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Vanadium in PDB 4dz6: Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp

Enzymatic activity of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp

All present enzymatic activity of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp:
2.7.4.6;

Protein crystallography data

The structure of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp, PDB code: 4dz6 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.47 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.650, 81.000, 181.430, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.3

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp (pdb code 4dz6). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 6 binding sites of Vanadium where determined in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp, PDB code: 4dz6:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6;

Vanadium binding site 1 out of 6 in 4dz6

Go back to Vanadium Binding Sites List in 4dz6
Vanadium binding site 1 out of 6 in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V1002

b:55.0
occ:0.75
 V A:VN41002 0.0 55.0 0.8
O3 A:VN41002 1.9 51.5 0.8
O1 A:VN41002 1.9 42.7 0.8
O2 A:VN41002 1.9 42.9 0.8
O3B A:ADP1001 2.0 37.6 0.8
ND1 A:HIS134 2.5 25.1 1.0
PB A:ADP1001 3.2 39.2 0.8
CE1 A:HIS134 3.3 26.0 1.0
O1B A:ADP1001 3.4 41.5 0.8
CG A:HIS134 3.5 25.0 1.0
O3' A:ADP1001 3.8 35.4 0.8
CB A:HIS134 3.9 24.4 1.0
CA A:HIS134 4.0 24.4 1.0
O1A A:ADP1001 4.1 39.1 0.8
C5' A:ADP1001 4.1 38.9 0.8
O3A A:ADP1001 4.2 39.9 0.8
O2B A:ADP1001 4.2 35.6 0.8
N A:ALA135 4.2 24.7 1.0
O A:ALA135 4.3 26.2 1.0
NH2 A:ARG111 4.3 26.6 1.0
OH A:TYR53 4.4 40.1 1.0
NE2 A:HIS134 4.4 26.1 1.0
NH2 A:ARG94 4.5 40.5 1.0
NZ A:LYS13 4.5 32.8 1.0
CD2 A:HIS134 4.6 24.7 1.0
C4' A:ADP1001 4.6 38.6 0.8
C A:HIS134 4.7 24.8 1.0
C3' A:ADP1001 4.7 38.7 0.8
PA A:ADP1001 4.7 39.8 0.8
CE1 A:TYR53 4.8 37.7 1.0
O5' A:ADP1001 4.9 39.3 0.8
CE A:LYS13 5.0 31.4 1.0

Vanadium binding site 2 out of 6 in 4dz6

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Vanadium binding site 2 out of 6 in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:V201

b:51.8
occ:0.75
 V B:VO4201 0.0 51.8 0.8
O4 B:VO4201 1.9 40.3 0.8
O1 B:VO4201 1.9 50.6 0.8
O3 B:VO4201 1.9 43.9 0.8
O2 B:VO4201 1.9 43.6 0.8
ND1 B:HIS134 2.7 27.3 1.0
CE1 B:HIS134 3.5 26.7 1.0
CG B:HIS134 3.7 25.4 1.0
CB B:HIS134 4.0 24.8 1.0
NZ B:LYS13 4.1 28.3 1.0
OH B:TYR53 4.2 26.7 1.0
CA B:HIS134 4.2 24.9 1.0
CE1 B:TYR53 4.4 26.8 1.0
N B:ALA135 4.6 25.4 1.0
NH2 B:ARG111 4.6 28.0 1.0
NE2 B:HIS134 4.7 26.1 1.0
CE B:LYS13 4.7 28.6 1.0
O B:ALA135 4.8 27.1 1.0
CZ B:TYR53 4.8 27.1 1.0
CD2 B:HIS134 4.8 25.0 1.0
NH2 B:ARG94 4.9 43.3 1.0
C B:HIS134 5.0 24.7 1.0

Vanadium binding site 3 out of 6 in 4dz6

Go back to Vanadium Binding Sites List in 4dz6
Vanadium binding site 3 out of 6 in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:V1002

b:55.2
occ:0.75
 V C:VN41002 0.0 55.2 0.8
O3 C:VN41002 1.9 46.4 0.8
O1 C:VN41002 1.9 46.1 0.8
O1B C:ADP1001 1.9 44.4 0.8
O2 C:VN41002 1.9 56.2 0.8
ND1 C:HIS134 2.5 33.0 1.0
PB C:ADP1001 3.0 49.0 0.8
O3B C:ADP1001 3.2 50.2 0.8
CE1 C:HIS134 3.4 33.5 1.0
CG C:HIS134 3.5 32.1 1.0
O3' C:ADP1001 3.6 37.0 0.8
CB C:HIS134 3.8 30.6 1.0
CA C:HIS134 4.0 30.2 1.0
O2B C:ADP1001 4.0 45.4 0.8
O1A C:ADP1001 4.1 43.0 0.8
C5' C:ADP1001 4.1 43.0 0.8
O3A C:ADP1001 4.2 47.6 0.8
NH2 C:ARG111 4.2 30.4 1.0
N C:ALA135 4.2 31.0 1.0
NH2 C:ARG94 4.4 44.1 1.0
C3' C:ADP1001 4.5 41.5 0.8
O C:ALA135 4.5 31.3 1.0
OH C:TYR53 4.5 44.0 1.0
C4' C:ADP1001 4.5 42.5 0.8
NZ C:LYS13 4.5 29.4 1.0
NE2 C:HIS134 4.6 33.5 1.0
CD2 C:HIS134 4.6 32.3 1.0
C C:HIS134 4.6 30.8 1.0
PA C:ADP1001 4.7 45.3 0.8
CE1 C:TYR53 4.8 43.1 1.0
O5' C:ADP1001 4.9 42.9 0.8
CE C:LYS13 4.9 30.1 1.0
O C:ILE133 5.0 29.8 1.0

