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Manganese in PDB 2g8i: B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ 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 MN2+ 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 MN2+ 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 MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8i 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 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.118, 37.084, 61.772, 90.00, 96.53, 90.00
R / Rfree (%) 17.3 / 20.2

Other elements in 2g8i:

The structure of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) (pdb code 2g8i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8i:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 2g8i

Go back to Manganese Binding Sites List in 2g8i
Manganese binding site 1 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:10.8
occ:1.00
 O B:HOH61 2.0 7.5 1.0
OD1 A:ASP71 2.1 8.5 1.0
OE2 A:GLU109 2.1 9.3 1.0
OD1 A:ASP132 2.3 10.7 1.0
O3' B:A6 2.3 9.5 1.0
OD2 A:ASP132 2.8 12.2 1.0
CG A:ASP132 2.9 10.5 1.0
CD A:GLU109 3.0 12.7 1.0
CG A:ASP71 3.1 11.3 1.0
OE1 A:GLU109 3.2 12.3 1.0
OD2 A:ASP71 3.5 9.7 1.0
C3' B:A6 3.6 9.8 1.0
MN A:MN402 3.6 13.2 1.0
O A:HOH512 3.7 7.9 1.0
O A:HOH505 3.7 14.5 1.0
O2' B:A6 3.9 10.4 1.0
C4' B:A6 4.0 11.5 1.0
C2' B:A6 4.3 10.5 1.0
CG1 A:VAL72 4.3 10.9 1.0
CB A:ASP132 4.4 9.6 1.0
CB A:ASP71 4.4 9.8 1.0
CG A:GLU109 4.5 9.6 1.0
N A:VAL72 4.5 10.1 1.0
O B:HOH87 4.6 22.9 1.0
C5' B:A6 4.6 11.9 1.0
O A:HOH503 4.8 14.1 1.0
CA A:ASP71 4.8 9.8 1.0
O A:VAL72 4.8 10.6 1.0
O A:HOH559 4.9 11.3 1.0
C A:ASP132 5.0 10.5 1.0

Manganese binding site 2 out of 4 in 2g8i

Go back to Manganese Binding Sites List in 2g8i
Manganese binding site 2 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:13.2
occ:1.00
 O B:HOH61 2.0 7.5 1.0
O A:HOH505 2.1 14.5 1.0
OD1 A:ASN192 2.1 13.7 1.0
OD2 A:ASP71 2.2 9.7 1.0
O A:HOH559 2.2 11.3 1.0
O A:HOH503 2.3 14.1 1.0
CG A:ASP71 3.2 11.3 1.0
CG A:ASN192 3.3 14.1 1.0
OD1 A:ASP71 3.5 8.5 1.0
MN A:MN401 3.6 10.8 1.0
CB A:ASN192 3.9 13.9 1.0
CA A:ASN192 3.9 13.2 1.0
O A:VAL72 4.0 10.6 1.0
N A:TYR193 4.0 16.4 1.0
O B:HOH87 4.1 22.9 1.0
O3' B:A6 4.1 9.5 1.0
OD2 A:ASP132 4.1 12.2 1.0
OE2 A:GLU188 4.3 24.2 1.0
N A:GLY194 4.3 26.8 1.0
ND2 A:ASN192 4.4 14.5 1.0
O A:HOH504 4.4 28.6 1.0
CB A:ASP71 4.5 9.8 1.0
C A:ASN192 4.5 15.2 1.0
CG2 A:ILE189 4.8 11.0 1.0
CA A:GLY194 4.9 30.8 1.0

Manganese binding site 3 out of 4 in 2g8i

Go back to Manganese Binding Sites List in 2g8i
Manganese binding site 3 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:17.6
occ:1.00
 O A:HOH673 2.0 18.3 1.0
OE2 A:GLU166 2.1 13.3 1.0
O A:HOH638 2.2 13.1 1.0
O A:HOH718 2.2 15.7 1.0
OD1 A:ASP163 2.2 16.5 1.0
O A:HOH577 2.3 17.7 1.0
CD A:GLU166 3.1 14.6 1.0
CG A:ASP163 3.4 15.6 1.0
OE1 A:GLU166 3.4 14.3 1.0
NZ A:LYS144 3.9 29.0 1.0
NH2 A:ARG151 3.9 14.9 1.0
CB A:ASP163 4.1 10.5 1.0
CA A:ASP163 4.1 10.6 1.0
O A:HOH536 4.2 13.5 1.0
OD2 A:ASP163 4.2 15.1 1.0
O A:HOH656 4.3 28.5 1.0
O A:HOH675 4.4 21.8 1.0
O A:HOH620 4.4 27.9 1.0
CG A:GLU166 4.5 11.9 1.0
CB A:GLU166 4.7 12.3 1.0
N A:ASP163 4.9 10.4 1.0
CE A:LYS144 4.9 28.8 1.0
CD A:LYS144 4.9 26.1 1.0

Manganese binding site 4 out of 4 in 2g8i

Go back to Manganese Binding Sites List in 2g8i
Manganese binding site 4 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with MN2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:84.0
occ:1.00
 OE1 A:GLU96 2.2 31.2 1.0
O A:HOH605 2.2 30.9 1.0
OE2 A:GLU82 2.2 25.3 1.0
O A:HOH648 2.4 35.3 1.0
CD A:GLU96 3.0 30.2 1.0
CD A:GLU82 3.1 24.3 1.0
CG A:GLU96 3.5 25.3 1.0
OE1 A:GLU82 3.6 27.1 1.0
OE2 A:GLU96 4.0 32.3 1.0
OH A:TYR193 4.1 11.2 1.0
CE2 A:TYR193 4.2 13.1 1.0
CG A:GLU82 4.2 17.7 1.0
O A:HOH686 4.3 43.6 1.0
CB A:GLU82 4.5 13.4 1.0
O A:ARG97 4.5 12.6 1.0
CZ A:TYR193 4.7 13.7 1.0
O A:HOH585 4.9 62.5 1.0
CB A:GLU96 4.9 18.6 1.0
CG A:PRO99 4.9 13.5 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: Sat Oct 5 14:09:30 2024

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