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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

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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

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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

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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

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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

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