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Calcium in PDB 2qkk: Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid

Enzymatic activity of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid

All present enzymatic activity of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid:
3.1.26.4;

Protein crystallography data

The structure of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid, PDB code: 2qkk was solved by M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crouch, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 151.065, 176.200, 125.845, 90.00, 90.22, 90.00
R / Rfree (%) 21.2 / 26.9

Other elements in 2qkk:

The structure of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid (pdb code 2qkk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid, PDB code: 2qkk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 2qkk

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Calcium binding site 1 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:44.3
occ:1.00
 OP1 C:C6 2.1 22.8 1.0
O3' C:A5 2.4 22.7 1.0
OD2 A:ASP145 2.6 19.6 1.0
OD1 A:ASN210 2.6 31.4 1.0
P C:C6 2.7 22.5 1.0
OE1 A:GLU186 3.1 33.1 1.0
CG A:ASN210 3.1 28.8 1.0
ND2 A:ASN210 3.2 26.8 1.0
OE2 A:GLU186 3.3 33.9 1.0
CA A:CA1002 3.4 23.5 1.0
CG A:ASP145 3.4 20.9 1.0
O A:HOH2004 3.5 46.8 1.0
O A:HOH2007 3.5 64.5 1.0
CD A:GLU186 3.5 32.5 1.0
O2' C:A5 3.6 16.5 1.0
C5' C:C6 3.6 18.4 1.0
O5' C:C6 3.6 18.7 1.0
C3' C:A5 3.7 20.5 1.0
OD1 A:ASP145 3.7 20.5 1.0
O A:GLY146 3.9 27.1 1.0
OP2 C:C6 4.0 23.1 1.0
C4' C:A5 4.1 21.6 1.0
C2' C:A5 4.2 17.8 1.0
CB A:ASN210 4.5 26.5 1.0
O C:HOH15 4.5 35.6 1.0
O A:HOH2003 4.6 21.9 1.0
CB A:ASP145 4.7 20.6 1.0
N A:GLY146 4.7 24.1 1.0
C5' C:A5 4.8 23.6 1.0
CG A:GLU186 5.0 29.1 1.0

Calcium binding site 2 out of 14 in 2qkk

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Calcium binding site 2 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:23.5
occ:1.00
 OD1 A:ASP145 2.1 20.5 1.0
OP1 C:C6 2.1 22.8 1.0
O A:HOH2007 2.2 64.5 1.0
O A:HOH2003 2.2 21.9 1.0
OD1 A:ASP274 2.5 28.0 1.0
O C:HOH15 2.7 35.6 1.0
CG A:ASP145 3.1 20.9 1.0
OD2 A:ASP145 3.3 19.6 1.0
CA A:CA1001 3.4 44.3 1.0
CG A:ASP274 3.4 26.3 1.0
P C:C6 3.5 22.5 1.0
CB A:ASP274 3.6 26.7 1.0
OP2 C:C6 4.0 23.1 1.0
CA A:ASP274 4.2 25.4 1.0
ND2 A:ASN210 4.3 26.8 1.0
O A:GLY146 4.3 27.1 1.0
O5' C:C6 4.4 18.7 1.0
CB A:ASP145 4.4 20.6 1.0
O3' C:A5 4.5 22.7 1.0
OD2 A:ASP274 4.5 24.6 1.0
OP2 C:C7 4.5 25.1 1.0
C5' C:C6 4.6 18.4 1.0

Calcium binding site 3 out of 14 in 2qkk

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Calcium binding site 3 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1009

b:38.1
occ:1.00
 O B:HOH2004 2.1 2.6 1.0
OD1 B:ASP145 2.2 29.0 1.0
OD1 B:ASP274 2.4 48.8 1.0
OD1 B:ASN210 2.6 37.2 1.0
O B:HOH2002 2.6 41.2 1.0
O B:HOH2003 2.6 30.7 1.0
CG B:ASP145 3.2 30.1 1.0
CG B:ASN210 3.4 35.7 1.0
CG B:ASP274 3.6 46.7 1.0
CB B:ASN210 3.9 34.8 1.0
CB B:ASP145 3.9 31.1 1.0
OD2 B:ASP145 4.1 30.7 1.0
OP1 C:C13 4.2 22.9 1.0
OE2 B:GLU186 4.3 53.5 1.0
OD2 B:ASP274 4.4 47.6 1.0
ND2 B:ASN210 4.5 34.6 1.0
O3' C:U12 4.5 22.7 1.0
CB B:ASP274 4.6 44.8 1.0
CA B:ASP145 4.7 32.4 1.0
NH2 B:ARG278 4.7 39.5 1.0
C5' C:C13 4.9 26.7 1.0
N B:ASN210 4.9 32.2 1.0

Calcium binding site 4 out of 14 in 2qkk

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Calcium binding site 4 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1003

b:44.8
occ:1.00
 OD1 E:ASP274 1.9 55.4 1.0
OP1 G:C6 2.5 34.9 1.0
OD1 E:ASP145 2.8 41.1 1.0
CG E:ASP274 3.1 53.7 1.0
OD2 E:ASP145 3.4 39.8 1.0
CG E:ASP145 3.5 38.4 1.0
P G:C6 3.7 31.8 1.0
CA E:CA1004 3.7 68.3 1.0
O5' G:C6 3.7 32.2 1.0
CB E:ASP274 3.9 50.4 1.0
NH1 E:ARG278 3.9 62.7 1.0
O E:GLY146 3.9 37.0 1.0
C5' G:C6 4.0 31.4 1.0
OD2 E:ASP274 4.0 54.0 1.0
CA E:ASP274 4.2 46.9 1.0
NH2 E:ARG278 4.3 62.6 1.0
OP2 G:C6 4.5 32.2 1.0
CZ E:ARG278 4.5 60.7 1.0
OP2 G:C7 4.6 29.2 1.0
CB E:CYS147 4.8 44.0 1.0
O3' G:A5 4.8 31.4 1.0
CB E:ASP145 4.9 35.4 1.0
O E:ASP274 4.9 45.2 1.0
C E:GLY146 5.0 36.5 1.0

Calcium binding site 5 out of 14 in 2qkk

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Calcium binding site 5 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1004

b:68.3
occ:1.00
 OP1 G:C6 2.1 34.9 1.0
OD2 E:ASP145 2.5 39.8 1.0
O3' G:A5 2.7 31.4 1.0
OE1 E:GLU186 2.7 48.4 1.0
OD1 E:ASN210 2.8 41.9 1.0
P G:C6 2.9 31.8 1.0
OE2 E:GLU186 3.1 49.7 1.0
CD E:GLU186 3.2 48.6 1.0
CG E:ASN210 3.3 42.5 1.0
CG E:ASP145 3.4 38.4 1.0
ND2 E:ASN210 3.6 42.4 1.0
C5' G:C6 3.6 31.4 1.0
CA E:CA1003 3.7 44.8 1.0
O5' G:C6 3.8 32.2 1.0
O E:GLY146 3.8 37.0 1.0
OD1 E:ASP145 3.8 41.1 1.0
C3' G:A5 4.0 30.4 1.0
O2' G:A5 4.1 26.0 1.0
OP2 G:C6 4.2 32.2 1.0
O E:HOH1012 4.2 28.8 1.0
C4' G:A5 4.3 31.2 1.0
CB E:ASN210 4.4 41.8 1.0
N E:GLY146 4.4 33.4 1.0
CB E:ASP145 4.6 35.4 1.0
CG E:GLU186 4.6 45.5 1.0
C2' G:A5 4.7 29.3 1.0
CA E:ASP145 4.7 33.5 1.0
C E:GLY146 4.9 36.5 1.0

Calcium binding site 6 out of 14 in 2qkk

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Calcium binding site 6 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1013

b:32.4
occ:1.00
 OD1 F:ASP145 2.0 45.9 1.0
OD2 F:ASP274 2.5 53.0 1.0
ND2 F:ASN210 2.7 31.1 1.0
CG F:ASP145 2.8 43.8 1.0
CG F:ASN210 3.4 29.9 1.0
OD1 F:ASN210 3.4 25.7 1.0
CG F:ASP274 3.5 51.6 1.0
CB F:ASP145 3.5 41.5 1.0
OD2 F:ASP145 3.7 45.3 1.0
OD1 F:ASP274 3.8 50.6 1.0
O F:ASN270 4.4 42.5 1.0
O F:THR144 4.4 39.5 1.0
OE2 F:GLU186 4.5 51.3 1.0
CA F:ASP145 4.5 41.5 1.0
CB F:ASN210 4.7 32.7 1.0
CB F:ASP274 4.9 50.5 1.0
OP1 G:C13 4.9 28.6 1.0
N F:ASN210 4.9 35.6 1.0

Calcium binding site 7 out of 14 in 2qkk

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Calcium binding site 7 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1006

b:78.5
occ:1.00
 OP1 K:C6 2.2 60.7 1.0
OD1 I:ASP274 2.3 0.3 1.0
OD1 I:ASP145 2.4 79.2 1.0
O K:HOH26 3.0 46.8 1.0
CG I:ASP274 3.1 0.9 1.0
P K:C6 3.2 60.5 1.0
CG I:ASP145 3.3 79.6 1.0
OP2 K:C6 3.4 61.2 1.0
OD2 I:ASP145 3.5 79.8 1.0
O I:HOH76 3.7 37.5 1.0
CB I:ASP274 3.9 0.7 1.0
OD2 I:ASP274 3.9 0.1 1.0
O5' K:C6 4.0 60.7 1.0
OP2 K:C7 4.2 59.6 1.0
ND2 I:ASN210 4.3 76.1 1.0
OD1 I:ASN270 4.3 0.3 1.0
C5' K:C6 4.5 61.4 1.0
O3' K:A5 4.5 58.6 1.0
CA I:ASP274 4.6 99.9 1.0
CB I:ASP145 4.7 79.1 1.0
O I:GLY146 4.9 76.2 1.0

