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Manganese in PDB 7kt6: Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7kt6 was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.04 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.081, 68.692, 110.49, 90, 90, 90
R / Rfree (%) 16.5 / 19.3

Other elements in 7kt6:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) (pdb code 7kt6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7kt6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7kt6

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Manganese binding site 1 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:18.3
occ:1.00
 OD1 A:ASP330 2.1 19.4 0.3
O A:HOH617 2.2 18.6 1.0
OD2 A:ASP332 2.2 17.2 1.0
O2 A:GOA512 2.2 20.4 1.0
OD2 A:ASP330 2.2 18.6 0.7
OP1 P:8OG5 2.2 17.3 1.0
O12 A:GOA512 2.2 16.9 1.0
CG A:ASP330 3.0 19.7 0.7
C1 A:GOA512 3.0 18.3 1.0
CG A:ASP332 3.1 18.1 1.0
C2 A:GOA512 3.1 20.4 1.0
OD1 A:ASP330 3.1 20.2 0.7
CG A:ASP330 3.2 19.3 0.3
MN A:MN502 3.3 18.6 0.9
OD1 A:ASP332 3.4 18.8 1.0
P P:8OG5 3.4 17.5 1.0
OD2 A:ASP330 3.6 19.8 0.3
O5' P:8OG5 3.8 16.4 1.0
C5' P:8OG5 4.1 16.4 1.0
OP2 P:8OG5 4.1 18.9 1.0
O A:HOH814 4.2 20.1 1.0
O A:ASP330 4.2 16.7 0.3
O11 A:GOA512 4.2 16.5 1.0
O A:ASP330 4.3 16.6 0.7
O A:HOH606 4.3 18.6 1.0
O A:HOH608 4.3 19.6 1.0
O P:HOH103 4.4 33.1 1.0
CB A:ASP330 4.4 19.2 0.7
N A:GLY320 4.4 17.5 1.0
CB A:ASP332 4.4 16.8 1.0
CB A:ASP330 4.5 19.4 0.3
CA A:GLY319 4.5 16.6 1.0
O A:HOH676 4.5 30.3 1.0
C A:ASP330 4.5 17.5 0.3
C A:ASP330 4.5 17.5 0.7
O3' P:DA4 4.7 18.3 1.0
O A:HOH751 4.8 16.9 0.7
N A:ASP332 5.0 15.6 1.0
CA A:ASP330 5.0 18.9 0.7
CA A:ASP330 5.0 19.0 0.3
N A:VAL331 5.0 17.1 1.0

Manganese binding site 2 out of 6 in 7kt6

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Manganese binding site 2 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:18.6
occ:0.92
 OD2 A:ASP330 1.6 19.8 0.3
OD1 A:ASP332 2.0 18.8 1.0
OD2 A:ASP418 2.1 20.2 1.0
OP1 P:8OG5 2.2 17.3 1.0
OD2 A:ASP330 2.2 18.6 0.7
O A:HOH608 2.3 19.6 1.0
O A:HOH751 2.3 16.9 0.7
CG A:ASP330 2.5 19.3 0.3
OD1 A:ASP330 3.0 19.4 0.3
CG A:ASP418 3.0 20.4 1.0
CG A:ASP332 3.1 18.1 1.0
CG A:ASP330 3.2 19.7 0.7
P P:8OG5 3.3 17.5 1.0
MN A:MN501 3.3 18.3 1.0
O3' P:DA4 3.4 18.3 1.0
OD2 A:ASP332 3.5 17.2 1.0
CB A:ASP418 3.8 19.0 1.0
CB A:ASP330 3.8 19.2 0.7
CB A:ASP330 3.9 19.4 0.3
OD1 A:ASP418 3.9 20.9 1.0
OP2 P:8OG5 4.0 18.9 1.0
OD1 A:ASP330 4.2 20.2 0.7
C5' P:DA4 4.3 19.6 1.0
O A:VAL331 4.4 17.7 1.0
CB A:ASP332 4.4 16.8 1.0
O P:HOH103 4.4 33.1 1.0
NH2 A:ARG416 4.4 20.1 1.0
C3' P:DA4 4.4 19.1 1.0
O2 A:GOA512 4.5 20.4 1.0
C4' P:DA4 4.5 19.1 1.0
O5' P:8OG5 4.6 16.4 1.0
C A:VAL331 4.7 17.0 1.0
OP1 P:DA4 4.7 21.7 1.0
N A:ASP418 4.8 17.1 1.0
N A:VAL331 4.9 17.1 1.0
CA A:ASP332 4.9 16.3 1.0
CA A:ASP418 4.9 18.1 1.0
C5' P:8OG5 4.9 16.4 1.0
O A:HOH617 4.9 18.6 1.0
N A:ASP332 5.0 15.6 1.0
CZ3 A:TRP434 5.0 17.2 1.0
C A:ASP330 5.0 17.5 0.3

Manganese binding site 3 out of 6 in 7kt6

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Manganese binding site 3 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:30.5
occ:0.58
 OG A:SER458 2.6 27.2 1.0
N A:SER458 3.2 21.1 1.0
O A:HOH625 3.2 27.2 1.0
ND1 A:HIS459 3.2 38.9 1.0
CB A:SER458 3.5 24.4 1.0
C1' T:DA7 3.5 27.9 1.0
C2' T:DA7 3.6 28.9 1.0
CE1 A:HIS459 3.6 40.5 1.0
C4' T:DA7 3.6 29.2 1.0
O4' T:DA7 3.6 29.0 1.0
NH2 A:ARG387 3.7 28.1 1.0
CB A:ASN457 3.7 23.8 1.0
CA A:SER458 3.8 21.8 1.0
CG A:ASN457 3.9 26.4 1.0
C3' T:DA7 4.1 29.0 1.0
N A:HIS459 4.1 20.7 1.0
C A:SER458 4.2 21.5 1.0
O3' T:DA7 4.2 28.5 1.0
C A:ASN457 4.2 20.8 1.0
ND2 A:ASN457 4.3 31.7 1.0
OD1 A:ASN457 4.3 23.5 1.0
CA A:ASN457 4.4 21.3 1.0
CG A:HIS459 4.5 37.2 1.0
NH2 A:ARG445 4.8 20.0 1.0
O2 A:EDO508 4.9 29.3 1.0
CZ A:ARG387 4.9 25.8 1.0
NE2 A:HIS459 4.9 39.9 1.0
N9 T:DA7 5.0 26.4 1.0
O A:HOH713 5.0 23.9 1.0
C5' T:DA7 5.0 30.0 1.0

Manganese binding site 4 out of 6 in 7kt6

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Manganese binding site 4 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:30.0
occ:0.53
 OE2 A:GLU386 2.2 41.2 1.0
O A:HOH777 2.2 37.6 1.0
O A:HOH809 2.3 38.3 1.0
O T:HOH201 2.3 39.3 1.0
NE2 A:HIS459 2.4 39.9 1.0
OE1 A:GLU386 2.5 42.5 1.0
CD A:GLU386 2.7 41.2 1.0
CD2 A:HIS459 3.0 39.3 1.0
CE1 A:HIS459 3.5 40.5 1.0
O A:HOH681 4.1 38.6 1.0
CG A:GLU386 4.2 40.2 1.0
CG A:HIS459 4.3 37.2 1.0
OP1 T:DC8 4.3 27.6 1.0
O A:HOH615 4.3 27.8 1.0
ND1 A:HIS459 4.5 38.9 1.0
OE1 A:GLN426 4.6 27.6 1.0
C5' T:DC8 4.6 25.2 1.0

Manganese binding site 5 out of 6 in 7kt6

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Manganese binding site 5 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:74.4
occ:0.85
 O A:HOH797 2.0 65.6 0.9
O A:HOH740 2.2 53.3 0.8
NE2 A:HIS219 2.2 57.4 1.0
CE1 A:HIS219 3.0 59.8 1.0
CD2 A:HIS219 3.3 56.7 1.0
ND1 A:HIS219 4.2 58.5 1.0
CG A:HIS219 4.4 54.2 1.0
CB A:GLU218 4.8 46.5 1.0

Manganese binding site 6 out of 6 in 7kt6

Go back to Manganese Binding Sites List in 7kt6
Manganese binding site 6 out of 6 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:77.7
occ:0.74
 O T:HOH214 2.4 41.5 0.7
N7 T:DG2 2.8 36.7 1.0
C8 T:DG2 3.6 36.6 1.0
C5 T:DG2 3.9 35.6 1.0
O T:HOH202 4.0 39.4 1.0
O6 T:DG2 4.0 33.6 1.0
OP2 T:DG2 4.2 55.4 1.0
C6 T:DG2 4.4 33.0 1.0
O6 T:DG3 4.5 28.6 1.0
C6 T:DC1 4.8 45.1 1.0
C2' T:DC1 4.8 62.4 1.0
C3' T:DC1 4.9 63.2 1.0
N9 T:DG2 4.9 36.5 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN) To Be Published.
Page generated: Sun Oct 6 09:28:27 2024

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