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Manganese in PDB 6vfc: Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min), PDB code: 6vfc 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) 33.55 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.333, 62.44, 119.336, 90, 90, 90
R / Rfree (%) 17.2 / 19.2

Other elements in 6vfc:

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) 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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) (pdb code 6vfc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min), PDB code: 6vfc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6vfc

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Manganese binding site 1 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:20.5
occ:1.00
 OD1 A:ASP330 2.0 21.8 0.5
O A:HOH602 2.1 28.9 1.0
O3 A:PO4507 2.1 16.6 0.8
OD1 A:ASP330 2.2 20.8 0.6
OD2 A:ASP332 2.2 17.8 1.0
O A:HOH620 2.3 18.5 1.0
OP1 P:8GM5 2.6 22.4 0.8
CG A:ASP330 2.7 19.8 0.5
OD2 A:ASP330 2.9 23.4 0.5
CG A:ASP332 3.1 18.6 1.0
CG A:ASP330 3.2 20.2 0.6
P A:PO4507 3.2 30.2 0.8
O1 A:PO4507 3.4 33.0 0.8
OD1 A:ASP332 3.4 19.7 1.0
OD2 A:ASP330 3.4 24.4 0.6
MN P:MN101 3.5 20.6 0.8
P P:8GM5 3.6 22.5 0.8
O5' P:8GM5 3.8 23.1 0.8
O4 A:PO4507 3.8 38.1 0.8
O A:HOH604 3.8 49.6 1.0
O A:ASP330 3.8 13.9 0.5
O A:HOH656 4.0 41.0 1.0
C5' P:8GM5 4.1 23.8 0.8
CE1 A:HIS329 4.1 28.5 0.6
ND1 A:HIS329 4.1 27.4 0.6
CB A:ASP330 4.2 17.4 0.5
O P:HOH201 4.2 21.6 0.5
C A:ASP330 4.3 13.9 0.5
O A:HOH613 4.3 17.1 1.0
N A:GLY320 4.3 18.6 1.0
OP2 P:8GM5 4.4 21.9 0.8
O A:ASP330 4.4 14.2 0.6
O A:HOH601 4.4 22.9 1.0
O2 A:PO4507 4.4 24.9 0.8
CB A:ASP332 4.4 14.1 1.0
CA A:GLY319 4.5 17.7 1.0
C A:ASP330 4.5 14.1 0.6
CB A:ASP330 4.5 16.1 0.6
N A:ASP330 4.8 16.9 0.6
CA A:ASP330 4.8 16.0 0.5
O3' P:DA4 4.8 24.6 1.0
CA A:ASP330 4.9 15.4 0.6
N A:ASP332 4.9 14.1 1.0
N A:VAL331 4.9 17.1 1.0

Manganese binding site 2 out of 8 in 6vfc

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Manganese binding site 2 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:41.7
occ:0.81
 O A:HOH834 2.1 38.8 0.7
O A:HOH797 2.2 37.7 0.7
O A:HOH798 2.2 40.0 0.8
NE2 A:HIS152 2.4 49.6 1.0
CD2 A:HIS152 3.2 48.9 1.0
CE1 A:HIS152 3.4 51.4 1.0
O A:HOH670 4.4 31.5 1.0
CG A:HIS152 4.4 46.5 1.0
O A:HOH816 4.5 43.0 1.0
O A:PRO190 4.5 33.3 1.0
ND1 A:HIS152 4.5 50.4 1.0
O A:THR150 4.6 26.7 1.0

Manganese binding site 3 out of 8 in 6vfc

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Manganese binding site 3 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:41.2
occ:0.66
 OP3 D:DG1 2.2 35.2 1.0
O D:HOH217 2.3 42.5 0.9
O D:HOH218 2.4 36.5 0.7
ND1 A:HIS208 2.5 31.3 1.0
O D:HOH209 2.5 35.7 0.9
CE1 A:HIS208 3.4 32.7 1.0
P D:DG1 3.4 28.8 1.0
CG A:HIS208 3.4 28.1 1.0
O D:HOH214 3.5 42.5 1.0
CB A:HIS208 3.7 25.1 1.0
OP1 D:DG1 3.7 28.6 1.0
OP2 D:DG1 4.1 27.3 1.0
NE2 A:HIS208 4.4 30.5 1.0
CD2 A:HIS208 4.5 30.7 1.0
O5' D:DG1 4.6 26.8 1.0
CA A:HIS208 4.6 24.4 1.0
C5' D:DG1 5.0 25.1 1.0

Manganese binding site 4 out of 8 in 6vfc

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Manganese binding site 4 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:56.6
occ:0.80
 O A:HOH737 1.9 49.2 0.7
O A:HOH603 2.1 48.9 0.8
O A:HOH826 2.3 43.0 0.7
NE2 A:HIS219 2.3 47.6 1.0
OE2 A:GLU215 2.9 66.5 1.0
CD2 A:HIS219 3.1 46.6 1.0
CE1 A:HIS219 3.4 49.4 1.0
OE1 A:GLU215 3.5 67.2 1.0
CD A:GLU215 3.6 61.0 1.0
OE1 A:GLU218 3.7 69.0 1.0
OE2 A:GLU218 3.8 71.0 1.0
CD A:GLU218 3.9 68.0 1.0
CG A:HIS219 4.4 45.3 1.0
ND1 A:HIS219 4.4 48.5 1.0
CG A:GLU218 5.0 58.1 1.0

