Atomistry » Manganese » PDB 3ot9-3q4q » 3py8
Atomistry »
  Manganese »
    PDB 3ot9-3q4q »
      3py8 »

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: Tue Dec 15 04:14:06 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy