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Chlorine 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;

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:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where 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:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5k8b

Go back to Chlorine Binding Sites List in 5k8b
Chlorine binding site 1 out of 5 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

A full contact list of Chlorine with other atoms in the Cl 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:
probe atom residue distance (Å) B Occ
A:Cl502

b:25.6
occ:1.00
 CB A:ASN322 3.1 34.9 1.0
ND1 A:HIS325 3.2 12.0 1.0
N A:TRP324 3.6 18.1 1.0
C A:ASN322 3.8 28.8 1.0
N A:ASN323 3.8 23.3 1.0
N A:HIS325 3.9 14.4 1.0
CE3 A:TRP319 4.0 16.8 1.0
CA A:ASN322 4.0 31.3 1.0
CB A:TRP324 4.0 15.7 1.0
CE1 A:HIS325 4.1 11.8 1.0
CG A:HIS325 4.1 12.6 1.0
CZ3 A:TRP319 4.1 16.0 1.0
CG A:ASN322 4.1 38.3 1.0
CA A:TRP324 4.2 16.4 1.0
CB A:HIS325 4.2 12.5 1.0
O A:HOH692 4.3 23.0 1.0
O A:ASN322 4.3 28.8 1.0
C A:TRP324 4.4 15.7 1.0
CD1 A:TRP324 4.5 16.4 1.0
OD1 A:ASN322 4.6 42.7 1.0
C A:ASN323 4.6 20.1 1.0
CA A:HIS325 4.7 12.3 1.0
CG A:TRP324 4.7 15.8 1.0
CA A:ASN323 4.7 21.9 1.0
ND2 A:ASN322 4.9 38.3 1.0
CD1 A:PHE317 5.0 25.7 1.0

Chlorine binding site 2 out of 5 in 5k8b

Go back to Chlorine Binding Sites List in 5k8b
Chlorine binding site 2 out of 5 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

A full contact list of Chlorine with other atoms in the Cl binding site number 2 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:
probe atom residue distance (Å) B Occ
A:Cl503

b:17.9
occ:1.00
 NZ A:LYS262 3.1 16.1 1.0
O A:HOH723 3.1 25.6 1.0
O A:HOH648 3.1 11.6 1.0
N A:SER292 3.3 18.7 1.0
CE A:LYS262 3.5 15.9 1.0
O A:SER292 3.8 18.5 1.0
CB A:ARG278 3.8 18.3 1.0
O A:PHE290 3.9 15.6 1.0
CD A:ARG278 3.9 17.2 1.0
CB A:SER292 4.0 18.5 1.0
CD1 A:LEU291 4.0 19.9 1.0
CA A:LEU291 4.0 17.1 1.0
CD1 A:ILE280 4.1 24.0 1.0
CA A:SER292 4.1 18.4 1.0
C A:LEU291 4.2 17.9 1.0
C A:SER292 4.4 19.3 1.0
CG A:ARG278 4.4 17.7 1.0
OG A:SER292 4.5 16.7 1.0
CG1 A:ILE280 4.7 21.3 1.0
C A:PHE290 4.7 14.9 1.0
N A:ARG278 4.7 15.8 1.0
O A:ARG278 4.8 15.3 1.0
CA A:ARG278 4.8 16.7 1.0
N A:LEU291 4.9 16.1 1.0
CD A:LYS262 5.0 15.3 1.0
CB A:LEU291 5.0 17.9 1.0
O A:HOH667 5.0 15.5 1.0

Chlorine binding site 3 out of 5 in 5k8b

Go back to Chlorine Binding Sites List in 5k8b
Chlorine binding site 3 out of 5 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

A full contact list of Chlorine with other atoms in the Cl binding site number 3 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:
probe atom residue distance (Å) B Occ
B:Cl502