Calcium binding site 8 out of 14 in 2qkk

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Calcium binding site 8 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca1008

b:53.3
occ:1.00
 ND2 J:ASN210 2.0 58.6 1.0
OD1 J:ASP145 2.2 58.3 1.0
OD1 J:ASN210 2.4 58.5 1.0
OD1 J:ASP274 2.4 64.3 1.0
CG J:ASN210 2.5 59.0 1.0
CG J:ASP145 2.7 59.1 1.0
CB J:ASP145 3.1 59.6 1.0
CG J:ASP274 3.2 63.0 1.0
OD2 J:ASP274 3.3 63.2 1.0
OD2 J:ASP145 3.7 56.3 1.0
OE2 J:GLU186 3.9 70.1 1.0
CB J:ASN210 4.0 58.0 1.0
CA J:ASP145 4.1 60.3 1.0
O J:ASN270 4.2 66.9 1.0
O J:THR144 4.3 64.2 1.0
N J:ASN210 4.6 59.5 1.0
CB J:ASP274 4.6 61.8 1.0
OE1 J:GLU186 4.7 71.1 1.0
CD J:GLU186 4.7 70.5 1.0
CA J:ASN210 4.9 58.4 1.0
OP1 K:C13 4.9 59.3 1.0
CA J:ASP274 5.0 60.8 1.0

Calcium binding site 9 out of 14 in 2qkk

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Calcium binding site 9 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca1010

b:38.3
occ:1.00
 OD1 M:ASP274 2.2 55.7 1.0
OP1 O:C6 2.2 42.2 1.0
O M:HOH11 2.4 31.4 1.0
OD1 M:ASP145 2.7 45.7 1.0
O M:HOH12 2.8 67.6 1.0
O O:HOH15 2.8 36.6 1.0
CG M:ASP274 3.2 55.7 1.0
CA M:CA1014 3.3 0.3 1.0
P O:C6 3.5 44.0 1.0
CG M:ASP145 3.6 46.0 1.0
OD2 M:ASP145 3.8 44.0 1.0
CB M:ASP274 3.9 54.3 1.0
OP2 O:C6 4.0 43.3 1.0
OP2 O:C7 4.1 46.3 1.0
O5' O:C6 4.2 45.0 1.0
OD2 M:ASP274 4.2 56.0 1.0
O M:GLY146 4.6 47.6 1.0
CA M:ASP274 4.6 52.9 1.0
O3' O:A5 4.7 43.9 1.0
C5' O:C6 4.7 44.6 1.0
ND2 M:ASN210 4.8 56.4 1.0

Calcium binding site 10 out of 14 in 2qkk

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Calcium binding site 10 out of 14 in the Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Human Rnase H Catalytic Domain Mutant D210N in Complex with 14-Mer Rna/Dna Hybrid within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca1014

b:0.3
occ:1.00
 OP1 O:C6 2.0 42.2 1.0
OD2 M:ASP145 2.0 44.0 1.0
OE2 M:GLU186 2.2 52.7 1.0
ND2 M:ASN210 2.8 56.4 1.0
CG M:ASP145 2.9 46.0 1.0
O3' O:A5 2.9 43.9 1.0
P O:C6 2.9 44.0 1.0
OD1 M:ASP145 3.2 45.7 1.0
CA M:CA1010 3.3 38.3 1.0
CD M:GLU186 3.4 51.7 1.0
OD1 M:ASN210 3.5 55.9 1.0
CG M:ASN210 3.5 56.2 1.0
O M:GLY146 3.7 47.6 1.0
O M:HOH11 3.8 31.4 1.0
O5' O:C6 3.9 45.0 1.0
C5' O:C6 3.9 44.6 1.0
OE1 M:GLU186 3.9 51.8 1.0
O M:HOH12 4.0 67.6 1.0
N M:GLY146 4.1 45.1 1.0
OP2 O:C6 4.1 43.3 1.0
CB M:ASP145 4.2 47.1 1.0
C3' O:A5 4.3 44.4 1.0
CA M:ASP145 4.5 47.0 1.0
CG M:GLU186 4.6 48.8 1.0
C M:GLY146 4.7 46.5 1.0
C4' O:A5 4.8 45.9 1.0
O2' O:A5 4.8 41.7 1.0
C M:ASP145 4.8 45.9 1.0
CB M:ASN210 4.9 54.6 1.0
CA M:GLY146 4.9 45.9 1.0

Reference:

M.Nowotny, S.A.Gaidamakov, R.Ghirlando, S.M.Cerritelli, R.J.Crouch, W.Yang. Structure of Human Rnase H1 Complexed with An Rna/Dna Hybrid: Insight Into Hiv Reverse Transcription Mol.Cell V. 28 264 2007.
ISSN: ISSN 1097-2765
PubMed: 17964265
DOI: 10.1016/J.MOLCEL.2007.08.015
Page generated: Fri Jul 12 15:26:36 2024

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