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Calcium in PDB 3v6h: 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: 3v6h was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.80 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.532, 111.267, 98.942, 90.00, 102.68, 90.00
R / Rfree (%) 21.5 / 26.7

Other elements in 3v6h:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Replication of N2,3-Ethenoguanine By Dna Polymerases (pdb code 3v6h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6h:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3v6h

Go back to Calcium Binding Sites List in 3v6h
Calcium binding site 1 out of 3 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
D:Ca101

b:73.8
occ:1.00
O A:HOH536 2.3 47.3 1.0
C3' D:DOC13 3.0 63.9 1.0
N A:ILE104 3.5 33.3 1.0
C4' D:DOC13 3.7 68.7 1.0
CB A:SER103 3.8 34.1 1.0
NZ A:LYS78 4.0 51.0 1.0
CA A:SER103 4.1 34.0 1.0
CB A:ILE104 4.1 33.0 1.0
CG2 A:ILE104 4.1 31.7 1.0
C A:SER103 4.3 33.9 1.0
C2' D:DOC13 4.4 58.4 1.0
CA A:ILE104 4.4 34.5 1.0
C5' D:DOC13 4.5 73.3 1.0
NH2 A:ARG242 4.5 82.3 1.0
OG A:SER103 4.7 37.1 1.0
O4' D:DOC13 4.7 65.1 1.0
CE A:LYS78 4.8 45.9 1.0
O A:HOH615 4.9 64.9 1.0
C1' D:DOC13 5.0 57.1 1.0

Calcium binding site 2 out of 3 in 3v6h

Go back to Calcium Binding Sites List in 3v6h
Calcium binding site 2 out of 3 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:0.5
occ:1.00
O A:HOH585 2.7 47.1 1.0
O A:ILE186 2.8 58.6 1.0
O A:HOH535 2.8 58.2 1.0
O A:HOH613 2.9 70.0 1.0
O A:ALA181 3.0 54.5 1.0
O A:VAL183 3.6 46.9 1.0
OP2 D:DT12 3.7 59.9 1.0
C A:ILE186 3.9 56.3 1.0
C A:ALA181 4.1 52.3 1.0
CA A:ASP182 4.3 48.9 1.0
C A:VAL183 4.4 46.0 1.0
C A:ASP182 4.4 48.6 1.0
OP1 D:DT12 4.4 60.5 1.0
N A:ILE186 4.5 51.9 1.0
P D:DT12 4.6 58.5 1.0
N A:VAL183 4.6 47.4 1.0
CA A:ILE186 4.6 54.7 1.0
N A:ASP182 4.7 50.9 1.0
O A:ASP182 4.7 49.1 1.0
N A:GLY187 4.8 57.9 1.0
CA A:PRO184 4.9 42.9 1.0
CA A:GLY187 4.9 58.4 1.0
N A:PRO184 4.9 44.8 1.0
CB A:ILE186 4.9 55.6 1.0
N A:GLY185 4.9 45.5 1.0

Calcium binding site 3 out of 3 in 3v6h

Go back to Calcium Binding Sites List in 3v6h
Calcium binding site 3 out of 3 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:
probe atom residue distance (Å) B Occ
B:Ca403

b:77.3
occ:1.00
N B:ILE104 3.1 56.4 1.0
C3' P:DOC13 3.4 87.9 1.0
CG2 B:ILE104 3.5 58.2 1.0
CB B:ILE104 3.5 57.1 1.0
C4' P:DOC13 3.7 89.0 1.0
CB B:SER103 3.8 53.8 1.0
CA B:ILE104 3.9 57.1 1.0
CA B:SER103 4.1 55.3 1.0
C B:SER103 4.1 55.1 1.0
OG B:SER103 4.5 52.1 1.0
O4' P:DOC13 4.6 87.2 1.0
C2' P:DOC13 4.6 85.6 1.0
OH B:TYR12 4.7 60.0 1.0
C5' P:DOC13 4.9 89.2 1.0
CG1 B:ILE104 4.9 57.8 1.0
CE B:LYS78 5.0 71.5 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 04:33:57 2020

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