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Sodium in PDB 5k8b: X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate
Enzymatic activity of X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate
All present enzymatic activity of X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate:
2.6.1.109;
2.6.1.109;
Protein crystallography data
The structure of X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate, PDB code: 5k8b
was solved by
H.M.Holden,
J.B.Thoden,
T.R.Zachman-Brockmeyer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
| Resolution Low / High (Å) | 50.00 / 2.15 |
| Space group | C 1 2 1 |
| Cell size a, b, c (Å), α, β, γ (°) | 266.628, 61.675, 99.636, 90.00, 102.03, 90.00 |
| R / Rfree (%) | 17.1 / 22.6 |
Other elements in 5k8b:
The structure of X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate also contains other interesting chemical elements:
| Chlorine | (Cl) | 5 atoms |
Sodium Binding Sites:
The binding sites of Sodium atom in the X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate
(pdb code 5k8b). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate, PDB code: 5k8b:
In total only one binding site of Sodium was determined in the X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate, PDB code: 5k8b:
Sodium binding site 1 out of 1 in 5k8b
Go back to
Sodium Binding Sites List in 5k8b
Sodium binding site 1 out
of 1 in the X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Sodium with other atoms in the Na binding
site number 1 of X-Ray Structure of Kdna, 8-Amino-3,8-Dideoxy-Alpha-D-Manno- Octulosonate Transaminase, From Shewanella Oneidensis in the Presence of the External Aldimine with Plp and Glutamate within 5.0Å range:
|
Reference:
T.R.Zachman-Brockmeyer,
J.B.Thoden,
H.M.Holden.
Structures of Kdnb and Kdna From Shewanella Oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-D-Manno-Octulosonic Acid. Biochemistry V. 55 4485 2016.
ISSN: ISSN 0006-2960
PubMed: 27275764
DOI: 10.1021/ACS.BIOCHEM.6B00439
Page generated: Mon Aug 18 00:37:20 2025
ISSN: ISSN 0006-2960
PubMed: 27275764
DOI: 10.1021/ACS.BIOCHEM.6B00439
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