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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: Wed Dec 16 02:30:37 2020

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