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Manganese in PDB 7k97: Human Dna Polymerase Beta Dgdp Product Complex with MN2+

Enzymatic activity of Human Dna Polymerase Beta Dgdp Product Complex with MN2+

All present enzymatic activity of Human Dna Polymerase Beta Dgdp Product Complex with MN2+:
2.7.7.7;

Protein crystallography data

The structure of Human Dna Polymerase Beta Dgdp Product Complex with MN2+, PDB code: 7k97 was solved by F.A.Varela, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.58 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.102, 77.309, 55.111, 90, 114.85, 90
R / Rfree (%) 18.5 / 24

Other elements in 7k97:

The structure of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+ (pdb code 7k97). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+, PDB code: 7k97:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7k97

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Manganese binding site 1 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:25.6
occ:0.89
 OD2 A:ASP190 1.9 24.1 1.0
OD1 A:ASP192 2.1 29.1 1.0
OD2 A:ASP256 2.3 24.8 1.0
OP1 P:DG11 2.4 27.6 1.0
O3' P:DC10 2.4 41.9 1.0
CG A:ASP190 2.8 26.7 1.0
P P:DG11 2.9 35.5 1.0
CG A:ASP192 3.0 26.9 1.0
OD1 A:ASP190 3.1 35.6 1.0
MN A:MN402 3.3 34.2 0.9
OD2 A:ASP192 3.3 29.2 1.0
CG A:ASP256 3.4 24.4 1.0
C3' P:DC10 3.7 33.6 1.0
C4' P:DC10 3.9 33.5 1.0
OP2 P:DG11 4.0 42.0 1.0
CB A:ASP256 4.0 26.1 1.0
C5' P:DC10 4.1 30.9 1.0
O5' P:DG11 4.1 33.3 1.0
CB A:ASP190 4.2 26.1 1.0
C5' P:DG11 4.2 29.9 1.0
CB A:ASP192 4.4 24.7 1.0
OD1 A:ASP256 4.4 26.2 1.0
O1 P:PO4103 4.7 39.7 1.0
C2' P:DC10 4.7 29.1 1.0
OP1 P:DC10 4.7 28.3 1.0
O A:MET191 4.9 25.3 1.0
CA A:ASP192 4.9 28.1 1.0
O5' P:DC10 4.9 30.4 1.0
NH2 A:ARG254 5.0 31.4 1.0

Manganese binding site 2 out of 8 in 7k97

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Manganese binding site 2 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:34.2
occ:0.91
 O1 P:PO4103 1.8 39.7 1.0
OP1 P:DG11 1.9 27.6 1.0
OD1 A:ASP190 2.0 35.6 1.0
OD2 A:ASP192 2.0 29.2 1.0
O P:HOH203 2.4 33.0 1.0
CG A:ASP190 3.0 26.7 1.0
CG A:ASP192 3.0 26.9 1.0
P P:PO4103 3.1 44.2 1.0
MN A:MN401 3.3 25.6 0.9
P P:DG11 3.3 35.5 1.0
OD1 A:ASP192 3.4 29.1 1.0
OD2 A:ASP190 3.4 24.1 1.0
O4 P:PO4103 3.5 47.8 1.0
O5' P:DG11 3.8 33.3 1.0
O2 P:PO4103 3.9 37.9 1.0
C5' P:DG11 4.0 29.9 1.0
O3 P:PO4103 4.1 37.5 1.0
N A:ASP190 4.2 24.9 1.0
OP2 P:DG11 4.2 42.0 1.0
O3' P:DC10 4.3 41.9 1.0
CB A:ASP190 4.3 26.1 1.0
CB A:ASP192 4.4 24.7 1.0
CA A:ASP190 4.6 29.5 1.0
C A:ASP190 4.6 32.9 1.0
CA A:GLY179 4.6 27.1 1.0
N A:SER180 4.7 34.2 1.0
O A:ASP190 4.8 32.8 1.0
N A:ASP192 5.0 27.9 1.0
N A:MET191 5.0 28.5 1.0

Manganese binding site 3 out of 8 in 7k97

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Manganese binding site 3 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:76.1
occ:1.00
 OD1 A:ASP124 2.2 64.0 1.0
CG A:ASP124 3.0 55.3 1.0
OD2 A:ASP124 3.2 55.8 1.0
OG1 A:THR121 3.9 50.9 1.0
CB A:ASP124 4.4 44.6 1.0
N A:ASP124 4.7 46.1 1.0
CA A:ASP124 4.8 45.5 1.0
OE1 A:GLU123 5.0 69.0 1.0

Manganese binding site 4 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 4 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:86.7
occ:1.00
 CE1 A:HIS285 2.0 69.9 1.0
ND1 A:HIS285 2.0 64.1 1.0
OE1 A:GLU288 3.0 68.6 1.0
O A:HOH533 3.1 62.4 1.0
NE2 A:HIS285 3.3 82.7 1.0
CG A:HIS285 3.4 60.0 1.0
OE2 A:GLU288 3.5 75.4 1.0
CD A:GLU288 3.6 71.4 1.0
CD2 A:HIS285 4.0 59.5 1.0
CB A:HIS285 4.4 43.3 1.0
CA A:HIS285 4.7 46.8 1.0

Manganese binding site 5 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 5 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn405

b:93.6
occ:1.00
 NE2 A:HIS222 2.3 69.4 1.0
CE1 A:HIS222 3.1 64.1 1.0
CD2 A:HIS222 3.5 50.3 1.0
ND1 A:HIS222 4.3 64.7 1.0
CG A:HIS222 4.5 50.9 1.0

Manganese binding site 6 out of 8 in 7k97

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Manganese binding site 6 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:74.1
occ:1.00
 N7 P:DG4 2.2 61.4 1.0
C8 P:DG4 3.2 60.8 1.0
C5 P:DG4 3.3 55.4 1.0
O6 P:DG4 3.5 49.8 1.0
C6 P:DG4 3.8 50.6 1.0
O4 T:DT12 4.3 38.3 1.0
C2' P:DT3 4.3 55.4 1.0
N6 P:DA5 4.4 46.4 1.0
N9 P:DG4 4.4 53.8 1.0
C4 P:DG4 4.4 53.1 1.0

Manganese binding site 7 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 7 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:82.5
occ:1.00
 OP2 P:DG11 2.2 42.0 1.0
O4 P:PO4103 3.0 47.8 1.0
P P:DG11 3.6 35.5 1.0
O5' P:DG11 4.1 33.3 1.0
OD2 A:ASP276 4.2 42.8 1.0
OP1 P:DG11 4.4 27.6 1.0
P P:PO4103 4.5 44.2 1.0
O3' P:DC10 4.8 41.9 1.0
OP2 P:DC10 4.8 29.2 1.0
C8 P:DG11 4.8 29.3 1.0
N7 P:DG11 4.9 32.4 1.0

Manganese binding site 8 out of 8 in 7k97

Go back to Manganese Binding Sites List in 7k97
Manganese binding site 8 out of 8 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:66.2
occ:1.00
 O T:HOH205 2.7 51.1 1.0
N7 T:DG3 3.1 68.2 1.0
O6 T:DG3 3.3 58.7 1.0
C5 T:DG3 3.8 61.8 1.0
C6 T:DG3 3.9 57.9 1.0
C8 T:DG3 4.2 67.5 1.0
O4 D:DT2 4.2 42.7 1.0
N6 T:DA4 4.9 44.5 1.0
C6 T:DC2 5.0 59.3 1.0

Reference:

F.A.Varela, B.D.Freudenthal. Mechanism of Deoxyguanosine Diphosphate Insertion By Human Dna Polymerase Beta. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33475337
DOI: 10.1021/ACS.BIOCHEM.0C00847
Page generated: Sun Oct 6 08:55:19 2024

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