Vanadium binding site 4 out of 6 in 4dz6

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Vanadium binding site 4 out of 6 in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V1002

b:59.7
occ:0.75
 V D:VN41002 0.0 59.7 0.8
O3 D:VN41002 1.9 49.4 0.8
O1 D:VN41002 1.9 58.7 0.8
O2 D:VN41002 1.9 54.5 0.8
O3B D:ADP1001 2.0 48.4 0.8
ND1 D:HIS134 2.4 31.1 1.0
PB D:ADP1001 3.1 48.9 0.8
CE1 D:HIS134 3.3 31.3 1.0
O2B D:ADP1001 3.3 48.6 0.8
O3' D:ADP1001 3.3 40.7 0.8
CG D:HIS134 3.5 29.5 1.0
C5' D:ADP1001 3.6 51.8 0.8
CB D:HIS134 3.8 29.4 1.0
OH D:TYR53 3.9 40.4 1.0
C4' D:ADP1001 4.0 49.5 0.8
O3A D:ADP1001 4.1 52.5 0.8
O2A D:ADP1001 4.1 50.9 0.8
CA D:HIS134 4.1 28.4 1.0
C3' D:ADP1001 4.1 49.1 0.8
O1B D:ADP1001 4.2 47.2 0.8
CE1 D:TYR53 4.3 41.7 1.0
NZ D:LYS13 4.4 36.0 1.0
NE2 D:HIS134 4.5 32.2 1.0
PA D:ADP1001 4.5 53.4 0.8
O5' D:ADP1001 4.5 50.2 0.8
N D:ALA135 4.5 29.6 1.0
CD2 D:HIS134 4.6 30.6 1.0
NH2 D:ARG111 4.6 29.9 1.0
CZ D:TYR53 4.6 42.1 1.0
O D:ALA135 4.7 33.5 1.0
CE D:LYS13 4.7 35.3 1.0
C D:HIS134 4.9 29.2 1.0

Vanadium binding site 5 out of 6 in 4dz6

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Vanadium binding site 5 out of 6 in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:V201

b:42.6
occ:0.75
 V E:VO4201 0.0 42.6 0.8
O3 E:VO4201 1.9 38.1 0.8
O4 E:VO4201 1.9 37.0 0.8
O2 E:VO4201 2.0 42.8 0.8
O1 E:VO4201 2.0 38.3 0.8
ND1 E:HIS134 2.4 32.8 1.0
CE1 E:HIS134 3.2 33.8 1.0
CG E:HIS134 3.4 32.5 1.0
CB E:HIS134 3.7 32.1 1.0
CA E:HIS134 4.0 31.8 1.0
OH E:TYR53 4.1 47.1 1.0
N E:ALA135 4.3 32.5 1.0
CE1 E:TYR53 4.4 46.1 1.0
NE2 E:HIS134 4.4 33.6 1.0
NZ E:LYS13 4.5 33.9 1.0
CD2 E:HIS134 4.5 32.5 1.0
O E:ALA135 4.5 35.7 1.0
NH2 E:ARG111 4.6 34.2 1.0
C E:HIS134 4.7 32.6 1.0
NH1 E:ARG94 4.7 50.5 1.0
CZ E:TYR53 4.7 47.8 1.0
CE E:LYS13 4.8 33.5 1.0

Vanadium binding site 6 out of 6 in 4dz6

Go back to Vanadium Binding Sites List in 4dz6
Vanadium binding site 6 out of 6 in the Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of Transition State Mimic of Nucleoside-Diphosphate Kinase From Borrelia Burgdorferi with Bound Vanadate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:V201

b:59.6
occ:0.75
 V F:VO4201 0.0 59.6 0.8
O2 F:VO4201 1.9 48.6 0.8
O4 F:VO4201 1.9 53.0 0.8
O1 F:VO4201 1.9 47.7 0.8
O3 F:VO4201 1.9 54.5 0.8
ND1 F:HIS134 2.9 37.0 1.0
CE1 F:HIS134 3.7 36.7 1.0
CG F:HIS134 3.9 35.9 1.0
CB F:HIS134 4.1 35.0 1.0
NZ F:LYS13 4.2 38.2 1.0
CA F:HIS134 4.3 34.5 1.0
NH2 F:ARG111 4.3 36.9 1.0
OH F:TYR53 4.4 54.7 1.0
NH1 F:ARG94 4.6 53.3 1.0
CE1 F:TYR53 4.7 51.7 1.0
N F:ALA135 4.7 33.7 1.0
CE F:LYS13 4.7 36.5 1.0
O F:ALA135 4.8 35.9 1.0
NE2 F:HIS134 4.9 35.5 1.0
O F:ILE133 4.9 35.3 1.0
CD2 F:HIS134 5.0 35.9 1.0

Reference:

M.Dumais, D.R.Davies, T.Lin, B.L.Staker, P.J.Myler, W.C.Van Voorhis. Structure and Analysis of Nucleoside Diphosphate Kinase From Borrelia Burgdorferi Prepared in A Transition-State Complex with Adp and Vanadate Moieties. Acta Crystallogr F Struct V. 74 373 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29870023
DOI: 10.1107/S2053230X18007392
Page generated: Fri Oct 11 19:35:36 2024

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