Chlorine in PDB 7owh: Odinarchaeota Adenylate Kinase (Odinak) Native Structure

Enzymatic activity of Odinarchaeota Adenylate Kinase (Odinak) Native Structure

All present enzymatic activity of Odinarchaeota Adenylate Kinase (Odinak) Native Structure:
2.7.4.3;

Protein crystallography data

The structure of Odinarchaeota Adenylate Kinase (Odinak) Native Structure, PDB code: 7owh was solved by E.Aberg-Zingmark, C.Grundstrom, A.Verma, M.Wolf-Watz, U.H.Sauer, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.08 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.761, 77.772, 217.611, 90, 90, 90
R / Rfree (%) 19.5 / 24.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure (pdb code 7owh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure, PDB code: 7owh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7owh

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Chlorine binding site 1 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:48.6
occ:1.00
 N A:GLY12 3.1 31.0 1.0
N A:THR14 3.3 31.6 1.0
N A:LYS13 3.4 27.1 1.0
OG1 A:THR14 3.4 36.4 1.0
CA A:GLY12 3.5 37.3 1.0
O A:HOH347 3.5 29.4 1.0
C A:GLY12 3.6 38.3 1.0
CB A:THR14 3.6 35.7 1.0
O A:HOH388 3.6 36.9 1.0
N A:ALA11 3.8 31.2 1.0
C A:GLY10 3.9 31.3 1.0
CA A:GLY10 3.9 32.5 1.0
CA A:THR14 4.0 31.9 1.0
C A:ALA11 4.2 34.7 1.0
C A:LYS13 4.2 28.8 1.0
N A:GLY10 4.3 29.4 1.0
CA A:LYS13 4.3 30.7 1.0
O A:GLY12 4.5 30.3 1.0
N A:THR15 4.5 30.9 1.0
O A:GLY10 4.5 31.6 1.0
CA A:ALA11 4.6 32.6 1.0
CB A:LYS13 4.8 29.9 1.0
C A:THR14 4.8 28.5 1.0
CG2 A:THR14 5.0 42.3 1.0

Chlorine binding site 2 out of 8 in 7owh

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Chlorine binding site 2 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl201

b:68.9
occ:1.00
 N B:GLY12 3.1 45.9 1.0
O B:HOH354 3.3 38.5 1.0
N B:LYS13 3.3 44.4 1.0
O B:HOH317 3.4 47.8 1.0
N B:THR14 3.4 44.0 1.0
OG1 B:THR14 3.4 75.4 1.0
N B:ALA11 3.6 44.6 1.0
CA B:GLY12 3.6 52.4 1.0
CA B:GLY10 3.6 40.8 1.0
C B:GLY10 3.7 45.7 1.0
C B:GLY12 3.7 51.1 1.0
CB B:THR14 3.8 53.2 1.0
N B:GLY10 3.9 45.8 1.0
C B:ALA11 4.2 51.2 1.0
CA B:THR14 4.2 61.8 1.0
CA B:LYS13 4.3 44.1 1.0
C B:LYS13 4.3 44.0 1.0
O B:GLY10 4.4 51.1 1.0
CA B:ALA11 4.5 42.9 1.0
CB B:LYS13 4.6 43.1 1.0
O B:GLY12 4.6 45.1 1.0
N B:THR15 4.8 44.9 1.0

Chlorine binding site 3 out of 8 in 7owh

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Chlorine binding site 3 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:54.8
occ:1.00
 O C:HOH373 2.8 44.8 1.0
OG1 C:THR14 3.1 46.7 1.0
N C:THR14 3.2 41.8 1.0
O C:HOH342 3.3 40.6 1.0
N C:LYS13 3.3 39.7 1.0
N C:GLY12 3.4 38.9 1.0
CB C:THR14 3.6 45.7 1.0
C C:GLY12 3.8 35.0 1.0
CA C:GLY12 3.8 41.6 1.0
CA C:GLY10 3.9 43.8 1.0
N C:ALA11 3.9 44.7 1.0
C C:GLY10 4.0 43.6 1.0
CA C:THR14 4.0 38.6 1.0
N C:GLY10 4.1 36.1 1.0
CA C:LYS13 4.1 33.5 1.0
C C:LYS13 4.1 35.1 1.0
CB C:LYS13 4.3 37.0 1.0
O C:HOH301 4.4 45.2 1.0
C C:ALA11 4.5 42.8 1.0
O C:GLY12 4.6 36.9 1.0
CA C:ALA11 4.8 32.8 1.0
N C:THR15 4.8 37.9 1.0
O C:GLY10 4.8 39.1 1.0

Chlorine binding site 4 out of 8 in 7owh

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Chlorine binding site 4 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl201

b:48.1
occ:1.00
 O D:HOH312 2.9 57.0 1.0
N D:GLY12 3.1 34.8 1.0
N D:THR14 3.4 34.2 1.0
OG1 D:THR14 3.4 39.5 1.0
O D:HOH362 3.4 31.3 1.0
N D:LYS13 3.5 30.1 1.0
CA D:GLY12 3.5 36.4 1.0
O D:HOH402 3.6 39.4 1.0
CB D:THR14 3.6 45.1 1.0
C D:GLY12 3.6 32.2 1.0
N D:ALA11 3.8 33.6 1.0
CA D:GLY10 3.9 30.9 1.0
C D:GLY10 3.9 36.0 1.0
N D:GLY10 4.1 30.3 1.0
CA D:THR14 4.1 37.7 1.0
C D:ALA11 4.2 32.1 1.0
C D:LYS13 4.3 32.8 1.0
CA D:LYS13 4.4 32.3 1.0
O D:GLY12 4.5 34.0 1.0
O D:GLY10 4.6 37.9 1.0
CA D:ALA11 4.6 37.4 1.0
N D:THR15 4.7 32.9 1.0
NH2 D:ARG124 4.7 77.2 1.0
CB D:LYS13 4.8 30.3 1.0
C D:THR14 4.9 30.8 1.0
CG2 D:THR14 5.0 39.7 1.0

Chlorine binding site 5 out of 8 in 7owh

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Chlorine binding site 5 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl202

b:50.1
occ:1.00
 O D:HOH415 2.8 41.2 1.0
O D:HOH412 2.9 47.6 1.0
N D:ASP171 3.0 25.9 1.0
CA D:ILE170 3.7 30.2 1.0
OH D:TYR185 3.7 50.2 1.0
C D:ILE170 3.8 30.1 1.0
CA D:ASP171 3.9 25.6 1.0
CB D:ASP171 3.9 30.8 1.0
O D:ASP171 4.0 24.4 1.0
O D:HOH336 4.0 35.7 1.0
CG2 D:ILE170 4.0 25.4 1.0
O D:ILE169 4.0 27.3 1.0
CE2 D:TYR185 4.1 27.8 1.0
C D:ASP171 4.4 30.1 1.0
CB D:ILE170 4.4 25.5 1.0
CZ D:TYR185 4.4 40.7 1.0
O D:HOH399 4.7 51.0 1.0
N D:ILE170 4.7 27.5 1.0
C D:ILE169 4.8 25.5 1.0
O D:ILE170 4.9 26.4 1.0
CG1 D:ILE170 5.0 26.0 1.0

Chlorine binding site 6 out of 8 in 7owh

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Chlorine binding site 6 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:59.5
occ:1.00
 N E:GLY12 2.9 46.2 1.0
N E:LYS13 3.2 41.5 1.0
CA E:GLY12 3.3 49.5 1.0
N E:THR14 3.3 44.2 1.0
O E:HOH323 3.4 45.2 1.0
C E:GLY12 3.5 49.5 1.0
O E:HOH339 3.6 44.9 1.0
OG1 E:THR14 3.6 64.2 1.0
CB E:THR14 3.7 55.4 1.0
N E:ALA11 3.8 41.0 1.0
C E:GLY10 4.0 45.6 1.0
CA E:GLY10 4.1 40.4 1.0
CA E:THR14 4.1 54.1 1.0
C E:ALA11 4.1 42.9 1.0
CA E:LYS13 4.1 44.4 1.0
C E:LYS13 4.2 41.0 1.0
N E:GLY10 4.3 44.1 1.0
O E:GLY12 4.4 44.0 1.0
N E:THR15 4.4 44.6 1.0
CB E:LYS13 4.5 33.6 1.0
CA E:ALA11 4.6 45.1 1.0
O E:GLY10 4.6 46.7 1.0
C E:THR14 4.8 49.0 1.0

