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Manganese in PDB 4n5s: Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp

Enzymatic activity of Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp

All present enzymatic activity of Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp, PDB code: 4n5s was solved by E.Y.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.80 / 1.67
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 107.657, 107.657, 89.659, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 19.2

Other elements in 4n5s:

The structure of Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) 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 Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp (pdb code 4n5s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp, PDB code: 4n5s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4n5s

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Manganese binding site 1 out of 6 in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) 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 Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn201

b:22.3
occ:0.75
 O B:HOH330 2.1 31.6 1.0
O B:HOH329 2.1 19.3 1.0
O B:HOH328 2.2 20.5 1.0
O A:HOH1339 2.2 28.0 1.0
O B:HOH333 2.3 25.4 1.0
O B:HOH331 2.3 24.6 1.0
O B:HOH332 3.9 15.7 1.0
O B:HOH342 4.0 43.4 1.0
O C:HOH309 4.0 25.5 1.0
O6 B:DG108 4.1 16.8 1.0
O A:HOH1133 4.2 24.6 1.0
N7 B:DG107 4.3 16.9 1.0
O B:HOH323 4.4 37.1 1.0
O B:HOH327 4.4 25.0 1.0
O6 B:DG107 4.5 17.6 1.0
N4 C:DC209 4.6 15.9 1.0
O B:HOH324 4.6 35.6 1.0
C5 B:DC106 4.8 17.6 1.0

Manganese binding site 2 out of 6 in 4n5s

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Manganese binding site 2 out of 6 in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) 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 Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:15.2
occ:1.00
 OD2 A:ASP785 2.1 15.3 1.0
O1G A:DCT907 2.1 14.8 1.0
OD1 A:ASP610 2.1 16.6 1.0
O1B A:DCT907 2.1 14.9 1.0
O A:TYR611 2.2 14.1 1.0
O1A A:DCT907 2.3 14.1 1.0
CG A:ASP785 3.1 14.2 1.0
PB A:DCT907 3.2 15.7 1.0
CG A:ASP610 3.2 17.3 1.0
PG A:DCT907 3.3 16.8 1.0
C A:TYR611 3.4 14.5 1.0
MG A:MG901 3.5 16.8 1.0
OD1 A:ASP785 3.5 14.0 1.0
PA A:DCT907 3.5 15.6 1.0
O3B A:DCT907 3.5 16.1 1.0
O3A A:DCT907 3.7 15.2 1.0
OD2 A:ASP610 3.8 18.3 1.0
O A:HOH1018 3.9 17.8 1.0
N A:TYR611 4.0 13.3 1.0
C5' A:DCT907 4.2 14.3 1.0
CA A:TYR611 4.2 13.8 1.0
O2G A:DCT907 4.2 16.2 1.0
O A:HOH1365 4.2 22.1 1.0
O5' A:DCT907 4.3 14.1 1.0
C A:ASP610 4.3 14.6 1.0
N A:SER612 4.3 14.4 1.0
CB A:ASP785 4.4 13.8 1.0
N A:GLN613 4.4 14.5 1.0
O3G A:DCT907 4.4 15.3 1.0
CB A:ASP610 4.5 15.7 1.0
CA A:SER612 4.5 15.2 1.0
CG2 A:ILE614 4.5 15.9 1.0
CB A:TYR611 4.6 14.3 1.0
O2B A:DCT907 4.6 16.0 1.0
O2A A:DCT907 4.6 14.7 1.0
C A:SER612 4.7 13.9 1.0
N A:ILE614 4.7 14.9 1.0
O A:ASP610 4.7 15.2 1.0
CB A:ILE614 4.8 15.9 1.0
O A:ASP785 4.8 14.0 1.0
CA A:ASP610 4.8 15.1 1.0
O B:HOH305 5.0 16.9 1.0

Manganese binding site 3 out of 6 in 4n5s

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Manganese binding site 3 out of 6 in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) 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 Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn903

b:24.1
occ:0.75
 O A:HOH1331 2.1 27.4 1.0
O A:HOH1236 2.1 29.1 1.0
O A:HOH1334 2.2 30.3 1.0
O A:HOH1335 2.3 30.8 1.0
O A:HOH1332 2.3 25.1 1.0
O A:HOH1333 2.3 24.8 1.0
OE1 A:GLU400 4.1 34.5 1.0
O A:HOH1224 4.2 24.8 1.0
O A:HOH1146 4.2 34.3 1.0
OE2 A:GLU400 4.2 34.2 1.0
NH2 A:ARG405 4.2 22.5 1.0
O A:HOH1409 4.3 51.7 1.0
OXT A:ACT910 4.3 26.5 1.0
O A:HOH1126 4.3 30.0 1.0
O A:HOH1196 4.5 43.9 1.0
CD A:GLU400 4.6 34.5 1.0
O A:ACT910 4.6 23.5 1.0
CE A:LYS314 4.6 30.3 1.0
NE1 A:TRP398 4.7 23.4 1.0
C A:ACT910 4.8 24.2 1.0

