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Manganese in PDB 7ksv: Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

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

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ksv 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) 34.95 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.002, 68.825, 110.101, 90, 90, 90
R / Rfree (%) 16.2 / 18.8

Other elements in 7ksv:

The structure of Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) (pdb code 7ksv). 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ksv:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 7ksv

Go back to Manganese Binding Sites List in 7ksv
Manganese binding site 1 out of 6 in the Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:16.3
occ:1.00
 OD2 A:ASP330 1.6 16.3 0.5
OD2 A:ASP418 2.1 16.0 1.0
OD1 A:ASP332 2.1 16.0 1.0
OP1 P:DG5 2.2 12.2 1.0
O A:HOH629 2.3 17.1 1.0
OD2 A:ASP330 2.3 12.5 0.5
O A:HOH765 2.5 13.6 0.5
CG A:ASP330 2.5 19.8 0.5
OD1 A:ASP330 2.9 13.3 0.5
CG A:ASP418 3.1 16.0 1.0
CG A:ASP332 3.1 16.5 1.0
O3' P:DA4 3.2 15.3 1.0
P P:DG5 3.2 14.9 1.0
CG A:ASP330 3.3 12.8 0.5
MN A:MN502 3.4 14.1 1.0
OD2 A:ASP332 3.5 12.3 1.0
CB A:ASP418 3.8 14.7 1.0
OD1 A:ASP418 3.9 17.2 1.0
CB A:ASP330 3.9 17.6 0.5
CB A:ASP330 3.9 14.9 0.5
OP2 P:DG5 4.1 15.8 1.0
OD1 A:ASP330 4.2 18.2 0.5
C5' P:DA4 4.2 13.8 1.0
C3' P:DA4 4.3 16.0 1.0
O P:HOH104 4.4 31.7 1.0
C4' P:DA4 4.4 13.3 1.0
O5' P:DG5 4.4 15.8 1.0
CB A:ASP332 4.4 12.1 1.0
NH2 A:ARG416 4.5 16.2 1.0
O A:VAL331 4.5 15.1 1.0
OP1 P:DA4 4.6 16.2 1.0
C5' P:DG5 4.6 13.7 1.0
O2 A:GOA507 4.7 19.9 1.0
C A:VAL331 4.8 14.0 1.0
N A:ASP418 4.8 14.3 1.0
CA A:ASP332 4.9 12.6 1.0
CA A:ASP418 4.9 15.7 1.0
CZ3 A:TRP434 5.0 15.8 1.0
O5' P:DA4 5.0 16.6 1.0
N A:ASP332 5.0 12.7 1.0

Manganese binding site 2 out of 6 in 7ksv

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Manganese binding site 2 out of 6 in the Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:14.1
occ:1.00
 OD2 A:ASP330 2.1 12.5 0.5
OD2 A:ASP332 2.1 12.3 1.0
OD1 A:ASP330 2.2 13.3 0.5
O12 A:GOA507 2.2 13.8 1.0
O A:HOH616 2.2 15.4 1.0
OP1 P:DG5 2.2 12.2 1.0
O2 A:GOA507 2.3 19.9 1.0
CG A:ASP330 2.9 12.8 0.5
C1 A:GOA507 3.0 15.5 1.0
OD1 A:ASP330 3.1 18.2 0.5
CG A:ASP332 3.1 16.5 1.0
C2 A:GOA507 3.1 24.5 1.0
CG A:ASP330 3.3 19.8 0.5
MN A:MN501 3.4 16.3 1.0
OD1 A:ASP332 3.4 16.0 1.0
P P:DG5 3.5 14.9 1.0
OD2 A:ASP330 3.7 16.3 0.5
O5' P:DG5 3.8 15.8 1.0
C5' P:DG5 3.9 13.7 1.0
O A:ASP330 4.0 14.8 0.5
O A:HOH829 4.1 18.2 1.0
O11 A:GOA507 4.2 15.5 1.0
OP2 P:DG5 4.3 15.8 1.0
CB A:ASP330 4.3 17.6 0.5
O P:HOH104 4.3 31.7 1.0
O A:HOH620 4.3 14.2 1.0
O A:HOH629 4.3 17.1 1.0
C A:ASP330 4.4 15.7 0.5
N A:GLY320 4.4 13.8 1.0
CB A:ASP332 4.5 12.1 1.0
O A:ASP330 4.5 13.2 0.5
CB A:ASP330 4.5 14.9 0.5
O A:HOH706 4.5 27.0 1.0
CA A:GLY319 4.6 12.9 1.0
C A:ASP330 4.6 14.2 0.5
O3' P:DA4 4.6 15.3 1.0
O A:HOH765 4.9 13.6 0.5
CA A:ASP330 4.9 15.6 0.5
N A:ASP332 5.0 12.7 1.0
CA A:ASP330 5.0 16.0 0.5

