Atomistry » Manganese » PDB 6vf5-6wij » 6vfc
Atomistry »
  Manganese »
    PDB 6vf5-6wij »
      6vfc »

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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Go back to Manganese Binding Sites List in 6vfc
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

Last articles

Mg in 1HE8
Mg in 1HE1
Mg in 1HDI
Mg in 1HCK
Mg in 1HBO
Mg in 1HBM
Mg in 1H8E
Mg in 1H8H
Mg in 1H7U
Mg in 1HA3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy