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Magnesium in PDB 1t7p: T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin

Enzymatic activity of T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin

All present enzymatic activity of T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin:
2.7.7.7;

Protein crystallography data

The structure of T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin, PDB code: 1t7p was solved by S.Doublie, S.Tabor, A.M.Long, C.C.Richardson, T.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.600, 216.300, 52.100, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin (pdb code 1t7p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin, PDB code: 1t7p:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1t7p

Go back to Magnesium Binding Sites List in 1t7p
Magnesium binding site 1 out of 3 in the T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4001

b:23.2
occ:1.00
 O A:ALA476 2.2 14.7 1.0
O1G P:DG323 2.2 27.6 1.0
O2B P:DG323 2.2 20.7 1.0
O2A P:DG323 2.3 22.8 1.0
OD1 A:ASP475 2.3 32.7 1.0
OD2 A:ASP654 2.4 15.4 1.0
PB P:DG323 3.2 20.0 1.0
PG P:DG323 3.3 23.6 1.0
CG A:ASP654 3.4 14.1 1.0
C A:ALA476 3.4 13.6 1.0
O3B P:DG323 3.5 33.2 1.0
CG A:ASP475 3.5 26.8 1.0
PA P:DG323 3.5 21.9 1.0
O3A P:DG323 3.6 23.6 1.0
MG A:MG4002 3.7 31.6 1.0
OD1 A:ASP654 3.8 13.4 1.0
O P:HOH3107 4.1 32.2 1.0
N A:ALA476 4.1 10.9 1.0
O2G P:DG323 4.1 23.7 1.0
OD2 A:ASP475 4.1 34.5 1.0
O A:HOH3110 4.1 20.1 1.0
CA A:ALA476 4.2 14.4 1.0
N A:GLY478 4.2 15.5 1.0
C5' P:DG323 4.3 19.2 1.0
N A:SER477 4.4 14.2 1.0
O5' P:DG323 4.4 15.4 1.0
CB A:ALA476 4.5 13.2 1.0
CA A:SER477 4.5 16.8 1.0
N A:LEU479 4.6 19.9 1.0
CB A:ASP654 4.6 12.3 1.0
O3G P:DG323 4.6 22.2 1.0
C A:ASP475 4.6 17.1 1.0
O1B P:DG323 4.6 26.2 1.0
CB A:ASP475 4.7 19.7 1.0
O1A P:DG323 4.7 13.6 1.0
C A:SER477 4.7 13.3 1.0
CB A:LEU479 4.8 21.7 1.0
CA A:GLY478 5.0 11.2 1.0
O A:ASP654 5.0 14.9 1.0

Magnesium binding site 2 out of 3 in 1t7p

Go back to Magnesium Binding Sites List in 1t7p
Magnesium binding site 2 out of 3 in the T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4002

b:31.6
occ:1.00
 OD1 A:ASP654 2.3 13.4 1.0
O P:HOH3180 2.4 22.2 1.0
O2A P:DG323 2.4 22.8 1.0
O A:HOH3195 2.4 14.2 1.0
OD2 A:ASP475 2.5 34.5 1.0
CG A:ASP654 3.3 14.1 1.0
CG A:ASP475 3.3 26.8 1.0
OD1 A:ASP475 3.3 32.7 1.0
C3' P:2DA22 3.3 11.1 1.0
PA P:DG323 3.4 21.9 1.0
OD2 A:ASP654 3.5 15.4 1.0
MG A:MG4001 3.7 23.2 1.0
O P:HOH3107 3.7 32.2 1.0
O5' P:DG323 3.8 15.4 1.0
O1A P:DG323 3.9 13.6 1.0
C5' P:DG323 4.0 19.2 1.0
C4' P:2DA22 4.1 9.0 1.0
CE1 A:HIS704 4.2 36.6 1.0
C5' P:2DA22 4.3 14.2 1.0
CB A:GLU655 4.5 21.1 1.0
C2' P:2DA22 4.5 16.8 1.0
O A:VAL652 4.5 10.2 1.0
O1G P:DG323 4.5 27.6 1.0
CB A:ASP654 4.6 12.3 1.0
C A:ASP654 4.7 13.0 1.0
O5' P:2DA22 4.7 16.8 1.0
NE2 A:HIS704 4.7 31.4 1.0
O A:ASP654 4.7 14.9 1.0
CB A:ASP475 4.8 19.7 1.0
CG A:GLU655 4.8 32.2 1.0
N A:ASP654 4.8 10.4 1.0
O3A P:DG323 4.8 23.6 1.0
N A:GLU655 4.9 16.6 1.0
CA A:ASP654 4.9 11.2 1.0

Magnesium binding site 3 out of 3 in 1t7p

Go back to Magnesium Binding Sites List in 1t7p
Magnesium binding site 3 out of 3 in the T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T7 Dna Polymerase Complexed to Dna Primer/Template,A Nucleoside Triphosphate, and Its Processivity Factor Thioredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4003

b:23.5
occ:1.00
 O A:HOH3534 2.3 20.7 1.0
O A:HOH3535 2.3 17.9 1.0
O A:HOH3532 2.3 9.1 1.0
O A:HOH3533 2.5 15.5 1.0
OD1 A:ASP5 2.5 15.5 1.0
CG A:ASP5 3.5 18.5 1.0
OD2 A:ASP5 3.9 17.3 1.0
OD1 A:ASP65 3.9 18.4 1.0
O A:ILE6 4.0 14.0 1.0
OD2 A:ASP65 4.2 6.6 1.0
O A:HIS59 4.3 12.9 1.0
O A:HOH3297 4.4 18.8 1.0
O A:HOH3150 4.4 12.2 1.0
CG A:ASP65 4.5 7.3 1.0
O A:HOH3029 4.5 10.4 1.0
CB A:ASP5 4.8 14.8 1.0
CE A:MET107 4.9 20.0 1.0
OD2 A:ASP174 4.9 33.2 1.0
N A:ILE6 4.9 11.9 1.0
CD2 A:TYR64 5.0 5.2 1.0

Reference:

S.Doublie, S.Tabor, A.M.Long, C.C.Richardson, T.Ellenberger. Crystal Structure of A Bacteriophage T7 Dna Replication Complex at 2.2 A Resolution. Nature V. 391 251 1998.
ISSN: ISSN 0028-0836
PubMed: 9440688
DOI: 10.1038/34593
Page generated: Tue Aug 13 14:28:12 2024

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