Chlorine binding site 7 out of 8 in 7owh

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Chlorine binding site 7 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl201

b:54.3
occ:1.00
 O F:VAL8 2.8 30.8 1.0
N F:ALA11 2.9 36.8 1.0
O F:HOH368 2.9 36.1 1.0
N F:LYS13 3.0 31.3 1.0
N F:GLY12 3.2 34.9 1.0
CB F:LYS13 3.2 31.2 1.0
N F:GLY10 3.3 33.8 1.0
O F:HOH365 3.4 32.1 1.0
CA F:ALA11 3.6 37.7 1.0
CA F:LYS13 3.7 30.5 1.0
C F:ALA11 3.7 38.7 1.0
C F:PRO9 3.7 31.7 1.0
CB F:ALA11 3.7 38.5 1.0
C F:GLY10 3.9 42.3 1.0
C F:VAL8 4.0 32.1 1.0
CA F:PRO9 4.0 36.8 1.0
C F:GLY12 4.0 37.0 1.0
CA F:GLY10 4.0 42.8 1.0
CA F:GLY12 4.1 35.6 1.0
CE2 F:PHE116 4.4 39.0 1.0
CE F:LYS13 4.4 45.8 1.0
O F:PRO9 4.4 32.2 1.0
N F:PRO9 4.5 33.8 1.0
N F:THR14 4.6 32.7 1.0
CZ F:PHE116 4.6 36.6 1.0
CG F:LYS13 4.6 33.0 1.0
C F:LYS13 4.7 35.5 1.0
O F:GLY7 4.8 28.4 1.0
O F:ALA11 4.8 35.3 1.0
C F:GLY7 4.8 25.8 1.0
N F:VAL8 5.0 26.9 1.0

Chlorine binding site 8 out of 8 in 7owh

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Chlorine binding site 8 out of 8 in the Odinarchaeota Adenylate Kinase (Odinak) Native Structure


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Odinarchaeota Adenylate Kinase (Odinak) Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl202

b:68.2
occ:1.00
 N F:SER46 2.9 60.9 1.0
C F:TYR44 3.2 60.2 1.0
N F:PRO45 3.4 54.7 1.0
CA F:TYR44 3.4 50.3 1.0
CB F:SER46 3.4 80.3 1.0
N F:ILE47 3.4 51.3 1.0
OG F:SER46 3.5 79.8 1.0
CA F:SER46 3.6 69.0 1.0
CD F:PRO45 3.7 60.5 1.0
O F:TYR44 3.7 56.5 1.0
CG1 F:ILE47 3.9 59.5 1.0
C F:PRO45 3.9 62.2 1.0
CB F:TYR44 4.0 58.2 1.0
C F:SER46 4.0 68.5 1.0
CA F:PRO45 4.2 60.8 1.0
CD1 F:ILE47 4.2 62.7 1.0
CB F:ILE47 4.4 64.2 1.0
CA F:ILE47 4.5 62.0 1.0
N F:TYR44 4.8 55.6 1.0
CG F:PRO45 4.8 67.4 1.0
CB F:PRO45 4.8 54.0 1.0
CD1 F:TYR44 4.9 57.2 1.0
O F:LEU43 4.9 56.8 1.0
CG F:TYR44 5.0 55.2 1.0

Reference:

A.Verma, E.Aberg-Zingmark, T.Sparrman, A.U.Mushtaq, P.Rogne, C.Grundstrom, R.Berntsson, U.H.Sauer, L.Backman, K.Nam, E.Sauer-Eriksson, M.Wolf-Watz. Insights Into the Evolution of Enzymatic Specificity and Catalysis: From Asgard Archaea to Human Adenylate Kinases. Sci Adv V. 8 M4089 2022.
ISSN: ESSN 2375-2548
PubMed: 36332013
DOI: 10.1126/SCIADV.ABM4089
Page generated: Tue Apr 4 21:06:02 2023

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