Manganese binding site 4 out of 6 in 4n5s

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Manganese binding site 4 out of 6 in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) 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 Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn904

b:28.4
occ:0.75
 O A:HOH1343 2.1 30.8 1.0
O A:HOH1345 2.2 34.1 1.0
O A:HOH1342 2.2 33.3 1.0
O A:HOH1344 2.3 27.1 1.0
NE2 A:HIS443 2.3 26.8 1.0
CD2 A:HIS443 3.1 26.5 1.0
CE1 A:HIS443 3.4 28.1 1.0
O A:HOH1326 4.1 46.9 1.0
OE2 A:GLU773 4.1 45.5 1.0
O A:HOH1346 4.2 37.5 1.0
CG A:HIS443 4.3 24.3 1.0
ND1 A:HIS443 4.4 25.7 1.0
OG1 A:THR447 4.6 18.5 1.0
CG A:GLU773 4.6 38.1 1.0
CG A:ARG778 4.6 20.0 1.0
O A:ALA777 4.7 19.4 1.0
CD A:GLU773 4.9 42.2 1.0
CZ A:PHE769 5.0 24.9 1.0

Manganese binding site 5 out of 6 in 4n5s

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Manganese binding site 5 out of 6 in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) 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 Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn905

b:35.8
occ:0.75
 OE1 A:GLU825 1.8 37.1 1.0
O A:HOH1356 2.2 33.5 1.0
O A:HOH1357 2.5 31.7 1.0
CD A:GLU825 3.0 33.7 1.0
OE2 A:GLU825 3.5 37.5 1.0
O A:ALA600 4.2 22.8 1.0
CG A:GLU825 4.3 30.5 1.0
CB A:GLU825 4.5 25.8 1.0
CA A:GLU602 4.6 27.9 1.0
NZ A:LYS793 4.7 35.3 1.0
O A:GLU601 4.7 21.5 1.0
NH1 A:ARG450 4.7 32.9 1.0

Manganese binding site 6 out of 6 in 4n5s

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Manganese binding site 6 out of 6 in the Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Ternary Complex Structure of Klenow Fragment of Taq Dna Polymerase I707L Mutant (CS3C Klentaq) with Dna and Ddctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn906

b:36.9
occ:1.00
 OE2 A:GLU721 2.1 25.0 1.0
O A:HOH1442 2.2 30.9 1.0
O A:HOH1240 2.3 37.9 1.0
O A:HOH1111 2.3 25.3 1.0
O A:HOH1443 2.4 40.9 1.0
CD A:GLU721 3.2 24.9 1.0
CG A:GLU721 3.6 20.3 1.0
OE1 A:GLU713 4.1 32.6 1.0
O A:HOH1275 4.1 46.0 1.0
NH2 A:ARG425 4.2 34.0 1.0
O A:HOH1302 4.2 41.7 1.0
OE1 A:GLU721 4.2 25.5 1.0
NH2 A:ARG717 4.3 38.9 1.0
O A:HOH1269 4.3 33.2 1.0
OE2 A:GLU713 4.4 36.6 1.0
NH1 A:ARG425 4.5 31.1 1.0
CD A:GLU713 4.7 35.6 1.0
CZ A:ARG425 4.8 31.1 1.0
O A:THR722 4.9 17.4 1.0

Reference:

E.Y.Wu, A.R.Walsh, E.C.Materne, E.P.Hiltner, B.Zielinski, B.R.Miller, L.Mawby, E.Modeste, C.A.Parish, W.M.Barnes, M.B.Kermekchiev. A Conservative Isoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KLENTAQ1 Dna Polymerase. Biochemistry V. 54 881 2015.
ISSN: ISSN 0006-2960
PubMed: 25537790
DOI: 10.1021/BI501198F
Page generated: Sat Oct 5 20:29:48 2024

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