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Calcium in PDB 2g8k: B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ 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 CA2+ 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 CA2+ 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 CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8k 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 (°) 82.052, 36.925, 61.860, 90.00, 96.30, 90.00
R / Rfree (%) 18.2 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) (pdb code 2g8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site), PDB code: 2g8k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2g8k

Go back to Calcium Binding Sites List in 2g8k
Calcium binding site 1 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:13.7
occ:1.00
 OD1 A:ASP71 2.3 10.2 1.0
OD1 A:ASP132 2.4 12.6 1.0
OE2 A:GLU109 2.4 10.5 1.0
O3' B:A6 2.4 12.7 1.0
OD2 A:ASP132 2.4 13.9 1.0
O A:HOH514 2.4 12.2 1.0
CG A:ASP132 2.7 11.3 1.0
O A:HOH406 2.8 12.3 1.0
CG A:ASP71 3.2 12.3 1.0
CD A:GLU109 3.3 12.1 1.0
OE1 A:GLU109 3.5 12.3 1.0
C3' B:A6 3.7 11.5 1.0
OD2 A:ASP71 3.7 13.7 1.0
C4' B:A6 4.0 12.0 1.0
O2' B:A6 4.1 13.0 1.0
CB A:ASP132 4.2 11.2 1.0
CB A:ASP71 4.4 11.1 1.0
C5' B:A6 4.5 11.6 1.0
C2' B:A6 4.5 12.3 1.0
O A:HOH510 4.6 25.8 1.0
CG2 A:ILE189 4.7 12.8 1.0
CG A:GLU109 4.7 11.7 1.0
CA A:ASP71 4.7 9.9 1.0
N A:VAL72 4.8 11.4 1.0
O B:HOH252 4.8 48.6 1.0
N A:ASP132 4.9 11.5 1.0
O A:HOH415 4.9 15.8 1.0
O A:HOH472 5.0 30.3 1.0
CA A:ASP132 5.0 11.2 1.0
CG1 A:VAL72 5.0 12.4 1.0

Calcium binding site 2 out of 4 in 2g8k

Go back to Calcium Binding Sites List in 2g8k
Calcium binding site 2 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:16.9
occ:1.00
 O A:HOH476 2.3 28.0 1.0
O A:HOH472 2.4 30.3 1.0
O A:TYR193 2.4 22.0 1.0
OD1 A:ASN192 2.4 17.1 1.0
O A:HOH408 2.4 20.4 1.0
O A:HOH409 2.5 15.8 1.0
CG A:ASN192 3.4 18.4 1.0
C A:TYR193 3.5 20.9 1.0
ND2 A:ASN192 3.9 20.1 1.0
N A:TYR193 3.9 18.6 1.0
O A:HOH599 4.1 46.3 1.0
O A:HOH514 4.1 12.2 1.0
O A:HOH585 4.2 47.7 1.0
CA A:TYR193 4.3 20.1 1.0
OE2 A:GLU188 4.3 33.4 1.0
O A:ARG195 4.5 27.8 1.0
OD2 A:ASP71 4.5 13.7 1.0
N A:GLY194 4.6 23.9 1.0
CB A:TYR193 4.6 17.9 1.0
CB A:ASN192 4.7 17.4 1.0
CA A:GLY194 4.7 24.6 1.0
O A:GLY194 4.8 25.2 1.0
C A:GLY194 4.8 25.8 1.0
C A:ASN192 4.9 18.6 1.0
O A:HOH510 4.9 25.8 1.0
O B:HOH252 5.0 48.6 1.0
O A:VAL72 5.0 11.6 1.0

Calcium binding site 3 out of 4 in 2g8k

Go back to Calcium Binding Sites List in 2g8k
Calcium binding site 3 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:18.3
occ:1.00
 OH A:TYR83 3.0 15.1 1.0
O A:HOH439 3.1 20.7 1.0
O A:HOH422 3.2 15.7 1.0
O A:HOH414 3.2 18.4 1.0
CE2 A:TYR83 3.8 12.3 1.0
O A:HOH482 3.9 28.7 1.0
CZ A:TYR83 3.9 12.7 1.0
CD2 A:LEU111 3.9 11.2 1.0
CD2 A:LEU161 4.1 12.6 1.0
CB A:LEU161 4.1 12.8 1.0
CB A:LEU111 4.2 9.8 1.0
CD1 A:LEU161 4.2 14.8 1.0
CD1 A:LEU111 4.2 13.5 1.0
CG A:LEU111 4.3 11.0 1.0
CG A:LEU161 4.4 13.5 1.0
O A:HOH432 4.5 19.1 1.0
CD A:ARG97 4.6 15.3 1.0
O A:HOH425 4.7 24.1 1.0
O A:LEU111 4.8 9.7 1.0
NH1 A:ARG97 4.9 20.7 1.0
O A:HOH595 5.0 43.5 1.0
O A:LEU161 5.0 13.8 1.0

Calcium binding site 4 out of 4 in 2g8k

Go back to Calcium Binding Sites List in 2g8k
Calcium binding site 4 out of 4 in the B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of B. Halodurans Rnase H Catalytic Domain D192N Mutant in Complex with CA2+ and Rna/Dna Hybrid (Non-P Nick at the Active Site) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:41.3
occ:1.00
 O A:HOH416 2.7 16.6 1.0
O A:HOH502 2.7 27.4 1.0
O A:HOH433 2.8 22.6 1.0
O A:HOH417 2.9 21.1 1.0
CD1 A:ILE178 3.5 17.9 1.0
CA A:LYS141 3.8 17.7 1.0
N A:LYS141 4.1 14.6 1.0
O A:HOH423 4.1 19.9 1.0
O A:HOH430 4.1 21.9 1.0
CG1 A:VAL140 4.1 13.3 1.0
CG1 A:ILE178 4.2 13.7 1.0
CB A:LYS141 4.3 18.4 1.0
O A:HOH530 4.3 28.3 1.0
C A:VAL140 4.4 14.6 1.0
O A:VAL140 4.4 15.9 1.0
CE1 A:TYR174 4.5 20.1 1.0
O A:HOH528 4.5 37.4 1.0
O A:HOH450 4.5 31.4 1.0
CB A:ILE178 4.6 13.3 1.0
OH A:TYR174 4.7 23.1 1.0
O A:HOH581 4.8 48.0 1.0
CG A:LYS141 4.8 24.0 1.0
CB A:VAL140 4.8 11.6 1.0
C A:LYS141 5.0 17.6 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: Tue Jul 8 05:42:28 2025

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