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Manganese in PDB 3py8: Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp

Enzymatic activity of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp

All present enzymatic activity of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp, PDB code: 3py8 was solved by A.Schnur, A.Marx, W.Welte, K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.74 / 1.74
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.610, 108.610, 90.570, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 19.9

Other elements in 3py8:

The structure of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp (pdb code 3py8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp, PDB code: 3py8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 3py8

Go back to Manganese Binding Sites List in 3py8
Manganese binding site 1 out of 5 in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn833

b:29.0
occ:1.00
 OD1 A:ASP610 2.2 30.6 1.0
O A:TYR611 2.2 21.5 1.0
OD2 A:ASP785 2.2 27.2 1.0
O1G A:DCT113 2.2 30.4 1.0
O2A A:DCT113 2.3 26.6 1.0
O2B A:DCT113 2.3 26.1 1.0
CG A:ASP785 3.2 30.2 1.0
PB A:DCT113 3.2 31.2 1.0
CG A:ASP610 3.3 33.7 1.0
PG A:DCT113 3.3 31.9 1.0
C A:TYR611 3.3 25.3 1.0
MG A:MG2 3.5 29.3 1.0
PA A:DCT113 3.5 30.6 1.0
OD1 A:ASP785 3.5 24.6 1.0
O3B A:DCT113 3.6 30.8 1.0
OD2 A:ASP610 3.8 35.1 1.0
O3A A:DCT113 3.8 34.8 1.0
O A:HOH212 4.0 37.5 1.0
O A:HOH65 4.0 30.0 1.0
N A:TYR611 4.0 20.1 1.0
O2G A:DCT113 4.1 34.9 1.0
CA A:TYR611 4.2 21.5 1.0
C5' A:DCT113 4.2 27.0 1.0
N A:SER612 4.3 27.3 1.0
O5' A:DCT113 4.3 24.1 1.0
C A:ASP610 4.3 24.8 1.0
O3G A:DCT113 4.5 33.2 1.0
CA A:SER612 4.5 25.5 1.0
CB A:ASP785 4.5 24.3 1.0
O1A A:DCT113 4.5 29.9 1.0
CB A:ASP610 4.5 22.0 1.0
N A:GLN613 4.5 29.5 1.0
O1B A:DCT113 4.5 27.9 1.0
CB A:TYR611 4.6 22.2 1.0
O A:ASP785 4.7 20.7 1.0
C A:SER612 4.7 25.4 1.0
O A:ASP610 4.8 24.8 1.0
N A:LYS614 4.8 28.2 1.0
CA A:ASP610 4.8 22.1 1.0
CB A:LYS614 4.8 33.4 1.0
O A:HOH205 4.9 29.9 1.0

Manganese binding site 2 out of 5 in 3py8

Go back to Manganese Binding Sites List in 3py8
Manganese binding site 2 out of 5 in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn5

b:38.1
occ:1.00
 OE2 A:GLU462 2.2 49.3 1.0
O A:HOH904 2.3 32.5 1.0
O A:HOH213 2.4 35.2 1.0
OE1 A:GLU465 2.4 39.0 1.0
O A:HOH157 2.4 42.8 1.0
CD A:GLU462 3.3 55.8 1.0
CD A:GLU465 3.3 41.6 1.0
OE2 A:GLU465 3.6 37.1 1.0
OE1 A:GLU462 4.1 49.1 1.0
CG A:GLU462 4.1 51.6 1.0
O A:HOH994 4.1 76.9 1.0
O A:HOH203 4.2 44.0 1.0
CA A:GLU462 4.5 28.4 1.0
O A:HOH8 4.7 26.2 1.0
CG A:GLU465 4.7 32.7 1.0
CB A:GLU462 4.8 28.2 1.0
N A:GLU462 4.9 25.7 1.0

Manganese binding site 3 out of 5 in 3py8

Go back to Manganese Binding Sites List in 3py8
Manganese binding site 3 out of 5 in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn6

b:46.9
occ:1.00
 O A:HOH941 2.3 32.3 1.0
NE2 A:HIS443 2.3 29.6 1.0
O A:HOH274 2.4 49.7 1.0
O A:HOH278 2.4 50.8 1.0
O A:HOH263 2.6 51.3 1.0
CE1 A:HIS443 3.1 34.5 1.0
CD2 A:HIS443 3.4 32.1 1.0
O A:HOH214 4.0 35.6 1.0
O A:HOH227 4.1 39.2 1.0
ND1 A:HIS443 4.3 28.1 1.0
O A:HOH897 4.4 51.5 1.0
CG A:HIS443 4.4 24.8 1.0
OE1 A:GLU773 4.6 62.9 1.0

Manganese binding site 4 out of 5 in 3py8

Go back to Manganese Binding Sites List in 3py8
Manganese binding site 4 out of 5 in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3

b:38.5
occ:0.53
 O B:HOH312 2.1 13.4 1.0
O B:HOH469 2.4 55.7 1.0
O B:HOH410 2.6 41.9 1.0
N7 B:DG107 2.7 19.6 1.0
O B:HOH342 2.9 21.6 1.0
O B:HOH220 3.0 37.1 1.0
O C:HOH396 3.2 33.6 1.0
O B:HOH207 3.4 26.4 1.0
C8 B:DG107 3.5 23.8 1.0
O B:HOH350 3.6 39.4 1.0
C5 B:DG107 3.8 20.6 1.0
O B:HOH430 4.0 47.4 1.0
C6 B:DC106 4.1 19.4 1.0
O6 B:DG107 4.1 19.2 1.0
C5 B:DC106 4.2 26.0 1.0
O6 B:DG108 4.4 20.9 1.0
C6 B:DG107 4.4 22.8 1.0
O C:HOH451 4.4 52.6 1.0
N7 B:DG108 4.5 19.8 1.0
O B:HOH492 4.6 56.4 1.0
C2' B:DC106 4.6 21.0 1.0
N1 B:DC106 4.7 21.5 1.0
N9 B:DG107 4.8 20.4 1.0
C4 B:DG107 5.0 19.9 1.0
C6 B:DG108 5.0 18.5 1.0

Manganese binding site 5 out of 5 in 3py8

Go back to Manganese Binding Sites List in 3py8
Manganese binding site 5 out of 5 in the Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of A Mutant of the Large Fragment of Dna Polymerase I From Thermus Aquaticus in A Closed Ternary Complex with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4

b:53.6
occ:1.00
 O C:HOH218 2.3 40.0 1.0
O C:HOH240 2.6 41.2 1.0
O C:HOH186 2.6 40.8 1.0
N7 C:DG205 2.6 25.7 1.0
O C:HOH250 2.6 36.4 1.0
O C:HOH185 2.7 34.3 1.0
C8 C:DG205 3.4 21.9 1.0
C5 C:DG205 3.5 25.3 1.0
O6 C:DG205 3.8 23.6 1.0
C6 C:DG205 4.0 22.2 1.0
N7 C:DG206 4.1 18.2 1.0
O C:HOH471 4.2 60.5 1.0
O6 C:DG206 4.4 20.0 1.0
OP2 C:DG205 4.4 34.3 1.0
N9 C:DG205 4.5 23.5 1.0
C4 C:DG205 4.6 24.0 1.0
O C:HOH217 4.6 33.4 1.0
O B:HOH23 4.9 30.8 1.0
C5 C:DG206 4.9 17.8 1.0

Reference:

S.Obeid, A.Schnur, C.Gloeckner, N.Blatter, W.Welte, K.Diederichs, A.Marx. Learning From Directed Evolution: Thermus Aquaticus Dna Polymerase Mutants with Translesion Synthesis Activity. Chembiochem V. 12 1574 2011.
ISSN: ISSN 1439-4227
PubMed: 21480455
DOI: 10.1002/CBIC.201000783
Page generated: Sat Oct 5 17:34:29 2024

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