Manganese binding site 5 out of 8 in 6vfc

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Manganese binding site 5 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn505

b:25.8
occ:0.67
 O A:HOH802 2.0 34.6 1.0
O T:HOH204 2.2 31.4 1.0
OE2 A:GLU386 2.2 31.8 1.0
O A:HOH757 2.3 38.3 1.0
NE2 A:HIS459 2.3 39.1 1.0
OE1 A:GLU386 2.5 41.4 1.0
CD A:GLU386 2.7 36.4 1.0
CD2 A:HIS459 3.2 42.3 1.0
CE1 A:HIS459 3.3 40.5 1.0
O A:HOH734 4.2 29.4 1.0
OP1 T:DC8 4.2 26.0 1.0
CG A:GLU386 4.3 39.2 1.0
O A:HOH638 4.4 24.8 1.0
CG A:HIS459 4.4 35.2 1.0
ND1 A:HIS459 4.4 38.7 1.0
C5' T:DC8 4.5 20.7 1.0
OE1 A:GLN426 4.6 26.8 1.0

Manganese binding site 6 out of 8 in 6vfc

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Manganese binding site 6 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


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-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:56.7
occ:0.75
 N7 T:DG2 2.3 24.8 0.6
N7 T:DG2 2.3 24.4 0.5
O T:HOH211 2.4 37.8 1.0
O T:HOH201 2.8 36.2 0.8
C8 T:DG2 3.1 24.4 0.5
C8 T:DG2 3.1 24.5 0.6
C5 T:DG2 3.2 23.4 0.6
C5 T:DG2 3.5 23.4 0.5
O6 T:DG2 3.6 23.0 0.6
C6 T:DG2 3.8 22.4 0.6
O6 T:DG2 3.9 22.4 0.5
C6 T:DG2 4.1 22.4 0.5
O T:HOH213 4.2 40.5 1.0
O D:HOH216 4.2 43.1 0.8
N9 T:DG2 4.3 24.6 0.6
N9 T:DG2 4.3 24.4 0.5
C4 T:DG2 4.3 22.8 0.6
O6 T:DG3 4.4 22.7 1.0
C4 T:DG2 4.5 23.0 0.5
OP2 T:DG2 4.6 33.0 0.5
C2' T:DC1 4.7 29.3 0.4
C6 T:DC1 4.9 21.4 0.4
C5 T:DC1 5.0 21.1 0.6

Manganese binding site 7 out of 8 in 6vfc

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Manganese binding site 7 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:20.6
occ:0.83
 OP1 P:8GM5 1.6 22.4 0.8
OD2 A:ASP330 1.8 24.4 0.6
OD2 A:ASP418 2.0 17.1 1.0
OD1 A:ASP332 2.1 19.7 1.0
O A:HOH601 2.2 22.9 1.0
OD1 A:ASP330 2.4 21.8 0.5
CG A:ASP330 2.8 20.2 0.6
P P:8GM5 3.0 22.5 0.8
CG A:ASP418 3.0 17.8 1.0
O3' P:DA4 3.1 24.6 1.0
CG A:ASP332 3.2 18.6 1.0
OD1 A:ASP330 3.2 20.8 0.6
CG A:ASP330 3.2 19.8 0.5
MN A:MN501 3.5 20.5 1.0
OD2 A:ASP332 3.6 17.8 1.0
CB A:ASP418 3.7 16.0 1.0
OP2 P:8GM5 3.9 21.9 0.8
OD1 A:ASP418 3.9 17.9 1.0
CB A:ASP330 3.9 17.4 0.5
CB A:ASP330 4.0 16.1 0.6
OD2 A:ASP330 4.1 23.4 0.5
C5' P:DA4 4.1 27.3 1.0
CE1 A:HIS329 4.2 28.5 0.6
C3' P:DA4 4.2 27.1 1.0
O5' P:8GM5 4.2 23.1 0.8
C4' P:DA4 4.3 27.9 1.0
O P:HOH201 4.3 21.6 0.5
NH2 A:ARG416 4.4 19.6 1.0
O A:HOH602 4.4 28.9 1.0
CB A:ASP332 4.4 14.1 1.0
C5' P:8GM5 4.5 23.8 0.8
OP1 P:DA4 4.6 24.2 1.0
O A:VAL331 4.7 16.8 1.0
N A:ASP418 4.8 13.8 1.0
CZ3 A:TRP434 4.8 23.7 1.0
NE2 A:HIS329 4.8 30.9 0.6
O5' P:DA4 4.8 23.0 1.0
CA A:ASP418 4.9 15.1 1.0
CA A:ASP332 4.9 15.0 1.0
C A:VAL331 4.9 17.0 1.0

Manganese binding site 8 out of 8 in 6vfc

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Manganese binding site 8 out of 8 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn101

b:58.5
occ:0.66
 O D:HOH216 2.2 43.1 0.8
N7 D:DG1 2.3 21.3 1.0
O D:HOH210 2.6 35.4 0.8
C8 D:DG1 3.1 21.3 1.0
C5 D:DG1 3.4 19.4 1.0
O6 D:DG1 3.8 21.5 1.0
C6 D:DG1 4.0 20.0 1.0
N4 D:DC2 4.3 23.8 1.0
O D:HOH202 4.4 41.7 1.0
N9 D:DG1 4.4 19.6 1.0
C4 D:DG1 4.5 19.9 1.0
O T:HOH211 4.6 37.8 1.0
OP2 D:DG1 4.6 27.3 1.0
CG A:ARG175 4.9 28.4 1.0
O A:HOH804 5.0 27.6 1.0
C4 D:DC2 5.0 22.5 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (2160 Min) To Be Published.
Page generated: Sun Oct 6 07:32:12 2024

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