Manganese binding site 3 out of 6 in 7ksv

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Manganese binding site 3 out of 6 in the Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:35.4
occ:0.45
 OP3 D:DG1 2.2 28.1 1.0
ND1 A:HIS208 2.4 33.5 1.0
O D:HOH111 2.4 42.8 1.0
O A:HOH823 2.5 52.9 1.0
CE1 A:HIS208 3.2 31.4 1.0
CG A:HIS208 3.3 31.0 1.0
P D:DG1 3.5 28.4 1.0
O D:HOH112 3.6 44.1 1.0
CB A:HIS208 3.6 24.2 1.0
OP1 D:DG1 3.8 32.5 1.0
OP2 D:DG1 4.1 29.7 1.0
O D:HOH108 4.2 45.6 1.0
NE2 A:HIS208 4.3 30.1 1.0
CD2 A:HIS208 4.4 34.6 1.0
O A:HOH842 4.4 48.1 1.0
CA A:HIS208 4.6 23.2 1.0
O5' D:DG1 4.6 25.2 1.0
C5' D:DG1 5.0 26.1 1.0

Manganese binding site 4 out of 6 in 7ksv

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Manganese binding site 4 out of 6 in the Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:71.8
occ:1.00
 O A:HOH794 1.8 55.5 1.0
NE2 A:HIS219 2.2 58.9 1.0
O A:HOH602 2.2 53.9 0.8
O A:HOH631 2.2 58.4 1.0
CE1 A:HIS219 3.1 57.0 1.0
CD2 A:HIS219 3.2 53.2 1.0
OE1 A:GLU215 3.3 59.6 1.0
OE2 A:GLU215 3.4 56.5 1.0
CD A:GLU215 3.7 54.3 1.0
ND1 A:HIS219 4.2 52.5 1.0
CG A:HIS219 4.3 47.9 1.0

Manganese binding site 5 out of 6 in 7ksv

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Manganese binding site 5 out of 6 in the Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:24.3
occ:0.55
 OE2 A:GLU386 2.0 47.7 1.0
O A:HOH814 2.2 33.5 1.0
O A:HOH792 2.2 35.5 1.0
OE1 A:GLU386 2.2 28.4 1.0
O T:HOH203 2.3 33.7 1.0
NE2 A:HIS459 2.3 39.0 1.0
CD A:GLU386 2.4 44.5 1.0
CD2 A:HIS459 3.1 40.2 1.0
CE1 A:HIS459 3.4 43.0 1.0
CG A:GLU386 3.9 33.2 1.0
O A:HOH671 4.1 31.7 1.0
OP1 T:DC8 4.3 24.8 1.0
CG A:HIS459 4.3 28.6 1.0
O A:HOH683 4.4 25.6 1.0
ND1 A:HIS459 4.4 38.7 1.0
OE1 A:GLN426 4.6 24.3 1.0
C5' T:DC8 4.7 19.0 1.0
CB A:GLU386 4.8 25.3 1.0

Manganese binding site 6 out of 6 in 7ksv

Go back to Manganese Binding Sites List in 7ksv
Manganese binding site 6 out of 6 in the Dna Polymerase Mu, Dgtp:Ct 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:36.2
occ:0.50
 O T:HOH215 2.2 44.5 1.0
O T:HOH201 2.2 43.2 1.0
N7 T:DG2 2.6 36.3 1.0
C8 T:DG2 3.4 30.9 1.0
O T:HOH202 3.7 37.9 1.0
C5 T:DG2 3.8 28.0 1.0
OP2 T:DG2 4.0 47.0 1.0
O6 T:DG2 4.1 31.4 1.0
C6 T:DG2 4.4 27.4 1.0
O6 T:DG3 4.4 24.9 1.0
C2' T:DC1 4.5 47.6 1.0
O D:HOH110 4.6 47.8 1.0
N9 T:DG2 4.7 28.7 1.0
C3' T:DC1 4.8 57.0 1.0
C4 T:DG2 4.9 27.8 1.0
C6 T:DC1 4.9 48.1 1.0

Reference:

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

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