvm
Manganese binding site 1 out
of 4 in the Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
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 A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn3504
b:19.9
occ:1.00
|
OD1
|
A:ASP18
|
2.2
|
18.0
|
1.0
|
NE2
|
A:HIS202
|
2.3
|
19.8
|
1.0
|
O1
|
A:OXL3508
|
2.3
|
22.8
|
1.0
|
NE2
|
A:HIS200
|
2.3
|
18.6
|
1.0
|
O2
|
A:OXL3508
|
2.4
|
28.4
|
1.0
|
O
|
A:HOH3614
|
2.6
|
28.7
|
1.0
|
C2
|
A:OXL3508
|
2.9
|
28.6
|
1.0
|
C1
|
A:OXL3508
|
3.0
|
24.5
|
1.0
|
CE1
|
A:HIS202
|
3.2
|
23.3
|
1.0
|
CG
|
A:ASP18
|
3.2
|
19.5
|
1.0
|
CD2
|
A:HIS202
|
3.2
|
21.0
|
1.0
|
CD2
|
A:HIS200
|
3.2
|
18.6
|
1.0
|
CE1
|
A:HIS200
|
3.3
|
16.6
|
1.0
|
OD2
|
A:ASP18
|
3.5
|
19.9
|
1.0
|
ND2
|
A:ASN236
|
3.9
|
20.4
|
1.0
|
NH2
|
A:ARG17
|
4.1
|
20.4
|
1.0
|
O4
|
A:OXL3508
|
4.1
|
29.5
|
1.0
|
O3
|
A:OXL3508
|
4.1
|
22.3
|
1.0
|
ND1
|
A:HIS202
|
4.3
|
21.3
|
1.0
|
CG
|
A:HIS202
|
4.3
|
19.9
|
1.0
|
ND1
|
A:HIS200
|
4.4
|
16.4
|
1.0
|
CG
|
A:HIS200
|
4.4
|
16.1
|
1.0
|
NH1
|
A:ARG17
|
4.4
|
18.3
|
1.0
|
CB
|
A:ASP18
|
4.5
|
17.3
|
1.0
|
O
|
A:HOH3617
|
4.5
|
27.7
|
1.0
|
O
|
A:HOH3650
|
4.6
|
28.6
|
1.0
|
CZ
|
A:ARG17
|
4.8
|
17.5
|
1.0
|
CG
|
A:ASN236
|
4.8
|
22.1
|
1.0
|
OD1
|
A:ASN236
|
4.9
|
22.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1nvm
Go back to
Manganese Binding Sites List in 1nvm
Manganese binding site 2 out
of 4 in the Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
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 A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn3505
b:20.9
occ:1.00
|
OD2
|
C:ASP18
|
2.3
|
21.2
|
1.0
|
NE2
|
C:HIS202
|
2.4
|
21.4
|
1.0
|
O2
|
C:OXL3509
|
2.4
|
25.8
|
1.0
|
NE2
|
C:HIS200
|
2.4
|
20.0
|
1.0
|
O1
|
C:OXL3509
|
2.4
|
23.8
|
1.0
|
O
|
C:HOH3568
|
2.6
|
30.3
|
1.0
|
C2
|
C:OXL3509
|
2.9
|
27.0
|
1.0
|
C1
|
C:OXL3509
|
3.0
|
24.8
|
1.0
|
CD2
|
C:HIS200
|
3.3
|
16.4
|
1.0
|
CE1
|
C:HIS202
|
3.3
|
22.4
|
1.0
|
CD2
|
C:HIS202
|
3.3
|
19.9
|
1.0
|
CG
|
C:ASP18
|
3.3
|
21.4
|
1.0
|
CE1
|
C:HIS200
|
3.3
|
17.2
|
1.0
|
OD1
|
C:ASP18
|
3.5
|
21.0
|
1.0
|
ND2
|
C:ASN236
|
4.0
|
20.9
|
1.0
|
NH2
|
C:ARG17
|
4.0
|
18.7
|
1.0
|
O4
|
C:OXL3509
|
4.1
|
31.9
|
1.0
|
O3
|
C:OXL3509
|
4.1
|
21.9
|
1.0
|
O
|
C:HOH3637
|
4.3
|
28.8
|
1.0
|
ND1
|
C:HIS200
|
4.4
|
18.1
|
1.0
|
ND1
|
C:HIS202
|
4.4
|
20.6
|
1.0
|
CG
|
C:HIS202
|
4.4
|
19.2
|
1.0
|
CG
|
C:HIS200
|
4.4
|
17.7
|
1.0
|
O
|
C:HOH3651
|
4.4
|
30.0
|
1.0
|
NH1
|
C:ARG17
|
4.4
|
20.4
|
1.0
|
CB
|
C:ASP18
|
4.5
|
19.2
|
1.0
|
CZ
|
C:ARG17
|
4.8
|
17.0
|
1.0
|
CG
|
C:ASN236
|
4.9
|
20.7
|
1.0
|
OD1
|
C:ASN236
|
4.9
|
22.7
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1nvm
Go back to
Manganese Binding Sites List in 1nvm
Manganese binding site 3 out
of 4 in the Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
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 A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn3506
b:22.5
occ:1.00
|
OD1
|
E:ASP18
|
2.3
|
23.2
|
1.0
|
O1
|
E:OXL3510
|
2.3
|
25.6
|
1.0
|
NE2
|
E:HIS200
|
2.3
|
21.1
|
1.0
|
NE2
|
E:HIS202
|
2.4
|
26.4
|
1.0
|
O2
|
E:OXL3510
|
2.4
|
30.5
|
1.0
|
O
|
E:HOH3624
|
2.6
|
31.3
|
1.0
|
C1
|
E:OXL3510
|
3.0
|
28.7
|
1.0
|
C2
|
E:OXL3510
|
3.0
|
30.5
|
1.0
|
CD2
|
E:HIS202
|
3.2
|
26.7
|
1.0
|
CE1
|
E:HIS200
|
3.3
|
20.6
|
1.0
|
CD2
|
E:HIS200
|
3.3
|
21.1
|
1.0
|
CG
|
E:ASP18
|
3.3
|
22.9
|
1.0
|
CE1
|
E:HIS202
|
3.3
|
26.6
|
1.0
|
OD2
|
E:ASP18
|
3.5
|
22.6
|
1.0
|
ND2
|
E:ASN236
|
3.9
|
22.9
|
1.0
|
NH2
|
E:ARG17
|
4.1
|
20.4
|
1.0
|
O4
|
E:OXL3510
|
4.1
|
33.8
|
1.0
|
O3
|
E:OXL3510
|
4.1
|
25.6
|
1.0
|
O
|
E:HOH3693
|
4.2
|
30.8
|
1.0
|
ND1
|
E:HIS200
|
4.3
|
20.3
|
1.0
|
NH1
|
E:ARG17
|
4.4
|
20.4
|
1.0
|
ND1
|
E:HIS202
|
4.4
|
24.2
|
1.0
|
CG
|
E:HIS200
|
4.4
|
18.8
|
1.0
|
CG
|
E:HIS202
|
4.4
|
23.3
|
1.0
|
CB
|
E:ASP18
|
4.5
|
20.6
|
1.0
|
O
|
E:HOH3661
|
4.5
|
34.0
|
1.0
|
CZ
|
E:ARG17
|
4.7
|
19.3
|
1.0
|
CG
|
E:ASN236
|
4.9
|
22.6
|
1.0
|
OD1
|
E:ASN236
|
5.0
|
23.5
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1nvm
Go back to
Manganese Binding Sites List in 1nvm
Manganese binding site 4 out
of 4 in the Crystal Structure of A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate
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 A Bifunctional Aldolase-Dehydrogenase : Sequestering A Reactive and Volatile Intermediate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mn3507
b:24.4
occ:1.00
|
NE2
|
G:HIS202
|
2.3
|
22.2
|
1.0
|
NE2
|
G:HIS200
|
2.3
|
22.2
|
1.0
|
OD1
|
G:ASP18
|
2.3
|
25.9
|
1.0
|
O2
|
G:OXL3511
|
2.4
|
31.8
|
1.0
|
O1
|
G:OXL3511
|
2.4
|
29.1
|
1.0
|
O
|
G:HOH3679
|
2.6
|
34.3
|
1.0
|
C2
|
G:OXL3511
|
2.9
|
31.7
|
1.0
|
C1
|
G:OXL3511
|
3.0
|
29.4
|
1.0
|
CD2
|
G:HIS202
|
3.2
|
23.3
|
1.0
|
CE1
|
G:HIS200
|
3.2
|
22.3
|
1.0
|
CG
|
G:ASP18
|
3.3
|
24.8
|
1.0
|
CD2
|
G:HIS200
|
3.3
|
22.1
|
1.0
|
CE1
|
G:HIS202
|
3.3
|
23.3
|
1.0
|
OD2
|
G:ASP18
|
3.6
|
22.3
|
1.0
|
ND2
|
G:ASN236
|
3.9
|
24.0
|
1.0
|
NH2
|
G:ARG17
|
4.1
|
23.6
|
1.0
|
O4
|
G:OXL3511
|
4.1
|
35.0
|
1.0
|
O3
|
G:OXL3511
|
4.2
|
27.0
|
1.0
|
ND1
|
G:HIS200
|
4.3
|
22.4
|
1.0
|
CG
|
G:HIS202
|
4.3
|
20.1
|
1.0
|
ND1
|
G:HIS202
|
4.4
|
22.5
|
1.0
|
CG
|
G:HIS200
|
4.4
|
20.9
|
1.0
|
O
|
G:HOH3656
|
4.4
|
31.8
|
1.0
|
CB
|
G:ASP18
|
4.5
|
23.1
|
1.0
|
O
|
G:HOH3637
|
4.5
|
34.5
|
1.0
|
NH1
|
G:ARG17
|
4.5
|
22.2
|
1.0
|
CZ
|
G:ARG17
|
4.8
|
23.7
|
1.0
|
CG
|
G:ASN236
|
4.9
|
23.7
|
1.0
|
|
Reference:
A.B.Manjasetty,
J.Powlowski,
A.Vrielink.
Crystal Structure of A Bifunctional Aldolase-Dehydrogenase: Sequestering A Reactive and Volatile Intermediate Proc.Natl.Acad.Sci.Usa V. 100 6992 2003.
ISSN: ISSN 0027-8424
PubMed: 12764229
DOI: 10.1073/PNAS.1236794100
Page generated: Sat Oct 5 11:53:19 2024
|