b:17.1
occ:1.00
 NZ B:LYS262 2.9 21.3 1.0
O B:HOH678 3.0 11.6 1.0
O B:HOH675 3.0 19.7 1.0
N B:SER292 3.3 17.1 1.0
O B:SER292 3.7 16.9 1.0
CG B:ARG278 3.8 23.9 1.0
CE B:LYS262 3.8 24.4 1.0
O B:PHE290 3.9 19.5 1.0
CD1 B:ILE280 3.9 25.4 1.0
CB B:ARG278 3.9 23.5 1.0
CD1 B:LEU291 4.0 20.5 1.0
CA B:LEU291 4.1 17.3 1.0
CB B:SER292 4.1 17.3 1.0
CA B:SER292 4.1 16.9 1.0
C B:LEU291 4.2 17.2 1.0
C B:SER292 4.4 16.5 1.0
NE B:ARG278 4.4 24.3 1.0
CG1 B:ILE280 4.6 23.1 1.0
OG B:SER292 4.6 16.6 1.0
O B:ARG278 4.7 18.6 1.0
C B:PHE290 4.7 17.4 1.0
CD B:ARG278 4.8 26.3 1.0
CA B:ARG278 4.8 21.7 1.0
N B:ARG278 4.9 24.5 1.0
N B:LEU291 4.9 16.8 1.0
O B:HOH708 4.9 16.0 1.0
CG B:LEU291 5.0 19.1 1.0

Chlorine binding site 4 out of 5 in 5k8b

Go back to Chlorine Binding Sites List in 5k8b
Chlorine binding site 4 out of 5 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

A full contact list of Chlorine with other atoms in the Cl binding site number 4 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:
probe atom residue distance (Å) B Occ
C:Cl503

b:15.2
occ:1.00
 NZ C:LYS262 3.0 21.6 1.0
O C:HOH690 3.0 16.4 1.0
O C:HOH639 3.2 17.9 1.0
N C:SER292 3.2 17.7 1.0
CB C:ARG278 3.7 16.3 1.0
O C:PHE290 3.7 19.7 1.0
CE C:LYS262 3.7 20.0 1.0
O C:SER292 3.8 18.7 1.0
CD C:ARG278 3.9 15.2 1.0
CD1 C:ILE280 3.9 31.2 1.0
CA C:LEU291 4.0 17.9 1.0
CA C:SER292 4.1 19.1 1.0
C C:LEU291 4.1 17.5 1.0
CB C:SER292 4.1 19.5 1.0
CD1 C:LEU291 4.1 20.0 1.0
CG C:ARG278 4.3 15.5 1.0
C C:SER292 4.4 20.1 1.0
OG C:SER292 4.4 18.6 1.0
C C:PHE290 4.6 20.0 1.0
CG1 C:ILE280 4.7 24.2 1.0
N C:LEU291 4.8 20.0 1.0
CA C:ARG278 4.8 17.0 1.0
O C:HOH650 4.8 11.9 1.0
N C:ARG278 4.8 19.2 1.0
O C:ARG278 4.8 13.7 1.0

Chlorine binding site 5 out of 5 in 5k8b

Go back to Chlorine Binding Sites List in 5k8b
Chlorine binding site 5 out of 5 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

A full contact list of Chlorine with other atoms in the Cl binding site number 5 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:
probe atom residue distance (Å) B Occ
D:Cl502

b:16.7
occ:1.00
 NZ D:LYS262 3.0 19.7 1.0
O D:HOH709 3.1 14.6 1.0
N D:SER292 3.1 15.7 1.0
O D:HOH637 3.2 19.4 1.0
CE D:LYS262 3.5 20.9 1.0
CB D:ARG278 3.7 17.4 1.0
O D:SER292 3.7 19.9 1.0
CD D:ARG278 3.8 14.6 1.0
O D:PHE290 3.9 17.9 1.0
CA D:LEU291 3.9 14.8 1.0
CB D:SER292 4.0 15.8 1.0
CA D:SER292 4.0 16.4 1.0
C D:LEU291 4.0 15.2 1.0
CD1 D:LEU291 4.0 12.7 1.0
CD1 D:ILE280 4.1 23.6 1.0
CG D:ARG278 4.2 15.4 1.0
C D:SER292 4.3 18.6 1.0
OG D:SER292 4.6 17.7 1.0
C D:PHE290 4.6 15.0 1.0
N D:LEU291 4.7 13.8 1.0
O D:ARG278 4.7 18.3 1.0
CA D:ARG278 4.8 18.4 1.0
N D:ARG278 4.8 19.4 1.0
CG1 D:ILE280 4.8 19.4 1.0
CG D:LEU291 4.9 13.8 1.0
CB D:LEU291 5.0 14.0 1.0
CD D:LYS262 5.0 21.4 1.0

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: Sat Jul 12 03:55:10 2025

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