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Calcium in PDB 3v6k: Replication of N2,3-Ethenoguanine By Dna Polymerases

Enzymatic activity of Replication of N2,3-Ethenoguanine By Dna Polymerases

All present enzymatic activity of Replication of N2,3-Ethenoguanine By Dna Polymerases:
2.7.7.7;

Protein crystallography data

The structure of Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6k was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.855, 110.953, 100.238, 90.00, 102.70, 90.00
R / Rfree (%) 22.9 / 30.3

Other elements in 3v6k:

The structure of Replication of N2,3-Ethenoguanine By Dna Polymerases also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 4 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Replication of N2,3-Ethenoguanine By Dna Polymerases (pdb code 3v6k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 1 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:0.6
occ:1.00
 O A:ALA181 2.3 80.5 1.0
O A:ILE186 2.8 78.0 1.0
C A:ALA181 3.5 81.9 1.0
OP2 P:DC13 3.9 79.0 1.0
C A:ILE186 4.0 80.1 1.0
CA A:ASP182 4.1 76.9 1.0
N A:ASP182 4.3 80.5 1.0
O A:VAL183 4.3 75.4 1.0
C A:ASP182 4.5 75.7 1.0
CA A:ALA181 4.7 84.9 1.0
O A:ASP182 4.8 73.9 1.0
CA A:GLY187 4.8 82.6 1.0
N A:GLY187 4.9 82.0 1.0
OD1 A:ASP182 4.9 76.2 1.0
OP1 P:DC13 4.9 75.6 1.0
P P:DC13 5.0 77.3 1.0
N A:VAL183 5.0 77.2 1.0
CA A:ILE186 5.0 81.3 1.0

Calcium binding site 2 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 2 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:0.0
occ:1.00
 ND2 A:ASN234 3.7 0.7 1.0
CD A:PRO236 4.3 0.1 1.0
CG A:ASN234 4.4 0.6 1.0
O A:ASN234 4.6 0.7 1.0
CG A:PRO236 4.7 0.2 1.0
OD1 A:ASN234 4.7 0.8 1.0

Calcium binding site 3 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 3 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:

Calcium binding site 4 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 4 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca402

b:0.6
occ:1.00
 O J:ILE186 2.5 0.2 1.0
O J:ALA181 2.8 0.0 0.5
OP2 K:DC13 3.4 92.0 1.0
C J:ILE186 3.8 0.4 1.0
O J:VAL183 3.8 0.4 1.0
C J:ALA181 3.9 0.9 1.0
C J:ASP182 4.1 0.5 1.0
CA J:ASP182 4.2 0.7 1.0
O J:ASP182 4.2 0.3 1.0
C J:VAL183 4.5 0.4 1.0
N J:ASP182 4.5 0.2 1.0
N J:VAL183 4.5 0.2 1.0
P K:DC13 4.6 0.4 1.0
CA J:GLY187 4.7 0.6 1.0
N J:GLY187 4.7 0.9 1.0
CA J:ILE186 4.7 0.2 1.0
N J:ILE186 4.7 0.1 1.0
OP1 K:DC13 4.9 0.2 1.0

Calcium binding site 5 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 5 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca404

b:0.0
occ:1.00
 OP2 K:DA10 2.4 0.0 1.0
OD1 J:ASP294 2.7 0.6 1.0
OD2 J:ASP294 3.0 0.2 1.0
CG J:ASP294 3.2 0.8 1.0
P K:DA10 3.3 0.1 1.0
OP1 K:DA10 3.7 0.4 1.0
O3' K:DG9 3.7 0.1 1.0
C3' K:DG9 3.8 0.2 1.0
O J:ILE295 4.3 0.7 1.0
C2' K:DG9 4.5 0.6 1.0
CB J:ASP294 4.7 0.4 1.0
N J:ILE295 4.8 0.4 1.0
O5' K:DA10 4.8 0.5 1.0

Calcium binding site 6 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 6 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca405

b:0.0
occ:1.00
 O J:GLU94 3.9 0.7 1.0
CA J:TYR95 4.0 0.2 1.0
C J:GLU94 4.0 0.6 1.0
N J:TYR95 4.1 0.7 1.0
C J:TYR95 4.3 0.3 1.0
N J:SER96 4.4 0.0 1.0
CA J:GLU94 4.8 0.4 1.0
O J:TYR95 4.9 0.6 1.0

Calcium binding site 7 out of 7 in 3v6k

Go back to Calcium Binding Sites List in 3v6k
Calcium binding site 7 out of 7 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca406

b:0.0
occ:1.00
 CG2 J:ILE104 2.9 86.8 1.0
CB J:SER103 3.3 95.3 0.5
CA J:SER103 3.9 97.3 1.0
C J:SER103 4.0 95.2 1.0
OG J:SER103 4.1 93.8 0.5
N J:ILE104 4.1 93.0 1.0
CB J:ILE104 4.1 88.7 1.0
O J:SER103 4.6 96.7 1.0
CA J:ILE104 4.8 92.2 1.0

Reference:

L.Zhao, P.P.Christov, I.D.Kozekov, M.G.Pence, P.S.Pallan, C.J.Rizzo, M.Egli, F.P.Guengerich. Replication of N(2) ,3-Ethenoguanine By Dna Polymerases. Angew.Chem.Int.Ed.Engl. V. 51 5466 2012.
ISSN: ISSN 1433-7851
PubMed: 22488769
DOI: 10.1002/ANIE.201109004
Page generated: Sat Dec 12 04:33:58 2020

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