Atomistry » Vanadium » PDB 1z12-3myh » 2g8h
Atomistry »
  Vanadium »
    PDB 1z12-3myh »
      2g8h »

Vanadium in PDB 2g8h: B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)

Enzymatic activity of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)

All present enzymatic activity of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site):
3.1.26.4;

Protein crystallography data

The structure of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8h was solved by M.Nowotny, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.441, 36.964, 61.810, 90.00, 96.38, 90.00
R / Rfree (%) 20.6 / 25.4

Other elements in 2g8h:

The structure of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) (pdb code 2g8h). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 6 binding sites of Vanadium where determined in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8h:
Jump to Vanadium binding site number: 1; 2; 3; 4; 5; 6;

Vanadium binding site 1 out of 6 in 2g8h

Go back to Vanadium Binding Sites List in 2g8h
Vanadium binding site 1 out of 6 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V401

b:28.4
occ:1.00
V A:VO4401 0.0 28.4 1.0
O1 A:VO4401 1.7 32.6 1.0
O2 A:VO4401 1.7 32.4 1.0
O4 A:VO4401 1.7 33.6 1.0
O3 A:VO4401 1.7 30.9 1.0
O1 A:VO4406 2.6 37.4 1.0
V A:VO4402 3.0 23.1 1.0
V A:VO4403 3.1 32.6 1.0
V A:VO4406 3.1 27.4 1.0
V A:VO4404 3.2 26.4 1.0
O3 A:VO4402 3.4 33.5 1.0
O1 A:VO4403 3.5 32.8 1.0
O2 A:VO4402 3.9 33.6 1.0
NE2 A:HIS172 4.0 29.4 1.0
O2 A:VO4404 4.1 30.2 1.0
NE1 A:TRP168 4.1 24.6 1.0
O2 A:VO4406 4.2 37.6 1.0
O1 A:VO4404 4.4 33.9 1.0
O1 A:VO4402 4.4 33.1 1.0
O2 A:VO4403 4.5 32.8 1.0
V A:VO4405 4.5 26.7 1.0
O A:HOH478 4.6 68.1 1.0
CD1 A:TRP168 4.7 25.0 1.0
CD2 A:HIS172 4.8 28.2 1.0
CE1 A:HIS172 4.9 27.9 1.0

Vanadium binding site 2 out of 6 in 2g8h

Go back to Vanadium Binding Sites List in 2g8h
Vanadium binding site 2 out of 6 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V402

b:23.1
occ:1.00
V A:VO4402 0.0 23.1 1.0
O1 A:VO4402 1.7 33.1 1.0
O2 A:VO4402 1.7 33.6 1.0
O3 A:VO4402 1.7 33.5 1.0
O3 A:VO4401 1.7 30.9 1.0
O1 A:VO4405 2.9 32.4 1.0
V A:VO4401 3.0 28.4 1.0
V A:VO4403 3.0 32.6 1.0
O4 A:VO4401 3.2 33.6 1.0
V A:VO4404 3.2 26.4 1.0
V A:VO4405 3.3 26.7 1.0
O1 A:VO4401 3.3 32.6 1.0
O2 A:VO4404 3.4 30.2 1.0
O1 A:VO4403 4.0 32.8 1.0
O1 A:VO4404 4.2 33.9 1.0
O2 A:VO4403 4.2 32.8 1.0
V A:VO4406 4.4 27.4 1.0
CD2 A:HIS172 4.4 28.2 1.0
NE1 A:TRP168 4.5 24.6 1.0
O2 A:VO4401 4.5 32.4 1.0
CD A:LYS121 4.5 28.7 1.0
CB A:GLU122 4.6 26.2 1.0
NE2 A:HIS172 4.6 29.4 1.0
CA A:GLU122 4.6 24.9 1.0
O2 A:VO4405 4.6 37.5 1.0
CZ2 A:TRP168 4.7 23.6 1.0
N A:GLU122 4.7 24.0 1.0
CG A:LYS121 4.8 27.5 1.0
O A:ARG118 4.9 18.2 1.0
CE A:LYS121 4.9 32.5 1.0
CE2 A:TRP168 5.0 22.3 1.0

Vanadium binding site 3 out of 6 in 2g8h

Go back to Vanadium Binding Sites List in 2g8h
Vanadium binding site 3 out of 6 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 3 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V403

b:32.6
occ:1.00
V A:VO4403 0.0 32.6 1.0
O2 A:VO4403 1.7 32.8 1.0
O4 A:VO4401 1.7 33.6 1.0
O3 A:VO4402 1.7 33.5 1.0
O1 A:VO4403 1.7 32.8 1.0
V A:VO4406 3.0 27.4 1.0
V A:VO4402 3.0 23.1 1.0
V A:VO4401 3.1 28.4 1.0
V A:VO4405 3.2 26.7 1.0
O3 A:VO4401 3.2 30.9 1.0
O2 A:VO4405 3.4 37.5 1.0
O1 A:VO4405 3.4 32.4 1.0
O A:HOH517 3.4 92.9 1.0
O1 A:VO4406 3.6 37.4 1.0
O1 A:VO4401 3.9 32.6 1.0
O2 A:VO4402 4.0 33.6 1.0
O2 A:VO4404 4.0 30.2 1.0
NE2 A:HIS172 4.0 29.4 1.0
O2 A:VO4406 4.4 37.6 1.0
O1 A:VO4402 4.4 33.1 1.0
CD2 A:HIS172 4.4 28.2 1.0
V A:VO4404 4.4 26.4 1.0
O2 A:VO4401 4.4 32.4 1.0
O A:HOH478 4.5 68.1 1.0

Vanadium binding site 4 out of 6 in 2g8h

Go back to Vanadium Binding Sites List in 2g8h
Vanadium binding site 4 out of 6 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 4 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V404

b:26.4
occ:1.00
V A:VO4404 0.0 26.4 1.0
O1 A:VO4401 1.7 32.6 1.0
O1 A:VO4404 1.7 33.9 1.0
O2 A:VO4404 1.7 30.2 1.0
O2 A:VO4402 2.5 33.6 1.0
O2 A:VO4406 2.9 37.6 1.0
V A:VO4401 3.2 28.4 1.0
V A:VO4405 3.2 26.7 1.0
V A:VO4402 3.2 23.1 1.0
V A:VO4406 3.2 27.4 1.0
O3 A:VO4401 3.4 30.9 1.0
O1 A:VO4406 4.0 37.4 1.0
O1 A:VO4403 4.1 32.8 1.0
CB A:GLU122 4.2 26.2 1.0
O4 A:VO4401 4.2 33.6 1.0
O3 A:VO4402 4.2 33.5 1.0
O1 A:VO4405 4.2 32.4 1.0
V A:VO4403 4.4 32.6 1.0
O2 A:VO4401 4.5 32.4 1.0
O2 A:VO4405 4.5 37.5 1.0
OE1 A:GLU122 4.6 29.1 0.0
O1 A:VO4402 4.6 33.1 1.0
CD A:GLU122 4.9 28.6 0.0

Vanadium binding site 5 out of 6 in 2g8h

Go back to Vanadium Binding Sites List in 2g8h
Vanadium binding site 5 out of 6 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 5 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V405

b:26.7
occ:1.00
V A:VO4405 0.0 26.7 1.0
O1 A:VO4405 1.7 32.4 1.0
O2 A:VO4405 1.7 37.5 1.0
O2 A:VO4404 1.7 30.2 1.0
O2 A:VO4402 2.6 33.6 1.0
O1 A:VO4403 2.8 32.8 1.0
O3 A:VO4402 3.0 33.5 1.0
V A:VO4404 3.2 26.4 1.0
V A:VO4403 3.2 32.6 1.0
V A:VO4402 3.3 23.1 1.0
V A:VO4406 3.3 27.4 1.0
O2 A:VO4406 3.3 37.6 1.0
O1 A:VO4401 4.0 32.6 1.0
O A:HOH517 4.2 92.9 1.0
O4 A:VO4401 4.3 33.6 1.0
O3 A:VO4401 4.4 30.9 1.0
O2 A:VO4403 4.4 32.8 1.0
V A:VO4401 4.5 28.4 1.0
O1 A:VO4404 4.5 33.9 1.0
O1 A:VO4402 4.6 33.1 1.0
CB A:GLU122 4.7 26.2 1.0
CA A:GLU122 4.7 24.9 1.0
O1 A:VO4406 4.9 37.4 1.0

Vanadium binding site 6 out of 6 in 2g8h

Go back to Vanadium Binding Sites List in 2g8h
Vanadium binding site 6 out of 6 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 6 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MG2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V406

b:27.4
occ:1.00
V A:VO4406 0.0 27.4 1.0
O2 A:VO4406 1.7 37.6 1.0
O1 A:VO4406 1.7 37.4 1.0
O1 A:VO4403 1.7 32.8 1.0
O1 A:VO4401 2.7 32.6 1.0
O4 A:VO4401 2.9 33.6 1.0
V A:VO4403 3.0 32.6 1.0
O2 A:VO4404 3.0 30.2 1.0
V A:VO4401 3.1 28.4 1.0
V A:VO4404 3.2 26.4 1.0
V A:VO4405 3.3 26.7 1.0
O2 A:VO4405 3.4 37.5 1.0
O3 A:VO4402 4.1 33.5 1.0
O2 A:VO4401 4.2 32.4 1.0
O3 A:VO4401 4.3 30.9 1.0
V A:VO4402 4.4 23.1 1.0
O2 A:VO4403 4.5 32.8 1.0
O2 A:VO4402 4.6 33.6 1.0
O A:HOH517 4.6 92.9 1.0
O1 A:VO4405 4.7 32.4 1.0
O1 A:VO4404 4.9 33.9 1.0

Reference:

M.Nowotny, W.Yang. Stepwise Analyses of Metal Ions in Rnase H Catalysis From Substrate Destabilization to Product Release. Embo J. V. 25 1924 2006.
ISSN: ISSN 0261-4189
PubMed: 16601679
DOI: 10.1038/SJ.EMBOJ.7601076
Page generated: Thu Oct 29 07:04:46 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy