Atomistry » Vanadium » PDB 3omx-4zg4 » 4dz6
Atomistry »
  Vanadium »
    PDB 3omx-4zg4 »
      4dz6 »

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

Go back to Vanadium Binding Sites List in 4dz6
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

Go back to Vanadium Binding Sites List in 4dz6
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

Go back to Vanadium Binding Sites List in 4dz6
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

Last articles

As in 5HXD
As in 5J39
As in 5K6Z
As in 5IC5
As in 5HWA
As in 5HRS
As in 5HRN
As in 5HRR
As in 5HRP
As in 5HR7
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy